Warning: Permanently added '3.95.131.170' (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/9903006-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.6
PID: 179626
Logging PID: 179628
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 9903006,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '7eda71c535f9a03bc88ed5da91a0f1176dd7aa58',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jwakely/boost-190-rebuild.checker/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.08-1',
 'project_dirname': 'boost-190-rebuild.checker',
 'project_name': 'boost-190-rebuild.checker',
 'project_owner': 'jwakely',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jwakely/boost-190-rebuild.checker/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'jwakely/boost-190-rebuild.checker--jwakely',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'jwakely',
 'tags': [],
 'task_id': '9903006-fedora-rawhide-x86_64',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jwakely/boost-190-rebuild.checker/percolator /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jwakely/boost-190-rebuild.checker/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator'...

Running: git checkout 7eda71c535f9a03bc88ed5da91a0f1176dd7aa58 --

cmd: ['git', 'checkout', '7eda71c535f9a03bc88ed5da91a0f1176dd7aa58', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator
rc: 0
stdout: 
stderr: Note: switching to '7eda71c535f9a03bc88ed5da91a0f1176dd7aa58'.

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 7eda71c automatic import of percolator

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/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-3-08.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o percolator-rel-3-08.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/jwakely/boost-190-rebuild.checker/percolator/percolator-rel-3-08.tar.gz/md5/aeff68a2f7ef29ccc623edb0e1e8f53f/percolator-rel-3-08.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5138k  100 5138k    0     0   196M      0 --:--:-- --:--:-- --:--:--  200M
INFO: Reading stdout from command: md5sum percolator-rel-3-08.tar.gz

tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1765551765.922229 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.6 starting (python version = 3.13.7, NVR = mock-6.6-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1765551765.922229 -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-goiwco8e/percolator/percolator.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1765551765.922229/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using container image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Tagging container image as mock-bootstrap-54f80a33-a8d4-4d04-89c1-57eeb3696a9a
INFO: Checking that 670b0d5fef90acc76ada97460d64331389d67aad7e811d57f9960d9c421a29e0 image matches host's architecture
INFO: Copy content of container 670b0d5fef90acc76ada97460d64331389d67aad7e811d57f9960d9c421a29e0 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1765551765.922229/root
INFO: mounting 670b0d5fef90acc76ada97460d64331389d67aad7e811d57f9960d9c421a29e0 with podman image mount
INFO: image 670b0d5fef90acc76ada97460d64331389d67aad7e811d57f9960d9c421a29e0 as /var/lib/containers/storage/overlay/1aa9dd96706926d22cb313639fc78d330d9fc719180144bc62863260c7c5e5b6/merged
INFO: umounting image 670b0d5fef90acc76ada97460d64331389d67aad7e811d57f9960d9c421a29e0 (/var/lib/containers/storage/overlay/1aa9dd96706926d22cb313639fc78d330d9fc719180144bc62863260c7c5e5b6/merged) with podman image umount
INFO: Removing image mock-bootstrap-54f80a33-a8d4-4d04-89c1-57eeb3696a9a
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1765551765.922229/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-6.0.1-1.fc44.x86_64
  rpm-sequoia-1.9.0-2.fc43.x86_64
  dnf5-5.3.0.0-3.fc44.x86_64
  dnf5-plugins-5.3.0.0-3.fc44.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Copr repository                        100% |  80.4 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 151.1 KiB/s |  27.1 KiB |  00m00s
Repositories loaded.
Package                            Arch   Version                      Repository      Size
Installing group/module packages:
 bash                              x86_64 0:5.3.0-2.fc43               fedora       8.4 MiB
 bzip2                             x86_64 0:1.0.8-21.fc43              fedora      95.3 KiB
 coreutils                         x86_64 0:9.9-1.fc44                 fedora       5.4 MiB
 cpio                              x86_64 0:2.15-6.fc43                fedora       1.1 MiB
 diffutils                         x86_64 0:3.12-3.fc43                fedora       1.6 MiB
 fedora-release-common             noarch 0:44-0.8                     fedora      20.8 KiB
 findutils                         x86_64 1:4.10.0-6.fc43              fedora       1.8 MiB
 gawk                              x86_64 0:5.3.2-2.fc43               fedora       1.8 MiB
 glibc-minimal-langpack            x86_64 0:2.42.9000-15.fc44          fedora       0.0   B
 grep                              x86_64 0:3.12-2.fc43                fedora       1.0 MiB
 gzip                              x86_64 0:1.14-1.fc44                fedora     397.8 KiB
 info                              x86_64 0:7.2-7.fc44                 fedora     357.9 KiB
 patch                             x86_64 0:2.8-2.fc43                 fedora     222.8 KiB
 redhat-rpm-config                 noarch 0:343-16.fc44                fedora     183.6 KiB
 rpm-build                         x86_64 0:6.0.1-1.fc44               fedora     287.5 KiB
 sed                               x86_64 0:4.9-6.fc44                 fedora     857.3 KiB
 shadow-utils                      x86_64 2:4.18.0-7.fc44              fedora       3.9 MiB
 tar                               x86_64 2:1.35-6.fc43                fedora       2.9 MiB
 unzip                             x86_64 0:6.0-68.fc44                fedora     390.3 KiB
 util-linux                        x86_64 0:2.41.2-9.fc44              fedora       3.5 MiB
 which                             x86_64 0:2.23-3.fc43                fedora      83.5 KiB
 xz                                x86_64 1:5.8.1-4.fc44               fedora       1.3 MiB
Installing dependencies:
 add-determinism                   x86_64 0:0.7.2-2.fc44               fedora       2.3 MiB
 alternatives                      x86_64 0:1.33-3.fc44                fedora      62.2 KiB
 ansible-srpm-macros               noarch 0:1-18.1.fc43                fedora      35.7 KiB
 audit-libs                        x86_64 0:4.1.2-2.fc44               fedora     378.8 KiB
 binutils                          x86_64 0:2.45.50-9.fc44             fedora      27.0 MiB
 build-reproducibility-srpm-macros noarch 0:0.7.2-2.fc44               fedora       1.2 KiB
 bzip2-libs                        x86_64 0:1.0.8-21.fc43              fedora      80.6 KiB
 ca-certificates                   noarch 0:2025.2.80_v9.0.304-2.fc44  fedora       2.7 MiB
 coreutils-common                  x86_64 0:9.9-1.fc44                 fedora      11.2 MiB
 crypto-policies                   noarch 0:20251128-1.git19878fe.fc44 fedora     132.6 KiB
 curl                              x86_64 0:8.18.0~rc1-1.fc44          fedora     467.1 KiB
 cyrus-sasl-lib                    x86_64 0:2.1.28-33.fc44             fedora       2.3 MiB
 debugedit                         x86_64 0:5.2-3.fc44                 fedora     214.0 KiB
 dwz                               x86_64 0:0.16-2.fc43                fedora     287.1 KiB
 ed                                x86_64 0:1.22.3-1.fc44              fedora     148.9 KiB
 efi-srpm-macros                   noarch 0:6-5.fc44                   fedora      40.2 KiB
 elfutils                          x86_64 0:0.194-2.fc44               fedora       2.9 MiB
 elfutils-debuginfod-client        x86_64 0:0.194-2.fc44               fedora      84.0 KiB
 elfutils-default-yama-scope       noarch 0:0.194-2.fc44               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0:0.194-2.fc44               fedora       1.1 MiB
 elfutils-libs                     x86_64 0:0.194-2.fc44               fedora     687.5 KiB
 fedora-gpg-keys                   noarch 0:44-0.1                     fedora     131.2 KiB
 fedora-release                    noarch 0:44-0.8                     fedora       0.0   B
 fedora-release-identity-basic     noarch 0:44-0.8                     fedora     664.0   B
 fedora-repos                      noarch 0:44-0.1                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 0:44-0.1                     fedora       2.2 KiB
 file                              x86_64 0:5.46-8.fc44                fedora     100.2 KiB
 file-libs                         x86_64 0:5.46-8.fc44                fedora      11.9 MiB
 filesystem                        x86_64 0:3.18-50.fc43               fedora     112.0   B
 filesystem-srpm-macros            noarch 0:3.18-50.fc43               fedora      38.2 KiB
 fonts-srpm-macros                 noarch 1:5.0.0-1.fc44               fedora      55.8 KiB
 forge-srpm-macros                 noarch 0:0.4.0-3.fc43               fedora      38.9 KiB
 fpc-srpm-macros                   noarch 0:1.3-15.fc43                fedora     144.0   B
 gap-srpm-macros                   noarch 0:2-1.fc44                   fedora       2.1 KiB
 gdb-minimal                       x86_64 0:16.3-6.fc44                fedora      13.3 MiB
 gdbm-libs                         x86_64 1:1.23-10.fc43               fedora     129.9 KiB
 ghc-srpm-macros                   noarch 0:1.9.2-3.fc43               fedora     779.0   B
 glibc                             x86_64 0:2.42.9000-15.fc44          fedora       6.8 MiB
 glibc-common                      x86_64 0:2.42.9000-15.fc44          fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 0:2.42.9000-15.fc44          fedora       7.2 MiB
 gmp                               x86_64 1:6.3.0-4.fc44               fedora     815.3 KiB
 gnat-srpm-macros                  noarch 0:6-8.fc43                   fedora       1.0 KiB
 gnulib-l10n                       noarch 0:20241231-1.fc44            fedora     655.0 KiB
 gnupg2                            x86_64 0:2.4.8-4.fc43               fedora       6.5 MiB
 gnupg2-dirmngr                    x86_64 0:2.4.8-4.fc43               fedora     618.4 KiB
 gnupg2-gpg-agent                  x86_64 0:2.4.8-4.fc43               fedora     671.4 KiB
 gnupg2-gpgconf                    x86_64 0:2.4.8-4.fc43               fedora     250.0 KiB
 gnupg2-keyboxd                    x86_64 0:2.4.8-4.fc43               fedora     201.4 KiB
 gnupg2-verify                     x86_64 0:2.4.8-4.fc43               fedora     348.5 KiB
 gnutls                            x86_64 0:3.8.11-6.fc44              fedora       3.6 MiB
 go-srpm-macros                    noarch 0:3.8.0-1.fc44               fedora      61.9 KiB
 gpgverify                         noarch 0:2.2-3.fc43                 fedora       8.7 KiB
 ima-evm-utils-libs                x86_64 0:1.6.2-7.fc44               fedora      60.7 KiB
 jansson                           x86_64 0:2.14-3.fc43                fedora      89.1 KiB
 java-srpm-macros                  noarch 0:1-7.fc43                   fedora     870.0   B
 json-c                            x86_64 0:0.18-7.fc43                fedora      82.7 KiB
 kernel-srpm-macros                noarch 0:1.0-27.fc43                fedora       1.9 KiB
 keyutils-libs                     x86_64 0:1.6.3-6.fc43               fedora      54.3 KiB
 krb5-libs                         x86_64 0:1.21.3-10.fc44             fedora       2.3 MiB
 libacl                            x86_64 0:2.3.2-4.fc43               fedora      35.9 KiB
 libarchive                        x86_64 0:3.8.4-1.fc44               fedora     955.3 KiB
 libassuan                         x86_64 0:2.5.7-4.fc43               fedora     163.8 KiB
 libattr                           x86_64 0:2.5.2-6.fc43               fedora      24.4 KiB
 libblkid                          x86_64 0:2.41.2-9.fc44              fedora     262.4 KiB
 libbrotli                         x86_64 0:1.2.0-1.fc44               fedora     865.4 KiB
 libcap                            x86_64 0:2.77-1.fc44                fedora     209.1 KiB
 libcap-ng                         x86_64 0:0.8.5-8.fc44               fedora      68.9 KiB
 libcom_err                        x86_64 0:1.47.3-3.fc44              fedora      63.1 KiB
 libcurl                           x86_64 0:8.18.0~rc1-1.fc44          fedora     981.0 KiB
 libeconf                          x86_64 0:0.7.9-2.fc43               fedora      64.9 KiB
 libevent                          x86_64 0:2.1.12-16.fc43             fedora     883.1 KiB
 libfdisk                          x86_64 0:2.41.2-9.fc44              fedora     380.4 KiB
 libffi                            x86_64 0:3.5.2-1.fc44               fedora      83.8 KiB
 libfsverity                       x86_64 0:1.6-3.fc43                 fedora      28.5 KiB
 libgcc                            x86_64 0:15.2.1-4.fc44              fedora     266.6 KiB
 libgcrypt                         x86_64 0:1.11.2-1.fc44              fedora       1.6 MiB
 libgomp                           x86_64 0:15.2.1-4.fc44              fedora     541.6 KiB
 libgpg-error                      x86_64 0:1.57-1.fc44                fedora     941.7 KiB
 libidn2                           x86_64 0:2.3.8-2.fc43               fedora     552.5 KiB
 libksba                           x86_64 0:1.6.7-4.fc43               fedora     398.5 KiB
 liblastlog2                       x86_64 0:2.41.2-9.fc44              fedora      33.9 KiB
 libmount                          x86_64 0:2.41.2-9.fc44              fedora     372.7 KiB
 libnghttp2                        x86_64 0:1.68.0-2.fc44              fedora     162.2 KiB
 libnghttp3                        x86_64 0:1.13.1-1.fc44              fedora     155.3 KiB
 libpkgconf                        x86_64 0:2.3.0-3.fc43               fedora      78.1 KiB
 libpsl                            x86_64 0:0.21.5-6.fc43              fedora      76.4 KiB
 libselinux                        x86_64 0:3.9-5.fc44                 fedora     193.1 KiB
 libselinux-utils                  x86_64 0:3.9-5.fc44                 fedora     309.0 KiB
 libsemanage                       x86_64 0:3.9-4.fc44                 fedora     308.5 KiB
 libsepol                          x86_64 0:3.9-2.fc43                 fedora     822.0 KiB
 libsmartcols                      x86_64 0:2.41.2-9.fc44              fedora     180.5 KiB
 libssh                            x86_64 0:0.11.3-1.fc44              fedora     567.1 KiB
 libssh-config                     noarch 0:0.11.3-1.fc44              fedora     277.0   B
 libstdc++                         x86_64 0:15.2.1-4.fc44              fedora       2.8 MiB
 libtasn1                          x86_64 0:4.20.0-2.fc43              fedora     176.3 KiB
 libtool-ltdl                      x86_64 0:2.5.4-8.fc44               fedora      70.1 KiB
 libunistring                      x86_64 0:1.1-10.fc43                fedora       1.7 MiB
 libusb1                           x86_64 0:1.0.29-4.fc44              fedora     171.3 KiB
 libuuid                           x86_64 0:2.41.2-9.fc44              fedora      37.3 KiB
 libverto                          x86_64 0:0.3.2-11.fc43              fedora      25.4 KiB
 libxcrypt                         x86_64 0:4.5.2-2.fc44               fedora     285.3 KiB
 libxml2                           x86_64 0:2.12.10-5.fc44             fedora       1.7 MiB
 libzstd                           x86_64 0:1.5.7-3.fc44               fedora     940.3 KiB
 linkdupes                         x86_64 0:0.7.2-2.fc44               fedora     838.7 KiB
 lua-libs                          x86_64 0:5.4.8-4.fc44               fedora     281.9 KiB
 lua-srpm-macros                   noarch 0:1-16.fc43                  fedora       1.3 KiB
 lz4-libs                          x86_64 0:1.10.0-3.fc43              fedora     161.4 KiB
 mpfr                              x86_64 0:4.2.2-2.fc43               fedora     832.8 KiB
 ncurses-base                      noarch 0:6.5-8.20250614.fc44        fedora     328.1 KiB
 ncurses-libs                      x86_64 0:6.5-8.20250614.fc44        fedora     946.4 KiB
 nettle                            x86_64 0:3.10.1-2.fc43              fedora     790.6 KiB
 ngtcp2                            x86_64 0:1.18.0-1.fc44              fedora     314.3 KiB
 ngtcp2-crypto-ossl                x86_64 0:1.18.0-1.fc44              fedora      51.7 KiB
 npth                              x86_64 0:1.8-3.fc43                 fedora      49.6 KiB
 ocaml-srpm-macros                 noarch 0:11-2.fc43                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 0:2-20.fc43                  fedora     112.0   B
 openldap                          x86_64 0:2.6.10-4.fc44              fedora     659.8 KiB
 openssl-libs                      x86_64 1:3.5.4-1.fc44               fedora       8.9 MiB
 p11-kit                           x86_64 0:0.25.8-1.fc44              fedora       2.3 MiB
 p11-kit-trust                     x86_64 0:0.25.8-1.fc44              fedora     446.5 KiB
 package-notes-srpm-macros         noarch 0:0.5-14.fc43                fedora       1.6 KiB
 pam-libs                          x86_64 0:1.7.1-3.fc43               fedora     126.8 KiB
 pcre2                             x86_64 0:10.47-1.fc44               fedora     702.6 KiB
 pcre2-syntax                      noarch 0:10.47-1.fc44               fedora     281.9 KiB
 perl-srpm-macros                  noarch 0:1-60.fc43                  fedora     861.0   B
 pkgconf                           x86_64 0:2.3.0-3.fc43               fedora      88.5 KiB
 pkgconf-m4                        noarch 0:2.3.0-3.fc43               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 0:2.3.0-3.fc43               fedora     989.0   B
 policycoreutils                   x86_64 0:3.9-5.fc44                 fedora     683.5 KiB
 popt                              x86_64 0:1.19-9.fc43                fedora     132.8 KiB
 publicsuffix-list-dafsa           noarch 0:20250616-2.fc43            fedora      69.1 KiB
 pyproject-srpm-macros             noarch 0:1.18.6-1.fc44              fedora       1.9 KiB
 python-srpm-macros                noarch 0:3.14-9.fc44                fedora      51.6 KiB
 qt5-srpm-macros                   noarch 0:5.15.18-1.fc44             fedora     500.0   B
 qt6-srpm-macros                   noarch 0:6.10.1-1.fc44              fedora     464.0   B
 readline                          x86_64 0:8.3-2.fc43                 fedora     511.7 KiB
 rpm                               x86_64 0:6.0.1-1.fc44               fedora       3.1 MiB
 rpm-build-libs                    x86_64 0:6.0.1-1.fc44               fedora     264.4 KiB
 rpm-libs                          x86_64 0:6.0.1-1.fc44               fedora     933.8 KiB
 rpm-plugin-selinux                x86_64 0:6.0.1-1.fc44               fedora      12.0 KiB
 rpm-sequoia                       x86_64 0:1.9.0-2.fc43               fedora       2.5 MiB
 rpm-sign-libs                     x86_64 0:6.0.1-1.fc44               fedora      39.7 KiB
 rust-srpm-macros                  noarch 0:28.4-1.fc44                fedora       5.5 KiB
 selinux-policy                    noarch 0:42.19-1.fc44               fedora      32.0 KiB
 selinux-policy-targeted           noarch 0:42.19-1.fc44               fedora      18.7 MiB
 setup                             noarch 0:2.15.0-27.fc44             fedora     724.9 KiB
 sqlite-libs                       x86_64 0:3.51.0-1.fc44              fedora       1.5 MiB
 systemd-libs                      x86_64 0:259~rc3-1.fc44             fedora       2.3 MiB
 systemd-standalone-sysusers       x86_64 0:259~rc3-1.fc44             fedora     293.7 KiB
 tpm2-tss                          x86_64 0:4.1.3-8.fc43               fedora       1.6 MiB
 tree-sitter-srpm-macros           noarch 0:0.4.2-1.fc43               fedora       8.3 KiB
 util-linux-core                   x86_64 0:2.41.2-9.fc44              fedora       1.5 MiB
 xxhash-libs                       x86_64 0:0.8.3-3.fc43               fedora      90.2 KiB
 xz-libs                           x86_64 1:5.8.1-4.fc44               fedora     217.8 KiB
 zig-srpm-macros                   noarch 0:1-5.fc43                   fedora       1.1 KiB
 zip                               x86_64 0:3.0-44.fc43                fedora     694.5 KiB
 zlib-ng-compat                    x86_64 0:2.3.2-1.fc44               fedora     161.7 KiB
 zstd                              x86_64 0:1.5.7-3.fc44               fedora     506.2 KiB
Installing groups:
 Buildsystem building group                                                                

Transaction Summary:
 Installing:       180 packages

Total size of inbound packages is 67 MiB. Need to download 0 B.
After this operation, 219 MiB extra will be used (install 219 MiB, remove 0 B).
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--------------------------------------------------------------------------------
[180/180] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
Importing OpenPGP key 0xF577861E:
 UserID     : "Fedora (45) <fedora-45-primary@fedoraproject.org>"
 Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary
The key was successfully imported.
[  1/182] Verify package files          100% | 750.0   B/s | 180.0   B |  00m00s
[  2/182] Prepare transaction           100% |   3.5 KiB/s | 180.0   B |  00m00s
[  3/182] Installing libgcc-0:15.2.1-4. 100% | 262.0 MiB/s | 268.3 KiB |  00m00s
[  4/182] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/182] Installing publicsuffix-list- 100% |   0.0   B/s |  69.8 KiB |  00m00s
[  6/182] Installing fedora-release-ide 100% |   0.0   B/s | 920.0   B |  00m00s
[  7/182] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  8/182] Installing fedora-gpg-keys-0: 100% |  43.7 MiB/s | 179.0 KiB |  00m00s
[  9/182] Installing fedora-repos-0:44- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/182] Installing fedora-release-com 100% |  24.5 MiB/s |  25.1 KiB |  00m00s
[ 11/182] Installing fedora-release-0:4 100% |  17.3 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch
>>> Finished sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch
>>> Scriptlet output:
>>> Creating group 'adm' with GID 4.
>>> Creating group 'audio' with GID 63.
>>> Creating group 'cdrom' with GID 11.
>>> Creating group 'clock' with GID 103.
>>> Creating group 'dialout' with GID 18.
>>> Creating group 'disk' with GID 6.
>>> Creating group 'floppy' with GID 19.
>>> Creating group 'ftp' with GID 50.
>>> Creating group 'games' with GID 20.
>>> Creating group 'input' with GID 104.
>>> Creating group 'kmem' with GID 9.
>>> Creating group 'kvm' with GID 36.
>>> Creating group 'lock' with GID 54.
>>> Creating group 'lp' with GID 7.
>>> Creating group 'mail' with GID 12.
>>> Creating group 'man' with GID 15.
>>> Creating group 'mem' with GID 8.
>>> Creating group 'nobody' with GID 65534.
>>> Creating group 'render' with GID 105.
>>> Creating group 'root' with GID 0.
>>> Creating group 'sgx' with GID 106.
>>> Creating group 'sys' with GID 3.
>>> Creating group 'tape' with GID 33.
>>> Creating group 'tty' with GID 5.
>>> Creating group 'users' with GID 100.
>>> Creating group 'utmp' with GID 22.
>>> Creating group 'video' with GID 39.
>>> Creating group 'wheel' with GID 10.
>>> Creating user 'adm' (adm) with UID 3 and GID 4.
>>> Creating group 'bin' with GID 1.
>>> Creating user 'bin' (bin) with UID 1 and GID 1.
>>> Creating group 'daemon' with GID 2.
>>> Creating user 'daemon' (daemon) with UID 2 and GID 2.
>>> Creating user 'ftp' (FTP User) with UID 14 and GID 50.
>>> Creating user 'games' (games) with UID 12 and GID 100.
>>> Creating user 'halt' (halt) with UID 7 and GID 0.
>>> Creating user 'lp' (lp) with UID 4 and GID 7.
>>> Creating user 'mail' (mail) with UID 8 and GID 12.
>>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534.
>>> Creating user 'operator' (operator) with UID 11 and GID 0.
>>> Creating user 'root' (Super User) with UID 0 and GID 0.
>>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0.
>>> Creating user 'sync' (sync) with UID 5 and GID 0.
>>> 
[ 12/182] Installing setup-0:2.15.0-27. 100% |  54.9 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/182] Installing filesystem-0:3.18- 100% |   3.0 MiB/s | 212.8 KiB |  00m00s
[ 14/182] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 15/182] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB |  00m00s
[ 16/182] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB |  00m00s
[ 17/182] Installing coreutils-common-0 100% | 415.9 MiB/s |  11.2 MiB |  00m00s
[ 18/182] Installing ncurses-base-0:6.5 100% |  86.3 MiB/s | 353.5 KiB |  00m00s
[ 19/182] Installing bash-0:5.3.0-2.fc4 100% | 290.7 MiB/s |   8.4 MiB |  00m00s
[ 20/182] Installing glibc-common-0:2.4 100% |  68.1 MiB/s |   1.0 MiB |  00m00s
[ 21/182] Installing glibc-gconv-extra- 100% | 304.8 MiB/s |   7.3 MiB |  00m00s
[ 22/182] Installing glibc-0:2.42.9000- 100% | 195.8 MiB/s |   6.9 MiB |  00m00s
[ 23/182] Installing ncurses-libs-0:6.5 100% | 310.2 MiB/s | 953.0 KiB |  00m00s
[ 24/182] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 25/182] Installing zlib-ng-compat-0:2 100% | 158.7 MiB/s | 162.5 KiB |  00m00s
[ 26/182] Installing bzip2-libs-0:1.0.8 100% |   0.0   B/s |  81.7 KiB |  00m00s
[ 27/182] Installing libgpg-error-0:1.5 100% |  66.1 MiB/s | 947.6 KiB |  00m00s
[ 28/182] Installing libstdc++-0:15.2.1 100% | 406.3 MiB/s |   2.8 MiB |  00m00s
[ 29/182] Installing libassuan-0:2.5.7- 100% | 161.7 MiB/s | 165.6 KiB |  00m00s
[ 30/182] Installing libgcrypt-0:1.11.2 100% | 394.0 MiB/s |   1.6 MiB |  00m00s
[ 31/182] Installing readline-0:8.3-2.f 100% | 501.8 MiB/s | 513.9 KiB |  00m00s
[ 32/182] Installing gmp-1:6.3.0-4.fc44 100% | 399.2 MiB/s | 817.5 KiB |  00m00s
[ 33/182] Installing xz-libs-1:5.8.1-4. 100% | 213.8 MiB/s | 218.9 KiB |  00m00s
[ 34/182] Installing libuuid-0:2.41.2-9 100% |   0.0   B/s |  38.5 KiB |  00m00s
[ 35/182] Installing popt-0:1.19-9.fc43 100% |  68.1 MiB/s | 139.4 KiB |  00m00s
[ 36/182] Installing libzstd-0:1.5.7-3. 100% | 459.7 MiB/s | 941.6 KiB |  00m00s
[ 37/182] Installing elfutils-libelf-0: 100% | 373.7 MiB/s |   1.1 MiB |  00m00s
[ 38/182] Installing npth-0:1.8-3.fc43. 100% |   0.0   B/s |  50.7 KiB |  00m00s
[ 39/182] Installing libblkid-0:2.41.2- 100% | 257.2 MiB/s | 263.4 KiB |  00m00s
[ 40/182] Installing systemd-libs-0:259 100% | 390.1 MiB/s |   2.3 MiB |  00m00s
[ 41/182] Installing libxcrypt-0:4.5.2- 100% | 281.3 MiB/s | 288.0 KiB |  00m00s
[ 42/182] Installing libsepol-0:3.9-2.f 100% | 401.8 MiB/s | 822.9 KiB |  00m00s
[ 43/182] Installing sqlite-libs-0:3.51 100% | 383.0 MiB/s |   1.5 MiB |  00m00s
[ 44/182] Installing gnupg2-gpgconf-0:2 100% |  20.5 MiB/s | 252.0 KiB |  00m00s
[ 45/182] Installing libattr-0:2.5.2-6. 100% |   0.0   B/s |  25.4 KiB |  00m00s
[ 46/182] Installing libacl-0:2.3.2-4.f 100% |   0.0   B/s |  36.8 KiB |  00m00s
[ 47/182] Installing pcre2-0:10.47-1.fc 100% | 343.8 MiB/s | 704.1 KiB |  00m00s
[ 48/182] Installing libselinux-0:3.9-5 100% | 189.8 MiB/s | 194.4 KiB |  00m00s
[ 49/182] Installing grep-0:3.12-2.fc43 100% |  66.8 MiB/s |   1.0 MiB |  00m00s
[ 50/182] Installing sed-0:4.9-6.fc44.x 100% |  60.4 MiB/s | 865.5 KiB |  00m00s
[ 51/182] Installing findutils-1:4.10.0 100% | 116.1 MiB/s |   1.9 MiB |  00m00s
[ 52/182] Installing libtasn1-0:4.20.0- 100% | 173.9 MiB/s | 178.1 KiB |  00m00s
[ 53/182] Installing libunistring-0:1.1 100% | 431.7 MiB/s |   1.7 MiB |  00m00s
[ 54/182] Installing libidn2-0:2.3.8-2. 100% |  60.6 MiB/s | 558.7 KiB |  00m00s
[ 55/182] Installing crypto-policies-0: 100% |  38.5 MiB/s | 157.7 KiB |  00m00s
[ 56/182] Installing xz-1:5.8.1-4.fc44. 100% |  78.3 MiB/s |   1.3 MiB |  00m00s
[ 57/182] Installing libmount-0:2.41.2- 100% | 365.1 MiB/s | 373.8 KiB |  00m00s
[ 58/182] Installing gnupg2-verify-0:2. 100% |  28.5 MiB/s | 349.9 KiB |  00m00s
[ 59/182] Installing dwz-0:0.16-2.fc43. 100% |  25.6 MiB/s | 288.5 KiB |  00m00s
[ 60/182] Installing mpfr-0:4.2.2-2.fc4 100% | 407.4 MiB/s | 834.4 KiB |  00m00s
[ 61/182] Installing gawk-0:5.3.2-2.fc4 100% | 113.5 MiB/s |   1.8 MiB |  00m00s
[ 62/182] Installing libksba-0:1.6.7-4. 100% | 391.7 MiB/s | 401.1 KiB |  00m00s
[ 63/182] Installing unzip-0:6.0-68.fc4 100% |  32.1 MiB/s | 393.8 KiB |  00m00s
[ 64/182] Installing file-libs-0:5.46-8 100% | 697.5 MiB/s |  11.9 MiB |  00m00s
[ 65/182] Installing file-0:5.46-8.fc44 100% |   9.0 MiB/s | 101.7 KiB |  00m00s
[ 66/182] Installing diffutils-0:3.12-3 100% | 104.1 MiB/s |   1.6 MiB |  00m00s
[ 67/182] Installing libeconf-0:0.7.9-2 100% |  65.0 MiB/s |  66.5 KiB |  00m00s
[ 68/182] Installing libcap-ng-0:0.8.5- 100% |  69.2 MiB/s |  70.8 KiB |  00m00s
[ 69/182] Installing audit-libs-0:4.1.2 100% | 372.6 MiB/s | 381.5 KiB |  00m00s
[ 70/182] Installing pam-libs-0:1.7.1-3 100% | 126.0 MiB/s | 129.0 KiB |  00m00s
[ 71/182] Installing libcap-0:2.77-1.fc 100% |  17.4 MiB/s | 214.3 KiB |  00m00s
[ 72/182] Installing libsemanage-0:3.9- 100% | 303.0 MiB/s | 310.2 KiB |  00m00s
[ 73/182] Installing libsmartcols-0:2.4 100% | 177.4 MiB/s | 181.6 KiB |  00m00s
[ 74/182] Installing lua-libs-0:5.4.8-4 100% | 276.7 MiB/s | 283.3 KiB |  00m00s
[ 75/182] Installing json-c-0:0.18-7.fc 100% |  82.0 MiB/s |  84.0 KiB |  00m00s
[ 76/182] Installing libffi-0:3.5.2-1.f 100% |  83.2 MiB/s |  85.2 KiB |  00m00s
[ 77/182] Installing p11-kit-0:0.25.8-1 100% | 127.2 MiB/s |   2.3 MiB |  00m00s
[ 78/182] Installing alternatives-0:1.3 100% |   5.7 MiB/s |  63.8 KiB |  00m00s
[ 79/182] Installing p11-kit-trust-0:0. 100% |  21.9 MiB/s | 448.3 KiB |  00m00s
[ 80/182] Installing ngtcp2-0:1.18.0-1. 100% | 308.4 MiB/s | 315.8 KiB |  00m00s
[ 81/182] Installing openssl-libs-1:3.5 100% | 424.3 MiB/s |   8.9 MiB |  00m00s
[ 82/182] Installing coreutils-0:9.9-1. 100% | 182.9 MiB/s |   5.5 MiB |  00m00s
[ 83/182] Installing ca-certificates-0: 100% |   2.2 MiB/s |   2.5 MiB |  00m01s
[ 84/182] Installing gzip-0:1.14-1.fc44 100% |  28.1 MiB/s | 403.3 KiB |  00m00s
[ 85/182] Installing rpm-sequoia-0:1.9. 100% | 413.1 MiB/s |   2.5 MiB |  00m00s
[ 86/182] Installing libfsverity-0:1.6- 100% |   0.0   B/s |  29.5 KiB |  00m00s
[ 87/182] Installing libevent-0:2.1.12- 100% | 288.7 MiB/s | 886.8 KiB |  00m00s
[ 88/182] Installing ngtcp2-crypto-ossl 100% |  51.3 MiB/s |  52.6 KiB |  00m00s
[ 89/182] Installing util-linux-core-0: 100% |  92.5 MiB/s |   1.5 MiB |  00m00s
[ 90/182] Installing zip-0:3.0-44.fc43. 100% |  52.5 MiB/s | 698.4 KiB |  00m00s
[ 91/182] Installing gnupg2-keyboxd-0:2 100% |  28.3 MiB/s | 202.7 KiB |  00m00s
[ 92/182] Installing libpsl-0:0.21.5-6. 100% |  75.7 MiB/s |  77.5 KiB |  00m00s
[ 93/182] Installing tar-2:1.35-6.fc43. 100% | 155.7 MiB/s |   3.0 MiB |  00m00s
[ 94/182] Installing linkdupes-0:0.7.2- 100% |  63.1 MiB/s | 840.1 KiB |  00m00s
[ 95/182] Installing libselinux-utils-0 100% |  24.3 MiB/s | 323.4 KiB |  00m00s
[ 96/182] Installing liblastlog2-0:2.41 100% |   5.0 MiB/s |  35.9 KiB |  00m00s
[ 97/182] Installing systemd-standalone 100% |  22.1 MiB/s | 294.3 KiB |  00m00s
[ 98/182] Installing rpm-libs-0:6.0.1-1 100% | 304.5 MiB/s | 935.3 KiB |  00m00s
[ 99/182] Installing libusb1-0:1.0.29-4 100% |  21.1 MiB/s | 172.9 KiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64
>>> Scriptlet output:
>>> Creating group 'tss' with GID 59.
>>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59.
>>> 
[100/182] Installing tpm2-tss-0:4.1.3-8 100% | 314.4 MiB/s |   1.6 MiB |  00m00s
[101/182] Installing ima-evm-utils-libs 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[102/182] Installing gnupg2-gpg-agent-0 100% |  34.7 MiB/s | 675.4 KiB |  00m00s
[103/182] Installing libfdisk-0:2.41.2- 100% | 186.3 MiB/s | 381.5 KiB |  00m00s
[104/182] Installing util-linux-0:2.41. 100% | 108.3 MiB/s |   3.6 MiB |  00m00s
[105/182] Installing policycoreutils-0: 100% |  29.0 MiB/s | 711.8 KiB |  00m00s
[106/182] Installing selinux-policy-0:4 100% |   1.7 MiB/s |  33.6 KiB |  00m00s
[107/182] Installing selinux-policy-tar 100% | 207.1 MiB/s |  14.9 MiB |  00m00s
[108/182] Installing zstd-0:1.5.7-3.fc4 100% |  33.2 MiB/s | 509.8 KiB |  00m00s
[109/182] Installing libxml2-0:2.12.10- 100% | 106.5 MiB/s |   1.7 MiB |  00m00s
[110/182] Installing nettle-0:3.10.1-2. 100% | 258.4 MiB/s | 793.7 KiB |  00m00s
[111/182] Installing gnutls-0:3.8.11-6. 100% | 405.4 MiB/s |   3.6 MiB |  00m00s
[112/182] Installing bzip2-0:1.0.8-21.f 100% |   8.1 MiB/s |  99.8 KiB |  00m00s
[113/182] Installing add-determinism-0: 100% | 144.1 MiB/s |   2.3 MiB |  00m00s
[114/182] Installing build-reproducibil 100% |   0.0   B/s |   1.5 KiB |  00m00s
[115/182] Installing cpio-0:2.15-6.fc43 100% |  78.5 MiB/s |   1.1 MiB |  00m00s
[116/182] Installing ed-0:1.22.3-1.fc44 100% |  13.4 MiB/s | 151.2 KiB |  00m00s
[117/182] Installing patch-0:2.8-2.fc43 100% |  19.9 MiB/s | 224.3 KiB |  00m00s
[118/182] Installing lz4-libs-0:1.10.0- 100% | 158.6 MiB/s | 162.5 KiB |  00m00s
[119/182] Installing libarchive-0:3.8.4 100% | 311.6 MiB/s | 957.2 KiB |  00m00s
[120/182] Installing libgomp-0:15.2.1-4 100% | 265.1 MiB/s | 543.0 KiB |  00m00s
[121/182] Installing libtool-ltdl-0:2.5 100% |   0.0   B/s |  71.2 KiB |  00m00s
[122/182] Installing gdbm-libs-1:1.23-1 100% | 128.5 MiB/s | 131.6 KiB |  00m00s
[123/182] Installing cyrus-sasl-lib-0:2 100% | 143.7 MiB/s |   2.3 MiB |  00m00s
[124/182] Installing openldap-0:2.6.10- 100% | 324.0 MiB/s | 663.6 KiB |  00m00s
[125/182] Installing gnupg2-dirmngr-0:2 100% |  31.9 MiB/s | 621.1 KiB |  00m00s
[126/182] Installing gnupg2-0:2.4.8-4.f 100% | 242.6 MiB/s |   6.6 MiB |  00m00s
[127/182] Installing rpm-sign-libs-0:6. 100% |  39.6 MiB/s |  40.6 KiB |  00m00s
[128/182] Installing gpgverify-0:2.2-3. 100% |   0.0   B/s |   9.4 KiB |  00m00s
[129/182] Installing jansson-0:2.14-3.f 100% |  88.3 MiB/s |  90.5 KiB |  00m00s
[130/182] Installing libpkgconf-0:2.3.0 100% |   0.0   B/s |  79.2 KiB |  00m00s
[131/182] Installing pkgconf-0:2.3.0-3. 100% |   7.4 MiB/s |  91.0 KiB |  00m00s
[132/182] Installing pkgconf-pkg-config 100% | 161.2 KiB/s |   1.8 KiB |  00m00s
[133/182] Installing xxhash-libs-0:0.8. 100% |  89.4 MiB/s |  91.6 KiB |  00m00s
[134/182] Installing libbrotli-0:1.2.0- 100% | 282.4 MiB/s | 867.7 KiB |  00m00s
[135/182] Installing libnghttp2-0:1.68. 100% | 159.5 MiB/s | 163.4 KiB |  00m00s
[136/182] Installing libnghttp3-0:1.13. 100% | 153.0 MiB/s | 156.7 KiB |  00m00s
[137/182] Installing keyutils-libs-0:1. 100% |  54.4 MiB/s |  55.7 KiB |  00m00s
[138/182] Installing libcom_err-0:1.47. 100% |   0.0   B/s |  64.2 KiB |  00m00s
[139/182] Installing libverto-0:0.3.2-1 100% |  26.6 MiB/s |  27.2 KiB |  00m00s
[140/182] Installing krb5-libs-0:1.21.3 100% | 328.5 MiB/s |   2.3 MiB |  00m00s
[141/182] Installing libssh-0:0.11.3-1. 100% | 277.9 MiB/s | 569.2 KiB |  00m00s
[142/182] Installing libcurl-0:8.18.0~r 100% | 319.7 MiB/s | 982.1 KiB |  00m00s
[143/182] Installing curl-0:8.18.0~rc1- 100% |  21.8 MiB/s | 469.6 KiB |  00m00s
[144/182] Installing rpm-0:6.0.1-1.fc44 100% |  82.3 MiB/s |   2.6 MiB |  00m00s
[145/182] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[146/182] Installing java-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[147/182] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[148/182] Installing tree-sitter-srpm-m 100% |   0.0   B/s |   9.3 KiB |  00m00s
[149/182] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[150/182] Installing filesystem-srpm-ma 100% |   0.0   B/s |  38.9 KiB |  00m00s
[151/182] Installing elfutils-default-y 100% | 408.6 KiB/s |   2.0 KiB |  00m00s
[152/182] Installing elfutils-libs-0:0. 100% | 224.4 MiB/s | 689.3 KiB |  00m00s
[153/182] Installing elfutils-debuginfo 100% |   6.5 MiB/s |  86.3 KiB |  00m00s
[154/182] Installing elfutils-0:0.194-2 100% | 162.8 MiB/s |   2.9 MiB |  00m00s
[155/182] Installing binutils-0:2.45.50 100% | 351.5 MiB/s |  27.1 MiB |  00m00s
[156/182] Installing gdb-minimal-0:16.3 100% | 308.3 MiB/s |  13.3 MiB |  00m00s
[157/182] Installing debugedit-0:5.2-3. 100% |  17.7 MiB/s | 217.3 KiB |  00m00s
[158/182] Installing rpm-build-libs-0:6 100% | 259.0 MiB/s | 265.2 KiB |  00m00s
[159/182] Installing rust-srpm-macros-0 100% |   0.0   B/s |   6.4 KiB |  00m00s
[160/182] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 740.0   B |  00m00s
[161/182] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[162/182] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[163/182] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[164/182] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[165/182] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.1 KiB |  00m00s
[166/182] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[167/182] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[168/182] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[169/182] Installing gap-srpm-macros-0: 100% |   0.0   B/s |   2.7 KiB |  00m00s
[170/182] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[171/182] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[172/182] Installing rpm-build-0:6.0.1- 100% |  22.3 MiB/s | 296.6 KiB |  00m00s
[173/182] Installing pyproject-srpm-mac 100% |   0.0   B/s |   2.5 KiB |  00m00s
[174/182] Installing redhat-rpm-config- 100% |  30.9 MiB/s | 189.9 KiB |  00m00s
[175/182] Installing forge-srpm-macros- 100% |   0.0   B/s |  40.3 KiB |  00m00s
[176/182] Installing fonts-srpm-macros- 100% |   0.0   B/s |  57.0 KiB |  00m00s
[177/182] Installing go-srpm-macros-0:3 100% |   0.0   B/s |  63.0 KiB |  00m00s
[178/182] Installing python-srpm-macros 100% |   0.0   B/s |  52.9 KiB |  00m00s
[179/182] Installing rpm-plugin-selinux 100% |   0.0   B/s |  13.0 KiB |  00m00s
[180/182] Installing which-0:2.23-3.fc4 100% |   6.4 MiB/s |  85.7 KiB |  00m00s
[181/182] Installing shadow-utils-2:4.1 100% | 152.8 MiB/s |   4.0 MiB |  00m00s
[182/182] Installing info-0:7.2-7.fc44. 100% |  48.5 KiB/s | 358.3 KiB |  00m07s
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.7.2-2.fc44.x86_64
alternatives-1.33-3.fc44.x86_64
ansible-srpm-macros-1-18.1.fc43.noarch
audit-libs-4.1.2-2.fc44.x86_64
bash-5.3.0-2.fc43.x86_64
binutils-2.45.50-9.fc44.x86_64
build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch
bzip2-1.0.8-21.fc43.x86_64
bzip2-libs-1.0.8-21.fc43.x86_64
ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch
coreutils-9.9-1.fc44.x86_64
coreutils-common-9.9-1.fc44.x86_64
cpio-2.15-6.fc43.x86_64
crypto-policies-20251128-1.git19878fe.fc44.noarch
curl-8.18.0~rc1-1.fc44.x86_64
cyrus-sasl-lib-2.1.28-33.fc44.x86_64
debugedit-5.2-3.fc44.x86_64
diffutils-3.12-3.fc43.x86_64
dwz-0.16-2.fc43.x86_64
ed-1.22.3-1.fc44.x86_64
efi-srpm-macros-6-5.fc44.noarch
elfutils-0.194-2.fc44.x86_64
elfutils-debuginfod-client-0.194-2.fc44.x86_64
elfutils-default-yama-scope-0.194-2.fc44.noarch
elfutils-libelf-0.194-2.fc44.x86_64
elfutils-libs-0.194-2.fc44.x86_64
fedora-gpg-keys-44-0.1.noarch
fedora-release-44-0.8.noarch
fedora-release-common-44-0.8.noarch
fedora-release-identity-basic-44-0.8.noarch
fedora-repos-44-0.1.noarch
fedora-repos-rawhide-44-0.1.noarch
file-5.46-8.fc44.x86_64
file-libs-5.46-8.fc44.x86_64
filesystem-3.18-50.fc43.x86_64
filesystem-srpm-macros-3.18-50.fc43.noarch
findutils-4.10.0-6.fc43.x86_64
fonts-srpm-macros-5.0.0-1.fc44.noarch
forge-srpm-macros-0.4.0-3.fc43.noarch
fpc-srpm-macros-1.3-15.fc43.noarch
gap-srpm-macros-2-1.fc44.noarch
gawk-5.3.2-2.fc43.x86_64
gdb-minimal-16.3-6.fc44.x86_64
gdbm-libs-1.23-10.fc43.x86_64
ghc-srpm-macros-1.9.2-3.fc43.noarch
glibc-2.42.9000-15.fc44.x86_64
glibc-common-2.42.9000-15.fc44.x86_64
glibc-gconv-extra-2.42.9000-15.fc44.x86_64
glibc-minimal-langpack-2.42.9000-15.fc44.x86_64
gmp-6.3.0-4.fc44.x86_64
gnat-srpm-macros-6-8.fc43.noarch
gnulib-l10n-20241231-1.fc44.noarch
gnupg2-2.4.8-4.fc43.x86_64
gnupg2-dirmngr-2.4.8-4.fc43.x86_64
gnupg2-gpg-agent-2.4.8-4.fc43.x86_64
gnupg2-gpgconf-2.4.8-4.fc43.x86_64
gnupg2-keyboxd-2.4.8-4.fc43.x86_64
gnupg2-verify-2.4.8-4.fc43.x86_64
gnutls-3.8.11-6.fc44.x86_64
go-srpm-macros-3.8.0-1.fc44.noarch
gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b
gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-3.fc43.noarch
grep-3.12-2.fc43.x86_64
gzip-1.14-1.fc44.x86_64
ima-evm-utils-libs-1.6.2-7.fc44.x86_64
info-7.2-7.fc44.x86_64
jansson-2.14-3.fc43.x86_64
java-srpm-macros-1-7.fc43.noarch
json-c-0.18-7.fc43.x86_64
kernel-srpm-macros-1.0-27.fc43.noarch
keyutils-libs-1.6.3-6.fc43.x86_64
krb5-libs-1.21.3-10.fc44.x86_64
libacl-2.3.2-4.fc43.x86_64
libarchive-3.8.4-1.fc44.x86_64
libassuan-2.5.7-4.fc43.x86_64
libattr-2.5.2-6.fc43.x86_64
libblkid-2.41.2-9.fc44.x86_64
libbrotli-1.2.0-1.fc44.x86_64
libcap-2.77-1.fc44.x86_64
libcap-ng-0.8.5-8.fc44.x86_64
libcom_err-1.47.3-3.fc44.x86_64
libcurl-8.18.0~rc1-1.fc44.x86_64
libeconf-0.7.9-2.fc43.x86_64
libevent-2.1.12-16.fc43.x86_64
libfdisk-2.41.2-9.fc44.x86_64
libffi-3.5.2-1.fc44.x86_64
libfsverity-1.6-3.fc43.x86_64
libgcc-15.2.1-4.fc44.x86_64
libgcrypt-1.11.2-1.fc44.x86_64
libgomp-15.2.1-4.fc44.x86_64
libgpg-error-1.57-1.fc44.x86_64
libidn2-2.3.8-2.fc43.x86_64
libksba-1.6.7-4.fc43.x86_64
liblastlog2-2.41.2-9.fc44.x86_64
libmount-2.41.2-9.fc44.x86_64
libnghttp2-1.68.0-2.fc44.x86_64
libnghttp3-1.13.1-1.fc44.x86_64
libpkgconf-2.3.0-3.fc43.x86_64
libpsl-0.21.5-6.fc43.x86_64
libselinux-3.9-5.fc44.x86_64
libselinux-utils-3.9-5.fc44.x86_64
libsemanage-3.9-4.fc44.x86_64
libsepol-3.9-2.fc43.x86_64
libsmartcols-2.41.2-9.fc44.x86_64
libssh-0.11.3-1.fc44.x86_64
libssh-config-0.11.3-1.fc44.noarch
libstdc++-15.2.1-4.fc44.x86_64
libtasn1-4.20.0-2.fc43.x86_64
libtool-ltdl-2.5.4-8.fc44.x86_64
libunistring-1.1-10.fc43.x86_64
libusb1-1.0.29-4.fc44.x86_64
libuuid-2.41.2-9.fc44.x86_64
libverto-0.3.2-11.fc43.x86_64
libxcrypt-4.5.2-2.fc44.x86_64
libxml2-2.12.10-5.fc44.x86_64
libzstd-1.5.7-3.fc44.x86_64
linkdupes-0.7.2-2.fc44.x86_64
lua-libs-5.4.8-4.fc44.x86_64
lua-srpm-macros-1-16.fc43.noarch
lz4-libs-1.10.0-3.fc43.x86_64
mpfr-4.2.2-2.fc43.x86_64
ncurses-base-6.5-8.20250614.fc44.noarch
ncurses-libs-6.5-8.20250614.fc44.x86_64
nettle-3.10.1-2.fc43.x86_64
ngtcp2-1.18.0-1.fc44.x86_64
ngtcp2-crypto-ossl-1.18.0-1.fc44.x86_64
npth-1.8-3.fc43.x86_64
ocaml-srpm-macros-11-2.fc43.noarch
openblas-srpm-macros-2-20.fc43.noarch
openldap-2.6.10-4.fc44.x86_64
openssl-libs-3.5.4-1.fc44.x86_64
p11-kit-0.25.8-1.fc44.x86_64
p11-kit-trust-0.25.8-1.fc44.x86_64
package-notes-srpm-macros-0.5-14.fc43.noarch
pam-libs-1.7.1-3.fc43.x86_64
patch-2.8-2.fc43.x86_64
pcre2-10.47-1.fc44.x86_64
pcre2-syntax-10.47-1.fc44.noarch
perl-srpm-macros-1-60.fc43.noarch
pkgconf-2.3.0-3.fc43.x86_64
pkgconf-m4-2.3.0-3.fc43.noarch
pkgconf-pkg-config-2.3.0-3.fc43.x86_64
policycoreutils-3.9-5.fc44.x86_64
popt-1.19-9.fc43.x86_64
publicsuffix-list-dafsa-20250616-2.fc43.noarch
pyproject-srpm-macros-1.18.6-1.fc44.noarch
python-srpm-macros-3.14-9.fc44.noarch
qt5-srpm-macros-5.15.18-1.fc44.noarch
qt6-srpm-macros-6.10.1-1.fc44.noarch
readline-8.3-2.fc43.x86_64
redhat-rpm-config-343-16.fc44.noarch
rpm-6.0.1-1.fc44.x86_64
rpm-build-6.0.1-1.fc44.x86_64
rpm-build-libs-6.0.1-1.fc44.x86_64
rpm-libs-6.0.1-1.fc44.x86_64
rpm-plugin-selinux-6.0.1-1.fc44.x86_64
rpm-sequoia-1.9.0-2.fc43.x86_64
rpm-sign-libs-6.0.1-1.fc44.x86_64
rust-srpm-macros-28.4-1.fc44.noarch
sed-4.9-6.fc44.x86_64
selinux-policy-42.19-1.fc44.noarch
selinux-policy-targeted-42.19-1.fc44.noarch
setup-2.15.0-27.fc44.noarch
shadow-utils-4.18.0-7.fc44.x86_64
sqlite-libs-3.51.0-1.fc44.x86_64
systemd-libs-259~rc3-1.fc44.x86_64
systemd-standalone-sysusers-259~rc3-1.fc44.x86_64
tar-1.35-6.fc43.x86_64
tpm2-tss-4.1.3-8.fc43.x86_64
tree-sitter-srpm-macros-0.4.2-1.fc43.noarch
unzip-6.0-68.fc44.x86_64
util-linux-2.41.2-9.fc44.x86_64
util-linux-core-2.41.2-9.fc44.x86_64
which-2.23-3.fc43.x86_64
xxhash-libs-0.8.3-3.fc43.x86_64
xz-5.8.1-4.fc44.x86_64
xz-libs-5.8.1-4.fc44.x86_64
zig-srpm-macros-1-5.fc43.noarch
zip-3.0-44.fc43.x86_64
zlib-ng-compat-2.3.2-1.fc44.x86_64
zstd-1.5.7-3.fc44.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753228800
Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.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-x86_64-1765551765.922229/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-goiwco8e/percolator/percolator.spec) Config(child) 0 minutes 17 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-3.08-1.fc44.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1765551765.922229/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1765551765.922229/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-x86_64-1765551765.922229/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-6.0.1-1.fc44.x86_64
  rpm-sequoia-1.9.0-2.fc43.x86_64
  dnf5-5.3.0.0-3.fc44.x86_64
  dnf5-plugins-5.3.0.0-3.fc44.x86_64
Finish: chroot init
Start: build phase for percolator-3.08-1.fc44.src.rpm
Start: build setup for percolator-3.08-1.fc44.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753228800
Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |  84.9 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 129.4 KiB/s |  27.1 KiB |  00m00s
Repositories loaded.
Package                    Arch   Version               Repository      Size
Installing:
 boost-devel               x86_64 0:1.83.0-17.fc44      fedora     143.0 MiB
 boost-static              x86_64 0:1.83.0-17.fc44      fedora     383.3 MiB
 bzip2-devel               x86_64 0:1.0.8-21.fc43       fedora     309.8 KiB
 cmake                     x86_64 0:3.31.10-2.fc44      fedora      34.5 MiB
 eigen3-devel              noarch 0:5.0.1-1.fc44        fedora       9.5 MiB
 gcc                       x86_64 0:15.2.1-4.fc44       fedora     111.9 MiB
 gcc-c++                   x86_64 0:15.2.1-4.fc44       fedora      41.4 MiB
 gtest-devel               x86_64 0:1.17.0-1.fc44       fedora       1.1 MiB
 libtirpc-devel            x86_64 0:1.3.7-1.fc44        fedora     251.6 KiB
 make                      x86_64 1:4.4.1-11.fc43       fedora       1.8 MiB
 python3-devel             x86_64 0:3.14.2-1.fc44       fedora       1.9 MiB
 sqlite-devel              x86_64 0:3.51.0-1.fc44       fedora     694.0 KiB
 tokyocabinet-devel        x86_64 0:1.4.48-29.fc44      fedora     460.0 KiB
 xerces-c-devel            x86_64 0:3.3.0-8.fc43        fedora       4.1 MiB
 xsd                       x86_64 0:4.1.0-0.18.a11.fc43 fedora       5.0 MiB
 zlib-ng-compat-devel      x86_64 0:2.3.2-1.fc44        fedora     107.0 KiB
Installing dependencies:
 annobin-docs              noarch 0:13.03-1.fc44        fedora      99.2 KiB
 annobin-plugin-gcc        x86_64 0:13.03-1.fc44        fedora     695.8 KiB
 boost                     x86_64 0:1.83.0-17.fc44      fedora       1.3 KiB
 boost-atomic              x86_64 0:1.83.0-17.fc44      fedora      20.9 KiB
 boost-chrono              x86_64 0:1.83.0-17.fc44      fedora      37.5 KiB
 boost-container           x86_64 0:1.83.0-17.fc44      fedora      65.4 KiB
 boost-context             x86_64 0:1.83.0-17.fc44      fedora      12.4 KiB
 boost-contract            x86_64 0:1.83.0-17.fc44      fedora      99.1 KiB
 boost-coroutine           x86_64 0:1.83.0-17.fc44      fedora      21.1 KiB
 boost-date-time           x86_64 0:1.83.0-17.fc44      fedora      12.2 KiB
 boost-fiber               x86_64 0:1.83.0-17.fc44      fedora      78.7 KiB
 boost-filesystem          x86_64 0:1.83.0-17.fc44      fedora     143.6 KiB
 boost-graph               x86_64 0:1.83.0-17.fc44      fedora     363.1 KiB
 boost-iostreams           x86_64 0:1.83.0-17.fc44      fedora      90.6 KiB
 boost-json                x86_64 0:1.83.0-17.fc44      fedora     333.1 KiB
 boost-locale              x86_64 0:1.83.0-17.fc44      fedora     617.7 KiB
 boost-log                 x86_64 0:1.83.0-17.fc44      fedora       1.5 MiB
 boost-math                x86_64 0:1.83.0-17.fc44      fedora     642.6 KiB
 boost-nowide              x86_64 0:1.83.0-17.fc44      fedora      20.8 KiB
 boost-numpy3              x86_64 0:1.83.0-17.fc44      fedora      57.6 KiB
 boost-program-options     x86_64 0:1.83.0-17.fc44      fedora     280.8 KiB
 boost-python3             x86_64 0:1.83.0-17.fc44      fedora     258.2 KiB
 boost-random              x86_64 0:1.83.0-17.fc44      fedora      29.6 KiB
 boost-regex               x86_64 0:1.83.0-17.fc44      fedora     291.2 KiB
 boost-serialization       x86_64 0:1.83.0-17.fc44      fedora     441.6 KiB
 boost-stacktrace          x86_64 0:1.83.0-17.fc44      fedora      59.8 KiB
 boost-system              x86_64 0:1.83.0-17.fc44      fedora      12.2 KiB
 boost-test                x86_64 0:1.83.0-17.fc44      fedora     647.2 KiB
 boost-thread              x86_64 0:1.83.0-17.fc44      fedora     132.7 KiB
 boost-timer               x86_64 0:1.83.0-17.fc44      fedora      21.0 KiB
 boost-type_erasure        x86_64 0:1.83.0-17.fc44      fedora      54.1 KiB
 boost-wave                x86_64 0:1.83.0-17.fc44      fedora     868.3 KiB
 cmake-data                noarch 0:3.31.10-2.fc44      fedora       8.4 MiB
 cmake-filesystem          x86_64 0:3.31.10-2.fc44      fedora       0.0   B
 cmake-rpm-macros          noarch 0:3.31.10-2.fc44      fedora       8.2 KiB
 cpp                       x86_64 0:15.2.1-4.fc44       fedora      37.9 MiB
 emacs-filesystem          x86_64 1:30.2-1.fc44         fedora       0.0   B
 expat                     x86_64 0:2.7.3-1.fc44        fedora     301.1 KiB
 flexiblas                 x86_64 0:3.5.0-1.fc44        fedora      38.0 KiB
 flexiblas-netlib          x86_64 0:3.5.0-1.fc44        fedora      16.5 MiB
 flexiblas-openblas-openmp x86_64 0:3.5.0-1.fc44        fedora      39.2 KiB
 gcc-plugin-annobin        x86_64 0:15.2.1-4.fc44       fedora      57.1 KiB
 glibc-devel               x86_64 0:2.42.9000-15.fc44   fedora       2.3 MiB
 gmock                     x86_64 0:1.17.0-1.fc44       fedora     131.0 KiB
 gtest                     x86_64 0:1.17.0-1.fc44       fedora     505.8 KiB
 jsoncpp                   x86_64 0:1.9.6-2.fc43        fedora     257.6 KiB
 kernel-headers            x86_64 0:6.18.0-65.fc44      fedora       6.8 MiB
 libcutl                   x86_64 0:1.10.0-33.fc43      fedora       1.1 MiB
 libgfortran               x86_64 0:15.2.1-4.fc44       fedora       3.4 MiB
 libicu                    x86_64 0:77.1-1.fc43         fedora      36.4 MiB
 libicu-devel              x86_64 0:77.1-1.fc43         fedora       5.0 MiB
 libmpc                    x86_64 0:1.3.1-8.fc43        fedora     160.6 KiB
 libquadmath               x86_64 0:15.2.1-4.fc44       fedora     317.9 KiB
 libquadmath-devel         x86_64 0:15.2.1-4.fc44       fedora      22.2 KiB
 libstdc++-devel           x86_64 0:15.2.1-4.fc44       fedora      37.2 MiB
 libtirpc                  x86_64 0:1.3.7-1.fc44        fedora     200.4 KiB
 libuv                     x86_64 1:1.51.0-2.fc43       fedora     570.2 KiB
 libxcrypt-devel           x86_64 0:4.5.2-2.fc44        fedora      31.0 KiB
 mpdecimal                 x86_64 0:4.0.1-2.fc43        fedora     217.2 KiB
 openblas                  x86_64 0:0.3.29-2.fc43       fedora     111.7 KiB
 openblas-openmp           x86_64 0:0.3.29-2.fc43       fedora      43.7 MiB
 pyproject-rpm-macros      noarch 0:1.18.6-1.fc44       fedora     115.6 KiB
 python-pip-wheel          noarch 0:25.3-1.fc44         fedora       1.2 MiB
 python-rpm-macros         noarch 0:3.14-9.fc44         fedora      27.6 KiB
 python3                   x86_64 0:3.14.2-1.fc44       fedora      28.9 KiB
 python3-libs              x86_64 0:3.14.2-1.fc44       fedora      43.1 MiB
 python3-numpy             x86_64 1:2.3.5-1.fc44        fedora      41.4 MiB
 python3-numpy-f2py        x86_64 1:2.3.5-1.fc44        fedora       2.1 MiB
 python3-packaging         noarch 0:25.0-7.fc44         fedora     607.4 KiB
 python3-rpm-generators    noarch 0:14-13.fc43          fedora      81.7 KiB
 python3-rpm-macros        noarch 0:3.14-9.fc44         fedora       6.5 KiB
 rhash                     x86_64 0:1.4.5-3.fc43        fedora     351.1 KiB
 sqlite                    x86_64 0:3.51.0-1.fc44       fedora       1.9 MiB
 tokyocabinet              x86_64 0:1.4.48-29.fc44      fedora       1.5 MiB
 tzdata                    noarch 0:2025b-3.fc43        fedora       1.6 MiB
 vim-filesystem            noarch 2:9.1.1952-1.fc44     fedora      40.0   B
 xerces-c                  x86_64 0:3.3.0-8.fc43        fedora       3.8 MiB

Transaction Summary:
 Installing:        93 packages

Total size of inbound packages is 210 MiB. Need to download 57 MiB.
After this operation, 1 GiB extra will be used (install 1 GiB, remove 0 B).
[ 1/93] gcc-0:15.2.1-4.fc44.x86_64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
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[90/93] python-rpm-macros-0:3.14-9.fc44 100% |   9.6 MiB/s |  19.6 KiB |  00m00s
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[93/93] boost-static-0:1.83.0-17.fc44.x 100% | 115.1 MiB/s |  49.8 MiB |  00m00s
--------------------------------------------------------------------------------
[93/93] Total                           100% | 100.8 MiB/s |  57.0 MiB |  00m01s
Running transaction
[ 1/95] Verify package files            100% | 132.0   B/s |  93.0   B |  00m01s
[ 2/95] Prepare transaction             100% | 715.0   B/s |  93.0   B |  00m00s
[ 3/95] Installing boost-system-0:1.83. 100% |  12.8 MiB/s |  13.1 KiB |  00m00s
[ 4/95] Installing boost-chrono-0:1.83. 100% |  37.6 MiB/s |  38.5 KiB |  00m00s
[ 5/95] Installing cmake-filesystem-0:3 100% |   7.4 MiB/s |   7.6 KiB |  00m00s
[ 6/95] Installing boost-thread-0:1.83. 100% | 130.5 MiB/s | 133.7 KiB |  00m00s
[ 7/95] Installing libicu-0:77.1-1.fc43 100% | 413.5 MiB/s |  36.4 MiB |  00m00s
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[10/95] Installing boost-context-0:1.83 100% |   0.0   B/s |  13.4 KiB |  00m00s
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[12/95] Installing boost-filesystem-0:1 100% | 141.3 MiB/s | 144.6 KiB |  00m00s
[13/95] Installing expat-0:2.7.3-1.fc44 100% |  24.7 MiB/s | 303.2 KiB |  00m00s
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[19/95] Installing boost-container-0:1. 100% |   0.0   B/s |  66.4 KiB |  00m00s
[20/95] Installing gtest-0:1.17.0-1.fc4 100% | 247.7 MiB/s | 507.3 KiB |  00m00s
[21/95] Installing xerces-c-0:3.3.0-8.f 100% | 471.2 MiB/s |   3.8 MiB |  00m00s
[22/95] Installing make-1:4.4.1-11.fc43 100% | 112.5 MiB/s |   1.8 MiB |  00m00s
[23/95] Installing gmock-0:1.17.0-1.fc4 100% | 129.3 MiB/s | 132.4 KiB |  00m00s
[24/95] Installing boost-json-0:1.83.0- 100% | 326.2 MiB/s | 334.1 KiB |  00m00s
[25/95] Installing boost-wave-0:1.83.0- 100% | 424.5 MiB/s | 869.3 KiB |  00m00s
[26/95] Installing pyproject-rpm-macros 100% | 114.8 MiB/s | 117.5 KiB |  00m00s
[27/95] Installing cpp-0:15.2.1-4.fc44. 100% | 364.9 MiB/s |  38.0 MiB |  00m00s
[28/95] Installing libcutl-0:1.10.0-33. 100% | 356.5 MiB/s |   1.1 MiB |  00m00s
[29/95] Installing boost-fiber-0:1.83.0 100% |  77.8 MiB/s |  79.7 KiB |  00m00s
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[32/95] Installing boost-graph-0:1.83.0 100% | 177.8 MiB/s | 364.1 KiB |  00m00s
[33/95] Installing libicu-devel-0:77.1- 100% | 211.8 MiB/s |   5.1 MiB |  00m00s
[34/95] Installing boost-locale-0:1.83. 100% | 302.1 MiB/s | 618.7 KiB |  00m00s
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[38/95] Installing kernel-headers-0:6.1 100% | 216.9 MiB/s |   6.9 MiB |  00m00s
[39/95] Installing glibc-devel-0:2.42.9 100% | 182.4 MiB/s |   2.4 MiB |  00m00s
[40/95] Installing libxcrypt-devel-0:4. 100% |  32.5 MiB/s |  33.3 KiB |  00m00s
[41/95] Installing gcc-0:15.2.1-4.fc44. 100% | 416.3 MiB/s | 112.0 MiB |  00m00s
[42/95] Installing libquadmath-devel-0: 100% |   7.7 MiB/s |  23.6 KiB |  00m00s
[43/95] Installing libstdc++-devel-0:15 100% | 484.5 MiB/s |  37.3 MiB |  00m00s
[44/95] Installing openblas-0:0.3.29-2. 100% | 110.8 MiB/s | 113.5 KiB |  00m00s
[45/95] Installing openblas-openmp-0:0. 100% | 661.9 MiB/s |  43.7 MiB |  00m00s
[46/95] Installing flexiblas-netlib-0:3 100% | 343.9 MiB/s |  16.5 MiB |  00m00s
[47/95] Installing flexiblas-0:3.5.0-1. 100% |   0.0   B/s |  39.2 KiB |  00m00s
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[49/95] Installing tzdata-0:2025b-3.fc4 100% |  70.1 MiB/s |   1.9 MiB |  00m00s
[50/95] Installing python-pip-wheel-0:2 100% | 602.0 MiB/s |   1.2 MiB |  00m00s
[51/95] Installing mpdecimal-0:4.0.1-2. 100% |  35.6 MiB/s | 218.8 KiB |  00m00s
[52/95] Installing python3-libs-0:3.14. 100% | 359.4 MiB/s |  43.5 MiB |  00m00s
[53/95] Installing python3-0:3.14.2-1.f 100% |   2.3 MiB/s |  30.6 KiB |  00m00s
[54/95] Installing boost-python3-0:1.83 100% | 126.6 MiB/s | 259.2 KiB |  00m00s
[55/95] Installing python3-numpy-f2py-1 100% |  90.5 MiB/s |   2.2 MiB |  00m00s
[56/95] Installing python3-numpy-1:2.3. 100% | 359.3 MiB/s |  41.7 MiB |  00m00s
[57/95] Installing cmake-rpm-macros-0:3 100% |   0.0   B/s |   8.8 KiB |  00m00s
[58/95] Installing boost-numpy3-0:1.83. 100% |  57.3 MiB/s |  58.6 KiB |  00m00s
[59/95] Installing python3-packaging-0: 100% | 302.7 MiB/s | 619.9 KiB |  00m00s
[60/95] Installing python3-rpm-generato 100% |   0.0   B/s |  82.9 KiB |  00m00s
[61/95] Installing vim-filesystem-2:9.1 100% |   4.6 MiB/s |   4.7 KiB |  00m00s
[62/95] Installing emacs-filesystem-1:3 100% |   0.0   B/s | 812.0   B |  00m00s
[63/95] Installing boost-test-0:1.83.0- 100% | 316.7 MiB/s | 648.7 KiB |  00m00s
[64/95] Installing boost-stacktrace-0:1 100% |  60.3 MiB/s |  61.7 KiB |  00m00s
[65/95] Installing boost-serialization- 100% | 216.3 MiB/s | 443.1 KiB |  00m00s
[66/95] Installing boost-random-0:1.83. 100% |   0.0   B/s |  30.6 KiB |  00m00s
[67/95] Installing boost-program-option 100% | 275.2 MiB/s | 281.8 KiB |  00m00s
[68/95] Installing boost-nowide-0:1.83. 100% |   0.0   B/s |  21.8 KiB |  00m00s
[69/95] Installing boost-math-0:1.83.0- 100% | 315.4 MiB/s | 645.9 KiB |  00m00s
[70/95] Installing boost-iostreams-0:1. 100% |  89.5 MiB/s |  91.6 KiB |  00m00s
[71/95] Installing boost-contract-0:1.8 100% |  97.8 MiB/s | 100.1 KiB |  00m00s
[72/95] Installing boost-0:1.83.0-17.fc 100% |  57.3 KiB/s |   1.7 KiB |  00m00s
[73/95] Installing boost-devel-0:1.83.0 100% | 306.2 MiB/s | 145.8 MiB |  00m00s
[74/95] Installing tokyocabinet-0:1.4.4 100% |  87.4 MiB/s |   1.5 MiB |  00m00s
[75/95] Installing sqlite-0:3.51.0-1.fc 100% | 116.4 MiB/s |   1.9 MiB |  00m00s
[76/95] Installing libtirpc-0:1.3.7-1.f 100% | 197.7 MiB/s | 202.4 KiB |  00m00s
[77/95] Installing rhash-0:1.4.5-3.fc43 100% |  26.8 MiB/s | 356.4 KiB |  00m00s
[78/95] Installing libuv-1:1.51.0-2.fc4 100% | 279.8 MiB/s | 573.0 KiB |  00m00s
[79/95] Installing jsoncpp-0:1.9.6-2.fc 100% | 253.1 MiB/s | 259.2 KiB |  00m00s
[80/95] Installing cmake-0:3.31.10-2.fc 100% | 329.1 MiB/s |  34.6 MiB |  00m00s
[81/95] Installing cmake-data-0:3.31.10 100% | 124.5 MiB/s |   9.0 MiB |  00m00s
[82/95] Installing libtirpc-devel-0:1.3 100% | 128.5 MiB/s | 263.1 KiB |  00m00s
[83/95] Installing sqlite-devel-0:3.51. 100% | 678.4 MiB/s | 694.7 KiB |  00m00s
[84/95] Installing tokyocabinet-devel-0 100% | 452.2 MiB/s | 463.1 KiB |  00m00s
[85/95] Installing boost-static-0:1.83. 100% | 566.2 MiB/s | 383.3 MiB |  00m01s
[86/95] Installing python3-devel-0:3.14 100% |  90.7 MiB/s |   2.0 MiB |  00m00s
[87/95] Installing gcc-c++-0:15.2.1-4.f 100% | 339.1 MiB/s |  41.4 MiB |  00m00s
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[91/95] Installing gtest-devel-0:1.17.0 100% | 213.0 MiB/s |   1.1 MiB |  00m00s
[92/95] Installing xerces-c-devel-0:3.3 100% | 263.2 MiB/s |   4.2 MiB |  00m00s
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[95/95] Installing bzip2-devel-0:1.0.8- 100% |   2.3 MiB/s | 310.7 KiB |  00m00s
Complete!
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753228800
Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% |  19.1 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% |  74.3 KiB/s |  27.1 KiB |  00m00s
Repositories loaded.
Package "boost-devel-1.83.0-17.fc44.x86_64" is already installed.
Package "boost-static-1.83.0-17.fc44.x86_64" is already installed.
Package "bzip2-devel-1.0.8-21.fc43.x86_64" is already installed.
Package "cmake-3.31.10-2.fc44.x86_64" is already installed.
Package "eigen3-devel-5.0.1-1.fc44.noarch" is already installed.
Package "gcc-15.2.1-4.fc44.x86_64" is already installed.
Package "gcc-c++-15.2.1-4.fc44.x86_64" is already installed.
Package "gtest-devel-1.17.0-1.fc44.x86_64" is already installed.
Package "make-1:4.4.1-11.fc43.x86_64" is already installed.
Package "libtirpc-devel-1.3.7-1.fc44.x86_64" is already installed.
Package "sqlite-devel-3.51.0-1.fc44.x86_64" is already installed.
Package "tokyocabinet-devel-1.4.48-29.fc44.x86_64" is already installed.
Package "xerces-c-devel-3.3.0-8.fc43.x86_64" is already installed.
Package "python3-devel-3.14.2-1.fc44.x86_64" is already installed.
Package "xsd-4.1.0-0.18.a11.fc43.x86_64" is already installed.
Package "zlib-ng-compat-devel-2.3.2-1.fc44.x86_64" is already installed.

Nothing to do.
Finish: build setup for percolator-3.08-1.fc44.src.rpm
Start: rpmbuild percolator-3.08-1.fc44.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753228800
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.oRVlSw
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SDum78
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd /builddir/build/BUILD/percolator-3.08-build
+ rm -rf percolator-rel-3-08
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-08.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-08
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #0 (percolator-unbundle_eigen_gtest.patch):
+ echo 'Patch #0 (percolator-unbundle_eigen_gtest.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0
patching file src/CMakeLists.txt
patching file tests/unit_tests/percolator/CMakeLists.txt
+ 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 '{}' ';'
+ rm -rf 'percolator/_deps/*'
+ 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
+ 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.IO4L9q
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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-3-08
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ mkdir -p percolator
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -S . -B redhat-linux-build -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 -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -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 -B percolator -S ./ -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -DBUILD_TESTING:BOOL=ON -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = x86_64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.3.0
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Locating CodeSynthesis library with XSDDIR set to 
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from                  : /usr/lib64/libtirpc.so
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.0s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_INSTALL_FULL_SBINDIR
    CMAKE_INSTALL_SBINDIR
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
+ 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
+ /usr/bin/cmake --build percolator -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/CMakeFiles/generate_xsd.dir/build.make src/CMakeFiles/generate_xsd.dir/depend
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
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gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/generate_xsd.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
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gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
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[  2%] Generating percolator_out.* from XSD
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --std c++11 --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_in.xsd
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --std c++11 --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_out.xsd
[  3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[  4%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[  5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
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[  8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/parser.cxx
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:109:35: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
  109 |   std::unique_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                   ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:104:22: warning:   ‘xercesc_3_3::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  104 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:147:1: warning:   when initialized here [-Wreorder]
  147 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In member function ‘std::unique_ptr<xercesc_3_3::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:182:14: warning: unused variable ‘n’ [-Wunused-variable]
  182 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:174:9: warning: unused variable ‘i’ [-Wunused-variable]
  174 |     int i(1);
      |         ^
[ 20%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
[ 21%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/serializer.cxx
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[ 23%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[ 29%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 33%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 33%] Built target picked_protein
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                           ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                                          ^~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder]
  119 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  120 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning:   ‘bool XMLInterface::printExpMass_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |                      ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp: In member function ‘int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:239:32: warning: unused variable ‘numFeatures’ [-Wunused-variable]
  239 |             const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                                ^~~~~~~~~~~
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  122 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable]
  118 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  168 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable]
  157 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder]
  102 |       useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_;
      |       ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   86 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
   98 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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/IsotonicPEP.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/CompositionSorter.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/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.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/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.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/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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 -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 90%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 91%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
[ 92%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
[ 95%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 95%] Built target qvality
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a /usr/lib64/libxerces-c.so /usr/lib64/libtirpc.so -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[100%] Built target percolator
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_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_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[100%] Built target gtest_unit
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/CMakeFiles 0

+ mkdir -p src/fido
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -S . -B percolator -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 -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -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 -B src/fido -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64 -DBUILD_TESTING:BOOL=ON
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = OFF
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = x86_64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.0s)
-- Generating done (0.0s)
-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_INSTALL_FULL_SBINDIR
    CMAKE_INSTALL_SBINDIR
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR
    TokyoCabinet_INCLUDE_DIR
    TokyoCabinet_LIBRARY


+ /usr/bin/cmake --build src/fido -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
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gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
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gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
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[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[  5%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[  6%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[  7%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[  9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[ 11%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[ 13%] Linking C static library libdblas.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1
a - CMakeFiles/dblas.dir/daxpy.c.o
a - CMakeFiles/dblas.dir/ddot.c.o
a - CMakeFiles/dblas.dir/dgemv.c.o
a - CMakeFiles/dblas.dir/dnrm2.c.o
a - CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ranlib libdblas.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 13%] Built target dblas
[ 14%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[ 18%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
[ 21%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 25%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
[ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
[ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder]
  119 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  120 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning:   ‘bool XMLInterface::printExpMass_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |                      ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                           ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                                          ^~~~~
[ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 32%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
[ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 36%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/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
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 36%] Built target picked_protein
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder]
  102 |       useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_;
      |       ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   86 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
   98 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  122 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable]
  118 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  168 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable]
  157 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
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[ 84%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/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 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
[ 85%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
[ 86%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
[ 88%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 89%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 90%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 92%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 96%] Built target qvality
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[100%] Built target percolator
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_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_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[100%] Built target gtest_unit
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles 0

+ mkdir -p src/converters
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -S . -B src/fido -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 -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -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 -B src/converters -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=x86_64 -DBUILD_TESTING:BOOL=ON
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = OFF
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = x86_64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.0s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_INSTALL_FULL_SBINDIR
    CMAKE_INSTALL_SBINDIR
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    PERCOLATOR-CONVERTERS_BINARY_DIR
    SERIALIZE
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR
    TokyoCabinet_INCLUDE_DIR
    TokyoCabinet_LIBRARY


-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/cmake --build src/converters -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
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gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[  1%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o
[  2%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[  5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
[  5%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[  6%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[  7%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[  9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[ 11%] Linking C static library libdblas.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1
a - CMakeFiles/dblas.dir/daxpy.c.o
a - CMakeFiles/dblas.dir/ddot.c.o
a - CMakeFiles/dblas.dir/dgemv.c.o
a - CMakeFiles/dblas.dir/dnrm2.c.o
a - CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ranlib libdblas.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 11%] Built target dblas
[ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 15%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 18%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[ 21%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -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-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
[ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder]
  119 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  120 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning:   ‘bool XMLInterface::printExpMass_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |                      ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                           ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                                          ^~~~~
[ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 32%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
[ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
[ 38%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/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
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 38%] Built target picked_protein
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder]
  102 |       useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_;
      |       ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   86 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
   98 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  122 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable]
  118 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  168 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable]
  157 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/IsotonicPEP.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/CompositionSorter.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/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.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/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.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/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o
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cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/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 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
[ 85%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
[ 86%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
[ 88%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 89%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 90%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 92%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 96%] Built target qvality
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[100%] Built target percolator
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_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_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[100%] Built target gtest_unit
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/CMakeFiles 0

+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Zfgxz3
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ '[' /builddir/build/BUILD/percolator-3.08-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
++ dirname /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/percolator-3.08-build
+ mkdir /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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-3-08
+ DESTDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ /usr/bin/cmake --install percolator
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/percolator
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/qvality
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/./bin/gtest_unit
+ DESTDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ /usr/bin/cmake --install src/converters
-- Install configuration: "Release"
-- Up-to-date: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Up-to-date: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/percolator
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/qvality
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/./bin/gtest_unit
+ mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ rm -f /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.08-1.fc44 --unique-debug-suffix -3.08-1.fc44.x86_64 --unique-debug-src-base percolator-3.08-1.fc44.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08
find-debuginfo: starting
Extracting debug info from 5 files
DWARF-compressing 2 files
sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.08-1.fc44.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ COMPRESS='gzip -9 -n'
+ COMPRESS_EXT=.gz
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-det --brp -j4 /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libdblas.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libpicked_protein.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libperclibrary.a: replacing with normalized version
Scanned 27 directories and 125 files,
    processed 3 inodes,
    3 modified (3 replaced + 0 rewritten),
    0 unsupported format, 0 errors
+ /usr/bin/linkdupes --brp /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr
Scanned 26 directories and 125 files,
    considered 125 files, read 0 files, linked 0 files, 0 errors
    sum of sizes of linked files: 0 bytes
Reading /builddir/build/BUILD/percolator-3.08-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.mDsuRF
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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-3-08
+ /usr/bin/ctest --test-dir percolator --output-on-failure --force-new-ctest-process -j4 -VV
Internal ctest changing into directory: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
UpdateCTestConfiguration  from :/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/DartConfiguration.tcl
UpdateCTestConfiguration  from :/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/DartConfiguration.tcl
Test project /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
    Start 1: UnitTest_Percolator_RunAllTests

1: Test command: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator/gtest_unit
1: Working Directory: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator
1: Test timeout computed to be: 10000000
1: [==========] Running 29 tests from 8 test suites.
1: [----------] Global test environment set-up.
1: [----------] 1 test from CrossValidationTest
1: [ RUN      ] CrossValidationTest.doStepTest
1: [       OK ] CrossValidationTest.doStepTest (15 ms)
1: [----------] 1 test from CrossValidationTest (15 ms total)
1: 
1: [----------] 2 tests from ScoreHolderTest
1: [ RUN      ] ScoreHolderTest.CheckOrderingFunctions
1: 3
1: 4
1: 1
1: 2
1: 5
1: [       OK ] ScoreHolderTest.CheckOrderingFunctions (0 ms)
1: [ RUN      ] ScoreHolderTest.CheckUniquenessFilter
1: [       OK ] ScoreHolderTest.CheckUniquenessFilter (0 ms)
1: [----------] 2 tests from ScoreHolderTest (0 ms total)
1: 
1: [----------] 2 tests from ScoresTest
1: [ RUN      ] ScoresTest.CheckPopulating
1: [       OK ] ScoresTest.CheckPopulating (0 ms)
1: [ RUN      ] ScoresTest.CheckPopulatingEmpty
1: [       OK ] ScoresTest.CheckPopulatingEmpty (0 ms)
1: [----------] 2 tests from ScoresTest (0 ms total)
1: 
1: [----------] 7 tests from IsplineRegressionTest
1: [ RUN      ] IsplineRegressionTest.CubicIsplineBasicBehavior
1: [       OK ] IsplineRegressionTest.CubicIsplineBasicBehavior (0 ms)
1: [ RUN      ] IsplineRegressionTest.MonotonicityFitY
1: [       OK ] IsplineRegressionTest.MonotonicityFitY (0 ms)
1: [ RUN      ] IsplineRegressionTest.FitXYBinaryInputs
1: [       OK ] IsplineRegressionTest.FitXYBinaryInputs (0 ms)
1: [ RUN      ] IsplineRegressionTest.FitXYBinaryInputsLarge
1: [       OK ] IsplineRegressionTest.FitXYBinaryInputsLarge (2 ms)
1: [ RUN      ] IsplineRegressionTest.HandlesConstantInput
1: [       OK ] IsplineRegressionTest.HandlesConstantInput (0 ms)
1: [ RUN      ] IsplineRegressionTest.SmallDatasetUniformKnots
1: [       OK ] IsplineRegressionTest.SmallDatasetUniformKnots (0 ms)
1: [ RUN      ] IsplineRegressionTest.LargeDatasetAdaptiveKnots
1: [       OK ] IsplineRegressionTest.LargeDatasetAdaptiveKnots (0 ms)
1: [----------] 7 tests from IsplineRegressionTest (3 ms total)
1: 
1: [----------] 5 tests from DataSetTest
1: [ RUN      ] DataSetTest.ChecMinimalPsmParsing
1: Warning: protein decoy prefix dummyVariable_ doesn't match the decoy protein identifier ProteinList.
1: [       OK ] DataSetTest.ChecMinimalPsmParsing (0 ms)
1: [ RUN      ] DataSetTest.CheckInvalidPsmLines
1: [       OK ] DataSetTest.CheckInvalidPsmLines (0 ms)
1: [ RUN      ] DataSetTest.CheckPsmParsingWithFeatures
1: [       OK ] DataSetTest.CheckPsmParsingWithFeatures (0 ms)
1: [ RUN      ] DataSetTest.CheckFeatureParsing
1: [       OK ] DataSetTest.CheckFeatureParsing (0 ms)
1: [ RUN      ] DataSetTest.CheckOptionalFieldsParsing
1: [       OK ] DataSetTest.CheckOptionalFieldsParsing (0 ms)
1: [----------] 5 tests from DataSetTest (0 ms total)
1: 
1: [----------] 5 tests from SetHandlerTest
1: [ RUN      ] SetHandlerTest.TestSubsetStoring
1: [       OK ] SetHandlerTest.TestSubsetStoring (0 ms)
1: [ RUN      ] SetHandlerTest.TestGetOptionalFields
1: [       OK ] SetHandlerTest.TestGetOptionalFields (0 ms)
1: [ RUN      ] SetHandlerTest.TestBadReads
1: ERROR: Cannot read Tab delimited input from data stream.
1: Input file seems to be in XML format, use the -k flag for XML input.
1: [       OK ] SetHandlerTest.TestBadReads (0 ms)
1: [ RUN      ] SetHandlerTest.TestGoodReads
1: [       OK ] SetHandlerTest.TestGoodReads (0 ms)
1: [ RUN      ] SetHandlerTest.TestReadWithFeatures
1: [       OK ] SetHandlerTest.TestReadWithFeatures (0 ms)
1: [----------] 5 tests from SetHandlerTest (0 ms total)
1: 
1: [----------] 3 tests from TabReaderTest
1: [ RUN      ] TabReaderTest.CheckReadInt
1: [       OK ] TabReaderTest.CheckReadInt (0 ms)
1: [ RUN      ] TabReaderTest.CheckReadDouble
1: [       OK ] TabReaderTest.CheckReadDouble (0 ms)
1: [ RUN      ] TabReaderTest.CheckSequentialReading
1: [       OK ] TabReaderTest.CheckSequentialReading (0 ms)
1: [----------] 3 tests from TabReaderTest (0 ms total)
1: 
1: [----------] 4 tests from OptionTest
1: [ RUN      ] OptionTest.CheckBasicOptionParsing
1: [       OK ] OptionTest.CheckBasicOptionParsing (0 ms)
1: [ RUN      ] OptionTest.CheckThrowOnInvalidOption
1: [       OK ] OptionTest.CheckThrowOnInvalidOption (0 ms)
1: [ RUN      ] OptionTest.CheckThrowOnRangeExceeded
1: [       OK ] OptionTest.CheckThrowOnRangeExceeded (0 ms)
1: [ RUN      ] OptionTest.CheckSeparationOfOptionsAndArguments
1: [       OK ] OptionTest.CheckSeparationOfOptionsAndArguments (0 ms)
1: [----------] 4 tests from OptionTest (0 ms total)
1: 
1: [----------] Global test environment tear-down
1: [==========] 29 tests from 8 test suites ran. (21 ms total)
1: [  PASSED  ] 29 tests.
1/1 Test #1: UnitTest_Percolator_RunAllTests ...   Passed    0.02 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.02 sec
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.08-1.fc44.x86_64
Provides: percolator = 3.08-1.fc44 percolator(x86-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(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_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(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_3.4.9)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.08-1.fc44.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.CF7rvN
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ DOCDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-data
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/ReadMe.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.iZqi1S
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/license.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.08-1.fc44.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.rnuh64
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ DOCDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-static
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/ReadMe.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.lDvuhD
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/license.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.08-1.fc44 percolator-static(x86-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.08-1.fc44.x86_64
Provides: percolator-debugsource = 3.08-1.fc44 percolator-debugsource(x86-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.08-1.fc44.x86_64
Provides: debuginfo(build-id) = 97a32cd054a784df450b25e6e8152bc9a9c6e654 debuginfo(build-id) = e2eca8e8f087cf9cca4f89f6ac95764f5353f3f1 percolator-debuginfo = 3.08-1.fc44 percolator-debuginfo(x86-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(x86-64) = 3.08-1.fc44
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
Wrote: /builddir/build/RPMS/percolator-debugsource-3.08-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.08-1.fc44.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.08-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.08-1.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.08-1.fc44.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.sMsKVy
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ test -d /builddir/build/BUILD/percolator-3.08-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/percolator-3.08-build
+ rm -rf /builddir/build/BUILD/percolator-3.08-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.08-1.fc44.src.rpm
Finish: build phase for percolator-3.08-1.fc44.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1765551765.922229/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.08-1.fc44.src.rpm) Config(child) 6 minutes 47 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "src"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "noarch"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "x86_64"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished