Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c14e' (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/9329630-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.3
PID: 3242
Logging PID: 3243
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 9329630,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '08952a0782f09859f132b5e6020812e47ca25de1',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/lecris/cmake-ninja/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.08-1',
 'project_dirname': 'cmake-ninja',
 'project_name': 'cmake-ninja',
 'project_owner': 'lecris',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/lecris/cmake-ninja/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'lecris/cmake-ninja--lecris',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'lecris',
 'tags': [],
 'task_id': '9329630-fedora-rawhide-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/lecris/cmake-ninja/percolator /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/lecris/cmake-ninja/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator'...

Running: git checkout 08952a0782f09859f132b5e6020812e47ca25de1 --

cmd: ['git', 'checkout', '08952a0782f09859f132b5e6020812e47ca25de1', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator
rc: 0
stdout: 
stderr: Note: switching to '08952a0782f09859f132b5e6020812e47ca25de1'.

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 08952a0 automatic import of percolator

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/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
tail: /var/lib/copr-rpmbuild/main.log: file truncated
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/lecris/cmake-ninja/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  38.4M      0 --:--:-- --:--:-- --:--:-- 38.5M
INFO: Reading stdout from command: md5sum percolator-rel-3-08.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1753433315.726432 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.3 starting (python version = 3.13.3, NVR = mock-6.3-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-1qsyy_sr/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1753433315.726432 -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-1qsyy_sr/percolator/percolator.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.3
INFO: Mock Version: 6.3
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1753433315.726432/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-367232ff-24e3-4ba8-a4a0-4acf61b16821
INFO: Checking that 7cb41bfdf1d6ba1a48de30085c5b887b0f471c7d484d224b491f1f89bf614b94 image matches host's architecture
INFO: Copy content of container 7cb41bfdf1d6ba1a48de30085c5b887b0f471c7d484d224b491f1f89bf614b94 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1753433315.726432/root
INFO: mounting 7cb41bfdf1d6ba1a48de30085c5b887b0f471c7d484d224b491f1f89bf614b94 with podman image mount
INFO: image 7cb41bfdf1d6ba1a48de30085c5b887b0f471c7d484d224b491f1f89bf614b94 as /var/lib/containers/storage/overlay/8fb6137af852bf0cc38f3f5e442277ca09113297e0229daf3ac56dd3efc158ff/merged
INFO: umounting image 7cb41bfdf1d6ba1a48de30085c5b887b0f471c7d484d224b491f1f89bf614b94 (/var/lib/containers/storage/overlay/8fb6137af852bf0cc38f3f5e442277ca09113297e0229daf3ac56dd3efc158ff/merged) with podman image umount
INFO: Removing image mock-bootstrap-367232ff-24e3-4ba8-a4a0-4acf61b16821
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_64-1753433315.726432/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-5.99.91-1.fc43.x86_64
  rpm-sequoia-1.9.0-1.fc43.x86_64
  dnf5-5.2.15.0-3.fc43.x86_64
  dnf5-plugins-5.2.15.0-3.fc43.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Copr repository                        100% |   6.9 MiB/s |   3.6 MiB |  00m01s
 fedora                                 100% |  21.2 MiB/s |  21.9 MiB |  00m01s
Repositories loaded.
Package                            Arch   Version                    Repository      Size
Installing group/module packages:
 bash                              x86_64 5.3.0-1.fc43               fedora       8.4 MiB
 bzip2                             x86_64 1.0.8-20.fc42              fedora      99.3 KiB
 coreutils                         x86_64 9.7-4.fc43                 fedora       5.4 MiB
 cpio                              x86_64 2.15-2.fc41                fedora       1.1 MiB
 diffutils                         x86_64 3.12-2.fc43                fedora       1.6 MiB
 fedora-release-common             noarch 43-0.19                    fedora      20.4 KiB
 findutils                         x86_64 1:4.10.0-5.fc42            fedora       1.9 MiB
 gawk                              x86_64 5.3.2-1.fc43               fedora       1.8 MiB
 glibc-minimal-langpack            x86_64 2.41.9000-23.fc43          fedora       0.0   B
 grep                              x86_64 3.12-1.fc43                fedora       1.0 MiB
 gzip                              x86_64 1.13-3.fc42                fedora     392.9 KiB
 info                              x86_64 7.2-4.fc43                 fedora     353.9 KiB
 patch                             x86_64 2.8-1.fc43                 fedora     226.8 KiB
 redhat-rpm-config                 noarch 343-7.fc43                 fedora     181.7 KiB
 rpm-build                         x86_64 5.99.91-1.fc43             fedora     289.6 KiB
 sed                               x86_64 4.9-4.fc42                 fedora     857.3 KiB
 shadow-utils                      x86_64 2:4.18.0-1.fc43            fedora       3.9 MiB
 tar                               x86_64 2:1.35-5.fc42              fedora       3.0 MiB
 unzip                             x86_64 6.0-66.fc42                fedora     390.3 KiB
 util-linux                        x86_64 2.41.1-11.fc43             fedora       3.5 MiB
 which                             x86_64 2.23-2.fc43                fedora      83.5 KiB
 xz                                x86_64 1:5.8.1-1.fc43             fedora       1.3 MiB
Installing dependencies:
 add-determinism                   x86_64 0.6.0-1.fc43               fedora       2.5 MiB
 alternatives                      x86_64 1.33-1.fc43                fedora      62.2 KiB
 ansible-srpm-macros               noarch 1-17.1.fc42                fedora      35.7 KiB
 audit-libs                        x86_64 4.1.0-1.fc43               fedora     378.8 KiB
 binutils                          x86_64 2.44.90-2.fc43             fedora      26.4 MiB
 build-reproducibility-srpm-macros noarch 0.6.0-1.fc43               fedora     735.0   B
 bzip2-libs                        x86_64 1.0.8-20.fc42              fedora      84.6 KiB
 ca-certificates                   noarch 2024.2.69_v8.0.401-5.fc42  fedora       2.6 MiB
 coreutils-common                  x86_64 9.7-4.fc43                 fedora      11.3 MiB
 crypto-policies                   noarch 20250714-1.gitcd6043a.fc43 fedora     146.9 KiB
 curl                              x86_64 8.15.0-1.fc43              fedora     473.6 KiB
 cyrus-sasl-lib                    x86_64 2.1.28-30.fc42             fedora       2.3 MiB
 debugedit                         x86_64 5.2-1.fc43                 fedora     197.8 KiB
 dwz                               x86_64 0.16-1.fc43                fedora     287.1 KiB
 ed                                x86_64 1.22-1.fc43                fedora     147.1 KiB
 efi-srpm-macros                   noarch 6-3.fc43                   fedora      40.1 KiB
 elfutils                          x86_64 0.193-2.fc43               fedora       2.9 MiB
 elfutils-debuginfod-client        x86_64 0.193-2.fc43               fedora      83.9 KiB
 elfutils-default-yama-scope       noarch 0.193-2.fc43               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0.193-2.fc43               fedora       1.2 MiB
 elfutils-libs                     x86_64 0.193-2.fc43               fedora     683.4 KiB
 fedora-gpg-keys                   noarch 43-0.2                     fedora     129.0 KiB
 fedora-release                    noarch 43-0.19                    fedora       0.0   B
 fedora-release-identity-basic     noarch 43-0.19                    fedora     664.0   B
 fedora-repos                      noarch 43-0.2                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 43-0.2                     fedora       2.2 KiB
 file                              x86_64 5.46-5.fc43                fedora     100.2 KiB
 file-libs                         x86_64 5.46-5.fc43                fedora      11.9 MiB
 filesystem                        x86_64 3.18-44.fc43               fedora     112.0   B
 filesystem-srpm-macros            noarch 3.18-44.fc43               fedora      38.2 KiB
 fonts-srpm-macros                 noarch 1:2.0.5-22.fc43            fedora      55.8 KiB
 forge-srpm-macros                 noarch 0.4.0-2.fc42               fedora      38.9 KiB
 fpc-srpm-macros                   noarch 1.3-14.fc42                fedora     144.0   B
 gdb-minimal                       x86_64 16.3-3.fc43                fedora      13.2 MiB
 gdbm-libs                         x86_64 1:1.23-9.fc42              fedora     129.9 KiB
 ghc-srpm-macros                   noarch 1.9.2-2.fc42               fedora     779.0   B
 glibc                             x86_64 2.41.9000-23.fc43          fedora       6.7 MiB
 glibc-common                      x86_64 2.41.9000-23.fc43          fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 2.41.9000-23.fc43          fedora       7.2 MiB
 gmp                               x86_64 1:6.3.0-3.fc43             fedora     819.2 KiB
 gnat-srpm-macros                  noarch 6-7.fc42                   fedora       1.0 KiB
 gnupg2                            x86_64 2.4.8-2.fc43               fedora       6.5 MiB
 gnupg2-dirmngr                    x86_64 2.4.8-2.fc43               fedora     618.4 KiB
 gnupg2-gpg-agent                  x86_64 2.4.8-2.fc43               fedora     671.4 KiB
 gnupg2-gpgconf                    x86_64 2.4.8-2.fc43               fedora     250.0 KiB
 gnupg2-keyboxd                    x86_64 2.4.8-2.fc43               fedora     201.4 KiB
 gnupg2-verify                     x86_64 2.4.8-2.fc43               fedora     348.5 KiB
 gnutls                            x86_64 3.8.10-1.fc43              fedora       3.8 MiB
 go-srpm-macros                    noarch 3.7.0-1.fc43               fedora      61.6 KiB
 gpgverify                         noarch 2.2-2.fc43                 fedora       8.7 KiB
 ima-evm-utils-libs                x86_64 1.6.2-5.fc43               fedora      60.7 KiB
 jansson                           x86_64 2.14-2.fc42                fedora      93.1 KiB
 java-srpm-macros                  noarch 1-6.fc43                   fedora     870.0   B
 json-c                            x86_64 0.18-4.fc43                fedora      82.7 KiB
 kernel-srpm-macros                noarch 1.0-25.fc42                fedora       1.9 KiB
 keyutils-libs                     x86_64 1.6.3-5.fc42               fedora      58.3 KiB
 krb5-libs                         x86_64 1.21.3-6.fc43              fedora       2.3 MiB
 libacl                            x86_64 2.3.2-3.fc42               fedora      38.3 KiB
 libarchive                        x86_64 3.8.1-2.fc43               fedora     951.1 KiB
 libassuan                         x86_64 2.5.7-3.fc42               fedora     167.8 KiB
 libattr                           x86_64 2.5.2-5.fc42               fedora      27.1 KiB
 libblkid                          x86_64 2.41.1-11.fc43             fedora     262.4 KiB
 libbrotli                         x86_64 1.1.0-7.fc43               fedora     833.3 KiB
 libcap                            x86_64 2.76-1.fc43                fedora     209.2 KiB
 libcap-ng                         x86_64 0.8.5-5.fc43               fedora      68.9 KiB
 libcom_err                        x86_64 1.47.3-1.fc43              fedora      63.1 KiB
 libcurl                           x86_64 8.15.0-1.fc43              fedora     903.2 KiB
 libeconf                          x86_64 0.7.9-1.fc43               fedora      64.9 KiB
 libevent                          x86_64 2.1.12-15.fc42             fedora     903.1 KiB
 libfdisk                          x86_64 2.41.1-11.fc43             fedora     380.4 KiB
 libffi                            x86_64 3.5.1-1.fc43               fedora      83.6 KiB
 libfsverity                       x86_64 1.6-2.fc42                 fedora      32.5 KiB
 libgcc                            x86_64 15.1.1-2.fc43              fedora     266.6 KiB
 libgcrypt                         x86_64 1.11.1-1.fc43              fedora       1.6 MiB
 libgomp                           x86_64 15.1.1-2.fc43              fedora     539.1 KiB
 libgpg-error                      x86_64 1.55-1.fc43                fedora     915.3 KiB
 libidn2                           x86_64 2.3.8-1.fc43               fedora     552.5 KiB
 libksba                           x86_64 1.6.7-3.fc42               fedora     402.5 KiB
 liblastlog2                       x86_64 2.41.1-11.fc43             fedora      33.9 KiB
 libmount                          x86_64 2.41.1-11.fc43             fedora     372.7 KiB
 libnghttp2                        x86_64 1.66.0-1.fc43              fedora     162.2 KiB
 libpkgconf                        x86_64 2.3.0-2.fc42               fedora      78.1 KiB
 libpsl                            x86_64 0.21.5-5.fc42              fedora      76.4 KiB
 libselinux                        x86_64 3.9-1.fc43                 fedora     193.1 KiB
 libsemanage                       x86_64 3.9-1.fc43                 fedora     308.4 KiB
 libsepol                          x86_64 3.9-1.fc43                 fedora     821.9 KiB
 libsmartcols                      x86_64 2.41.1-11.fc43             fedora     180.5 KiB
 libssh                            x86_64 0.11.2-1.fc43              fedora     566.7 KiB
 libssh-config                     noarch 0.11.2-1.fc43              fedora     277.0   B
 libstdc++                         x86_64 15.1.1-2.fc43              fedora       2.8 MiB
 libtasn1                          x86_64 4.20.0-1.fc43              fedora     176.3 KiB
 libtool-ltdl                      x86_64 2.5.4-5.fc43               fedora      70.1 KiB
 libunistring                      x86_64 1.1-9.fc42                 fedora       1.7 MiB
 libusb1                           x86_64 1.0.28-2.fc43              fedora     171.0 KiB
 libuuid                           x86_64 2.41.1-11.fc43             fedora      37.4 KiB
 libverto                          x86_64 0.3.2-10.fc42              fedora      25.4 KiB
 libxcrypt                         x86_64 4.4.38-7.fc43              fedora     284.5 KiB
 libxml2                           x86_64 2.12.10-2.fc43             fedora       1.7 MiB
 libzstd                           x86_64 1.5.7-1.fc43               fedora     807.8 KiB
 lua-libs                          x86_64 5.4.8-1.fc43               fedora     280.8 KiB
 lua-srpm-macros                   noarch 1-15.fc42                  fedora       1.3 KiB
 lz4-libs                          x86_64 1.10.0-2.fc42              fedora     157.4 KiB
 mpfr                              x86_64 4.2.2-1.fc43               fedora     828.8 KiB
 ncurses-base                      noarch 6.5-6.20250614.fc43        fedora     328.1 KiB
 ncurses-libs                      x86_64 6.5-6.20250614.fc43        fedora     946.3 KiB
 nettle                            x86_64 3.10.1-1.fc43              fedora     790.5 KiB
 npth                              x86_64 1.8-2.fc42                 fedora      49.6 KiB
 ocaml-srpm-macros                 noarch 10-4.fc42                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 2-19.fc42                  fedora     112.0   B
 openldap                          x86_64 2.6.10-2.fc43              fedora     655.8 KiB
 openssl-libs                      x86_64 1:3.5.1-1.fc43             fedora       8.9 MiB
 p11-kit                           x86_64 0.25.5-8.fc43              fedora       2.2 MiB
 p11-kit-trust                     x86_64 0.25.5-8.fc43              fedora     395.5 KiB
 package-notes-srpm-macros         noarch 0.5-13.fc42                fedora       1.6 KiB
 pam-libs                          x86_64 1.7.1-2.fc43               fedora     126.8 KiB
 pcre2                             x86_64 10.45-1.fc43               fedora     697.7 KiB
 pcre2-syntax                      noarch 10.45-1.fc43               fedora     273.9 KiB
 perl-srpm-macros                  noarch 1-59.fc43                  fedora     861.0   B
 pkgconf                           x86_64 2.3.0-2.fc42               fedora      88.5 KiB
 pkgconf-m4                        noarch 2.3.0-2.fc42               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 2.3.0-2.fc42               fedora     989.0   B
 popt                              x86_64 1.19-8.fc42                fedora     132.8 KiB
 publicsuffix-list-dafsa           noarch 20250616-1.fc43            fedora      69.1 KiB
 pyproject-srpm-macros             noarch 1.18.3-1.fc43              fedora       1.9 KiB
 python-srpm-macros                noarch 3.14-3.fc43                fedora      51.5 KiB
 qt5-srpm-macros                   noarch 5.15.17-1.fc43             fedora     500.0   B
 qt6-srpm-macros                   noarch 6.9.1-1.fc43               fedora     464.0   B
 readline                          x86_64 8.3-1.fc43                 fedora     511.7 KiB
 rpm                               x86_64 5.99.91-1.fc43             fedora       3.0 MiB
 rpm-build-libs                    x86_64 5.99.91-1.fc43             fedora     268.4 KiB
 rpm-libs                          x86_64 5.99.91-1.fc43             fedora     933.7 KiB
 rpm-sequoia                       x86_64 1.9.0-1.fc43               fedora       2.5 MiB
 rpm-sign-libs                     x86_64 5.99.91-1.fc43             fedora      39.7 KiB
 rust-srpm-macros                  noarch 26.3-4.fc42                fedora       4.8 KiB
 setup                             noarch 2.15.0-25.fc43             fedora     725.0 KiB
 sqlite-libs                       x86_64 3.50.2-1.fc43              fedora       1.5 MiB
 systemd-libs                      x86_64 257.7-1.fc43               fedora       2.2 MiB
 systemd-standalone-sysusers       x86_64 257.7-1.fc43               fedora     277.3 KiB
 tpm2-tss                          x86_64 4.1.3-7.fc43               fedora       1.6 MiB
 tree-sitter-srpm-macros           noarch 0.4.1-1.fc43               fedora       8.2 KiB
 util-linux-core                   x86_64 2.41.1-11.fc43             fedora       1.5 MiB
 xxhash-libs                       x86_64 0.8.3-2.fc42               fedora      90.2 KiB
 xz-libs                           x86_64 1:5.8.1-1.fc43             fedora     217.8 KiB
 zig-srpm-macros                   noarch 1-4.fc42                   fedora       1.1 KiB
 zip                               x86_64 3.0-43.fc42                fedora     698.5 KiB
 zlib-ng-compat                    x86_64 2.2.4-2.fc43               copr_base  137.6 KiB
 zstd                              x86_64 1.5.7-1.fc43               fedora       1.7 MiB
Installing groups:
 Buildsystem building group                                                              

Transaction Summary:
 Installing:       169 packages

Total size of inbound packages is 59 MiB. Need to download 59 MiB.
After this operation, 198 MiB extra will be used (install 198 MiB, remove 0 B).
[  1/169] bzip2-0:1.0.8-20.fc42.x86_64  100% | 703.6 KiB/s |  52.1 KiB |  00m00s
[  2/169] cpio-0:2.15-2.fc41.x86_64     100% |   4.7 MiB/s | 291.8 KiB |  00m00s
[  3/169] coreutils-0:9.7-4.fc43.x86_64 100% |   7.5 MiB/s |   1.1 MiB |  00m00s
[  4/169] fedora-release-common-0:43-0. 100% |   1.8 MiB/s |  25.4 KiB |  00m00s
[  5/169] diffutils-0:3.12-2.fc43.x86_6 100% |  12.0 MiB/s | 392.7 KiB |  00m00s
[  6/169] bash-0:5.3.0-1.fc43.x86_64    100% |  10.7 MiB/s |   1.9 MiB |  00m00s
[  7/169] glibc-minimal-langpack-0:2.41 100% |   2.2 MiB/s |  35.2 KiB |  00m00s
[  8/169] gzip-0:1.13-3.fc42.x86_64     100% |  10.4 MiB/s | 170.4 KiB |  00m00s
[  9/169] grep-0:3.12-1.fc43.x86_64     100% |   6.8 MiB/s | 299.5 KiB |  00m00s
[ 10/169] info-0:7.2-4.fc43.x86_64      100% |  10.5 MiB/s | 182.8 KiB |  00m00s
[ 11/169] patch-0:2.8-1.fc43.x86_64     100% |   7.9 MiB/s | 113.7 KiB |  00m00s
[ 12/169] redhat-rpm-config-0:343-7.fc4 100% |   5.5 MiB/s |  78.9 KiB |  00m00s
[ 13/169] sed-0:4.9-4.fc42.x86_64       100% |  17.2 MiB/s | 317.3 KiB |  00m00s
[ 14/169] shadow-utils-2:4.18.0-1.fc43. 100% |  45.8 MiB/s |   1.3 MiB |  00m00s
[ 15/169] tar-2:1.35-5.fc42.x86_64      100% |  33.7 MiB/s | 862.5 KiB |  00m00s
[ 16/169] unzip-0:6.0-66.fc42.x86_64    100% |  11.3 MiB/s | 184.6 KiB |  00m00s
[ 17/169] which-0:2.23-2.fc43.x86_64    100% |   2.4 MiB/s |  41.8 KiB |  00m00s
[ 18/169] xz-1:5.8.1-1.fc43.x86_64      100% |  24.3 MiB/s | 572.5 KiB |  00m00s
[ 19/169] findutils-1:4.10.0-5.fc42.x86 100% |   3.7 MiB/s | 551.5 KiB |  00m00s
[ 20/169] gawk-0:5.3.2-1.fc43.x86_64    100% |  43.3 MiB/s |   1.1 MiB |  00m00s
[ 21/169] rpm-build-0:5.99.91-1.fc43.x8 100% |   7.0 MiB/s | 136.3 KiB |  00m00s
[ 22/169] glibc-0:2.41.9000-23.fc43.x86 100% |  35.5 MiB/s |   2.2 MiB |  00m00s
[ 23/169] filesystem-0:3.18-44.fc43.x86 100% |  20.5 MiB/s |   1.3 MiB |  00m00s
[ 24/169] util-linux-0:2.41.1-11.fc43.x 100% |  14.7 MiB/s |   1.2 MiB |  00m00s
[ 25/169] ncurses-libs-0:6.5-6.20250614 100% |  18.1 MiB/s | 333.1 KiB |  00m00s
[ 26/169] bzip2-libs-0:1.0.8-20.fc42.x8 100% |   2.7 MiB/s |  43.6 KiB |  00m00s
[ 27/169] libacl-0:2.3.2-3.fc42.x86_64  100% |   1.6 MiB/s |  23.0 KiB |  00m00s
[ 28/169] gmp-1:6.3.0-3.fc43.x86_64     100% |  18.5 MiB/s | 322.2 KiB |  00m00s
[ 29/169] libattr-0:2.5.2-5.fc42.x86_64 100% |   1.2 MiB/s |  17.1 KiB |  00m00s
[ 30/169] libcap-0:2.76-1.fc43.x86_64   100% |   6.1 MiB/s |  86.9 KiB |  00m00s
[ 31/169] libselinux-0:3.9-1.fc43.x86_6 100% |   6.8 MiB/s |  97.2 KiB |  00m00s
[ 32/169] systemd-libs-0:257.7-1.fc43.x 100% |  15.1 MiB/s | 789.7 KiB |  00m00s
[ 33/169] coreutils-common-0:9.7-4.fc43 100% |  18.4 MiB/s |   2.1 MiB |  00m00s
[ 34/169] openssl-libs-1:3.5.1-1.fc43.x 100% |  32.7 MiB/s |   2.6 MiB |  00m00s
[ 35/169] fedora-repos-0:43-0.2.noarch  100% | 542.9 KiB/s |   9.2 KiB |  00m00s
[ 36/169] ed-0:1.22-1.fc43.x86_64       100% |   5.4 MiB/s |  83.0 KiB |  00m00s
[ 37/169] pcre2-0:10.45-1.fc43.x86_64   100% |  15.1 MiB/s | 262.8 KiB |  00m00s
[ 38/169] glibc-common-0:2.41.9000-23.f 100% |  12.6 MiB/s | 322.1 KiB |  00m00s
[ 39/169] ansible-srpm-macros-0:1-17.1. 100% |   1.4 MiB/s |  20.3 KiB |  00m00s
[ 40/169] build-reproducibility-srpm-ma 100% | 898.7 KiB/s |  11.7 KiB |  00m00s
[ 41/169] dwz-0:0.16-1.fc43.x86_64      100% |   7.8 MiB/s | 135.5 KiB |  00m00s
[ 42/169] efi-srpm-macros-0:6-3.fc43.no 100% |   1.7 MiB/s |  22.5 KiB |  00m00s
[ 43/169] file-0:5.46-5.fc43.x86_64     100% |   3.4 MiB/s |  48.8 KiB |  00m00s
[ 44/169] filesystem-srpm-macros-0:3.18 100% |   2.0 MiB/s |  26.0 KiB |  00m00s
[ 45/169] fonts-srpm-macros-1:2.0.5-22. 100% |   2.0 MiB/s |  27.2 KiB |  00m00s
[ 46/169] forge-srpm-macros-0:0.4.0-2.f 100% |   1.5 MiB/s |  19.9 KiB |  00m00s
[ 47/169] fpc-srpm-macros-0:1.3-14.fc42 100% | 668.3 KiB/s |   8.0 KiB |  00m00s
[ 48/169] ghc-srpm-macros-0:1.9.2-2.fc4 100% | 704.3 KiB/s |   9.2 KiB |  00m00s
[ 49/169] gnat-srpm-macros-0:6-7.fc42.n 100% | 662.4 KiB/s |   8.6 KiB |  00m00s
[ 50/169] go-srpm-macros-0:3.7.0-1.fc43 100% |   2.1 MiB/s |  27.9 KiB |  00m00s
[ 51/169] java-srpm-macros-0:1-6.fc43.n 100% | 561.9 KiB/s |   7.9 KiB |  00m00s
[ 52/169] kernel-srpm-macros-0:1.0-25.f 100% | 705.1 KiB/s |   9.9 KiB |  00m00s
[ 53/169] lua-srpm-macros-0:1-15.fc42.n 100% | 743.1 KiB/s |   8.9 KiB |  00m00s
[ 54/169] ocaml-srpm-macros-0:10-4.fc42 100% | 657.5 KiB/s |   9.2 KiB |  00m00s
[ 55/169] openblas-srpm-macros-0:2-19.f 100% | 597.4 KiB/s |   7.8 KiB |  00m00s
[ 56/169] package-notes-srpm-macros-0:0 100% | 771.6 KiB/s |   9.3 KiB |  00m00s
[ 57/169] perl-srpm-macros-0:1-59.fc43. 100% | 650.9 KiB/s |   8.5 KiB |  00m00s
[ 58/169] pyproject-srpm-macros-0:1.18. 100% | 950.8 KiB/s |  13.3 KiB |  00m00s
[ 59/169] python-srpm-macros-0:3.14-3.f 100% |   1.7 MiB/s |  23.2 KiB |  00m00s
[ 60/169] rust-srpm-macros-0:26.3-4.fc4 100% | 900.4 KiB/s |  11.7 KiB |  00m00s
[ 61/169] tree-sitter-srpm-macros-0:0.4 100% |   1.0 MiB/s |  13.0 KiB |  00m00s
[ 62/169] zig-srpm-macros-0:1-4.fc42.no 100% | 687.0 KiB/s |   8.2 KiB |  00m00s
[ 63/169] zip-0:3.0-43.fc42.x86_64      100% |  15.1 MiB/s | 263.5 KiB |  00m00s
[ 64/169] audit-libs-0:4.1.0-1.fc43.x86 100% |   7.9 MiB/s | 138.3 KiB |  00m00s
[ 65/169] libsemanage-0:3.9-1.fc43.x86_ 100% |   7.1 MiB/s | 123.3 KiB |  00m00s
[ 66/169] libxcrypt-0:4.4.38-7.fc43.x86 100% |   8.9 MiB/s | 127.2 KiB |  00m00s
[ 67/169] pam-libs-0:1.7.1-2.fc43.x86_6 100% |   4.0 MiB/s |  57.7 KiB |  00m00s
[ 68/169] setup-0:2.15.0-25.fc43.noarch 100% |   8.5 MiB/s | 157.6 KiB |  00m00s
[ 69/169] xz-libs-1:5.8.1-1.fc43.x86_64 100% |   7.9 MiB/s | 113.0 KiB |  00m00s
[ 70/169] mpfr-0:4.2.2-1.fc43.x86_64    100% |  19.9 MiB/s | 346.7 KiB |  00m00s
[ 71/169] readline-0:8.3-1.fc43.x86_64  100% |  10.5 MiB/s | 224.7 KiB |  00m00s
[ 72/169] debugedit-0:5.2-1.fc43.x86_64 100% |   5.6 MiB/s |  80.6 KiB |  00m00s
[ 73/169] elfutils-0:0.193-2.fc43.x86_6 100% |  29.4 MiB/s | 571.5 KiB |  00m00s
[ 74/169] libarchive-0:3.8.1-2.fc43.x86 100% |  22.8 MiB/s | 421.0 KiB |  00m00s
[ 75/169] elfutils-libelf-0:0.193-2.fc4 100% |   9.2 MiB/s | 207.9 KiB |  00m00s
[ 76/169] libgcc-0:15.1.1-2.fc43.x86_64 100% |   7.8 MiB/s | 127.5 KiB |  00m00s
[ 77/169] popt-0:1.19-8.fc42.x86_64     100% |   3.6 MiB/s |  66.0 KiB |  00m00s
[ 78/169] libstdc++-0:15.1.1-2.fc43.x86 100% |  38.8 MiB/s | 912.8 KiB |  00m00s
[ 79/169] rpm-0:5.99.91-1.fc43.x86_64   100% |  25.0 MiB/s | 563.4 KiB |  00m00s
[ 80/169] libblkid-0:2.41.1-11.fc43.x86 100% |   8.1 MiB/s | 124.1 KiB |  00m00s
[ 81/169] libcap-ng-0:0.8.5-5.fc43.x86_ 100% |   2.2 MiB/s |  32.2 KiB |  00m00s
[ 82/169] zstd-0:1.5.7-1.fc43.x86_64    100% |  15.3 MiB/s | 485.8 KiB |  00m00s
[ 83/169] libfdisk-0:2.41.1-11.fc43.x86 100% |  10.6 MiB/s | 162.1 KiB |  00m00s
[ 84/169] liblastlog2-0:2.41.1-11.fc43. 100% |   1.7 MiB/s |  24.0 KiB |  00m00s
[ 85/169] libsmartcols-0:2.41.1-11.fc43 100% |   5.9 MiB/s |  84.9 KiB |  00m00s
[ 86/169] libmount-0:2.41.1-11.fc43.x86 100% |   8.9 MiB/s | 163.3 KiB |  00m00s
[ 87/169] libuuid-0:2.41.1-11.fc43.x86_ 100% |   1.9 MiB/s |  27.0 KiB |  00m00s
[ 88/169] ncurses-base-0:6.5-6.20250614 100% |   5.1 MiB/s |  88.3 KiB |  00m00s
[ 89/169] util-linux-core-0:2.41.1-11.f 100% |  26.9 MiB/s | 551.7 KiB |  00m00s
[ 90/169] libsepol-0:3.9-1.fc43.x86_64  100% |  18.7 MiB/s | 345.4 KiB |  00m00s
[ 91/169] ca-certificates-0:2024.2.69_v 100% |  36.9 MiB/s | 945.0 KiB |  00m00s
[ 92/169] crypto-policies-0:20250714-1. 100% |   6.9 MiB/s |  98.6 KiB |  00m00s
[ 93/169] fedora-gpg-keys-0:43-0.2.noar 100% |   8.9 MiB/s | 136.6 KiB |  00m00s
[ 94/169] fedora-repos-rawhide-0:43-0.2 100% | 677.2 KiB/s |   8.8 KiB |  00m00s
[ 95/169] glibc-gconv-extra-0:2.41.9000 100% |  22.3 MiB/s |   1.6 MiB |  00m00s
[ 96/169] pcre2-syntax-0:10.45-1.fc43.n 100% |  10.5 MiB/s | 161.7 KiB |  00m00s
[ 97/169] add-determinism-0:0.6.0-1.fc4 100% |  40.8 MiB/s | 918.3 KiB |  00m00s
[ 98/169] elfutils-libs-0:0.193-2.fc43. 100% |  16.5 MiB/s | 270.2 KiB |  00m00s
[ 99/169] elfutils-debuginfod-client-0: 100% |   3.3 MiB/s |  47.0 KiB |  00m00s
[100/169] libzstd-0:1.5.7-1.fc43.x86_64 100% |  18.1 MiB/s | 314.8 KiB |  00m00s
[101/169] file-libs-0:5.46-5.fc43.x86_6 100% |  20.2 MiB/s | 849.8 KiB |  00m00s
[102/169] lz4-libs-0:1.10.0-2.fc42.x86_ 100% |   5.4 MiB/s |  78.1 KiB |  00m00s
[103/169] curl-0:8.15.0-1.fc43.x86_64   100% |   9.5 MiB/s | 233.8 KiB |  00m00s
[104/169] elfutils-default-yama-scope-0 100% | 662.4 KiB/s |  12.6 KiB |  00m00s
[105/169] sqlite-libs-0:3.50.2-1.fc43.x 100% |  20.1 MiB/s | 761.3 KiB |  00m00s
[106/169] rpm-libs-0:5.99.91-1.fc43.x86 100% |  23.0 MiB/s | 399.9 KiB |  00m00s
[107/169] lua-libs-0:5.4.8-1.fc43.x86_6 100% |   7.6 MiB/s | 131.9 KiB |  00m00s
[108/169] rpm-build-libs-0:5.99.91-1.fc 100% |   8.3 MiB/s | 127.5 KiB |  00m00s
[109/169] rpm-sign-libs-0:5.99.91-1.fc4 100% |   1.8 MiB/s |  28.2 KiB |  00m00s
[110/169] libgomp-0:15.1.1-2.fc43.x86_6 100% |  18.8 MiB/s | 365.2 KiB |  00m00s
[111/169] rpm-sequoia-0:1.9.0-1.fc43.x8 100% |  19.0 MiB/s | 932.9 KiB |  00m00s
[112/169] ima-evm-utils-libs-0:1.6.2-5. 100% |   1.7 MiB/s |  29.5 KiB |  00m00s
[113/169] libfsverity-0:1.6-2.fc42.x86_ 100% |   1.3 MiB/s |  18.8 KiB |  00m00s
[114/169] gpgverify-0:2.2-2.fc43.noarch 100% | 780.1 KiB/s |  10.9 KiB |  00m00s
[115/169] gnupg2-dirmngr-0:2.4.8-2.fc43 100% |  13.4 MiB/s | 274.8 KiB |  00m00s
[116/169] gnupg2-gpg-agent-0:2.4.8-2.fc 100% |  15.7 MiB/s | 273.0 KiB |  00m00s
[117/169] gnupg2-gpgconf-0:2.4.8-2.fc43 100% |   7.5 MiB/s | 115.2 KiB |  00m00s
[118/169] gnupg2-keyboxd-0:2.4.8-2.fc43 100% |   6.6 MiB/s |  94.8 KiB |  00m00s
[119/169] gnupg2-verify-0:2.4.8-2.fc43. 100% |   9.8 MiB/s | 171.3 KiB |  00m00s
[120/169] libassuan-0:2.5.7-3.fc42.x86_ 100% |   4.7 MiB/s |  67.6 KiB |  00m00s
[121/169] libgpg-error-0:1.55-1.fc43.x8 100% |  14.9 MiB/s | 244.1 KiB |  00m00s
[122/169] gnupg2-0:2.4.8-2.fc43.x86_64  100% |  13.5 MiB/s |   1.6 MiB |  00m00s
[123/169] libgcrypt-0:1.11.1-1.fc43.x86 100% |  20.1 MiB/s | 596.1 KiB |  00m00s
[124/169] npth-0:1.8-2.fc42.x86_64      100% |   1.9 MiB/s |  25.8 KiB |  00m00s
[125/169] libksba-0:1.6.7-3.fc42.x86_64 100% |  10.5 MiB/s | 162.0 KiB |  00m00s
[126/169] openldap-0:2.6.10-2.fc43.x86_ 100% |  14.9 MiB/s | 259.1 KiB |  00m00s
[127/169] gnutls-0:3.8.10-1.fc43.x86_64 100% |  29.8 MiB/s |   1.4 MiB |  00m00s
[128/169] libusb1-0:1.0.28-2.fc43.x86_6 100% |   5.5 MiB/s |  79.3 KiB |  00m00s
[129/169] libidn2-0:2.3.8-1.fc43.x86_64 100% |  10.7 MiB/s | 174.8 KiB |  00m00s
[130/169] libtasn1-0:4.20.0-1.fc43.x86_ 100% |   5.2 MiB/s |  75.0 KiB |  00m00s
[131/169] libunistring-0:1.1-9.fc42.x86 100% |  12.9 MiB/s | 542.5 KiB |  00m00s
[132/169] p11-kit-0:0.25.5-8.fc43.x86_6 100% |  20.7 MiB/s | 488.2 KiB |  00m00s
[133/169] nettle-0:3.10.1-1.fc43.x86_64 100% |   6.4 MiB/s | 424.6 KiB |  00m00s
[134/169] cyrus-sasl-lib-0:2.1.28-30.fc 100% |  23.5 MiB/s | 793.5 KiB |  00m00s
[135/169] libtool-ltdl-0:2.5.4-5.fc43.x 100% |   2.7 MiB/s |  36.2 KiB |  00m00s
[136/169] libffi-0:3.5.1-1.fc43.x86_64  100% |   3.1 MiB/s |  40.9 KiB |  00m00s
[137/169] libevent-0:2.1.12-15.fc42.x86 100% |   3.8 MiB/s | 260.2 KiB |  00m00s
[138/169] gdbm-libs-1:1.23-9.fc42.x86_6 100% |   4.3 MiB/s |  57.0 KiB |  00m00s
[139/169] json-c-0:0.18-4.fc43.x86_64   100% |   2.0 MiB/s |  44.7 KiB |  00m00s
[140/169] libeconf-0:0.7.9-1.fc43.x86_6 100% |   1.7 MiB/s |  35.2 KiB |  00m00s
[141/169] zlib-ng-compat-0:2.2.4-2.fc43 100% | 895.0 KiB/s |  79.7 KiB |  00m00s
[142/169] alternatives-0:1.33-1.fc43.x8 100% |   3.0 MiB/s |  40.5 KiB |  00m00s
[143/169] tpm2-tss-0:4.1.3-7.fc43.x86_6 100% |   1.4 MiB/s | 423.4 KiB |  00m00s
[144/169] jansson-0:2.14-2.fc42.x86_64  100% |   3.4 MiB/s |  45.7 KiB |  00m00s
[145/169] pkgconf-pkg-config-0:2.3.0-2. 100% | 620.3 KiB/s |   9.9 KiB |  00m00s
[146/169] pkgconf-0:2.3.0-2.fc42.x86_64 100% |   3.4 MiB/s |  44.9 KiB |  00m00s
[147/169] pkgconf-m4-0:2.3.0-2.fc42.noa 100% | 889.7 KiB/s |  14.2 KiB |  00m00s
[148/169] libpkgconf-0:2.3.0-2.fc42.x86 100% |   2.9 MiB/s |  38.4 KiB |  00m00s
[149/169] qt5-srpm-macros-0:5.15.17-1.f 100% | 581.2 KiB/s |   8.7 KiB |  00m00s
[150/169] qt6-srpm-macros-0:6.9.1-1.fc4 100% | 782.1 KiB/s |   9.4 KiB |  00m00s
[151/169] p11-kit-trust-0:0.25.5-8.fc43 100% |   8.6 MiB/s | 132.4 KiB |  00m00s
[152/169] fedora-release-0:43-0.19.noar 100% |   1.1 MiB/s |  14.3 KiB |  00m00s
[153/169] systemd-standalone-sysusers-0 100% |   8.8 MiB/s | 134.8 KiB |  00m00s
[154/169] libxml2-0:2.12.10-2.fc43.x86_ 100% |   5.3 MiB/s | 691.3 KiB |  00m00s
[155/169] gdb-minimal-0:16.3-3.fc43.x86 100% |  45.0 MiB/s |   4.4 MiB |  00m00s
[156/169] xxhash-libs-0:0.8.3-2.fc42.x8 100% |   2.2 MiB/s |  39.1 KiB |  00m00s
[157/169] fedora-release-identity-basic 100% |   1.2 MiB/s |  15.1 KiB |  00m00s
[158/169] krb5-libs-0:1.21.3-6.fc43.x86 100% |  29.7 MiB/s | 759.5 KiB |  00m00s
[159/169] libnghttp2-0:1.66.0-1.fc43.x8 100% |   5.5 MiB/s |  72.7 KiB |  00m00s
[160/169] binutils-0:2.44.90-2.fc43.x86 100% |  18.5 MiB/s |   5.8 MiB |  00m00s
[161/169] libcurl-0:8.15.0-1.fc43.x86_6 100% |   6.4 MiB/s | 404.5 KiB |  00m00s
[162/169] libpsl-0:0.21.5-5.fc42.x86_64 100% |   4.8 MiB/s |  64.0 KiB |  00m00s
[163/169] libcom_err-0:1.47.3-1.fc43.x8 100% |   2.0 MiB/s |  26.8 KiB |  00m00s
[164/169] keyutils-libs-0:1.6.3-5.fc42. 100% |   1.9 MiB/s |  31.5 KiB |  00m00s
[165/169] libssh-0:0.11.2-1.fc43.x86_64 100% |  12.0 MiB/s | 232.8 KiB |  00m00s
[166/169] libverto-0:0.3.2-10.fc42.x86_ 100% |   1.6 MiB/s |  20.8 KiB |  00m00s
[167/169] libssh-config-0:0.11.2-1.fc43 100% | 680.9 KiB/s |   8.9 KiB |  00m00s
[168/169] publicsuffix-list-dafsa-0:202 100% |   3.2 MiB/s |  59.2 KiB |  00m00s
[169/169] libbrotli-0:1.1.0-7.fc43.x86_ 100% |  17.4 MiB/s | 339.1 KiB |  00m00s
--------------------------------------------------------------------------------
[169/169] Total                         100% |  34.3 MiB/s |  58.8 MiB |  00m02s
Running transaction
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 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 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing OpenPGP key 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.
[  1/171] Verify package files          100% | 684.0   B/s | 169.0   B |  00m00s
>>> Running %pretrans scriptlet: filesystem-0:3.18-44.fc43.x86_64               
>>> Finished %pretrans scriptlet: filesystem-0:3.18-44.fc43.x86_64              
>>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1753433315.726432/root/var/cache/d
[  2/171] Prepare transaction           100% |   1.9 KiB/s | 169.0   B |  00m00s
[  3/171] Installing libgcc-0:15.1.1-2. 100% | 131.0 MiB/s | 268.3 KiB |  00m00s
[  4/171] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/171] Installing publicsuffix-list- 100% |  68.2 MiB/s |  69.8 KiB |  00m00s
[  6/171] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0   B |  00m00s
[  7/171] Installing fedora-gpg-keys-0: 100% |  19.1 MiB/s | 175.9 KiB |  00m00s
[  8/171] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  9/171] Installing fedora-repos-0:43- 100% |   5.6 MiB/s |   5.7 KiB |  00m00s
[ 10/171] Installing fedora-release-com 100% |  12.1 MiB/s |  24.8 KiB |  00m00s
[ 11/171] Installing fedora-release-0:4 100% |   7.1 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-25.fc43.noarch                   
>>> Finished sysusers scriptlet: setup-0:2.15.0-25.fc43.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.                           
>>>                                                                             
[ 12/171] Installing setup-0:2.15.0-25. 100% |  39.6 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew                               
[ 13/171] Installing filesystem-0:3.18- 100% |   1.4 MiB/s | 212.5 KiB |  00m00s
[ 14/171] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 740.0   B |  00m00s
[ 15/171] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[ 16/171] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 17/171] Installing pcre2-syntax-0:10. 100% | 135.0 MiB/s | 276.4 KiB |  00m00s
[ 18/171] Installing ncurses-base-0:6.5 100% |  38.4 MiB/s | 353.5 KiB |  00m00s
[ 19/171] Installing bash-0:5.3.0-1.fc4 100% | 196.1 MiB/s |   8.4 MiB |  00m00s
[ 20/171] Installing glibc-common-0:2.4 100% |  53.7 MiB/s |   1.0 MiB |  00m00s
[ 21/171] Installing glibc-gconv-extra- 100% | 146.2 MiB/s |   7.3 MiB |  00m00s
[ 22/171] Installing glibc-0:2.41.9000- 100% | 145.5 MiB/s |   6.7 MiB |  00m00s
[ 23/171] Installing ncurses-libs-0:6.5 100% | 186.1 MiB/s | 952.9 KiB |  00m00s
[ 24/171] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 25/171] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB |  00m00s
[ 26/171] Installing bzip2-libs-0:1.0.8 100% |  83.7 MiB/s |  85.7 KiB |  00m00s
[ 27/171] Installing libgpg-error-0:1.5 100% |  52.9 MiB/s | 921.1 KiB |  00m00s
[ 28/171] Installing libstdc++-0:15.1.1 100% | 257.8 MiB/s |   2.8 MiB |  00m00s
[ 29/171] Installing xz-libs-1:5.8.1-1. 100% | 213.8 MiB/s | 218.9 KiB |  00m00s
[ 30/171] Installing libassuan-0:2.5.7- 100% | 165.6 MiB/s | 169.6 KiB |  00m00s
[ 31/171] Installing libgcrypt-0:1.11.1 100% | 262.5 MiB/s |   1.6 MiB |  00m00s
[ 32/171] Installing readline-0:8.3-1.f 100% | 167.3 MiB/s | 513.9 KiB |  00m00s
[ 33/171] Installing gmp-1:6.3.0-3.fc43 100% | 267.4 MiB/s | 821.5 KiB |  00m00s
[ 34/171] Installing libuuid-0:2.41.1-1 100% |  37.4 MiB/s |  38.3 KiB |  00m00s
[ 35/171] Installing popt-0:1.19-8.fc42 100% |  34.0 MiB/s | 139.4 KiB |  00m00s
[ 36/171] Installing npth-0:1.8-2.fc42. 100% |  49.5 MiB/s |  50.7 KiB |  00m00s
[ 37/171] Installing libblkid-0:2.41.1- 100% | 128.7 MiB/s | 263.5 KiB |  00m00s
[ 38/171] Installing libxcrypt-0:4.4.38 100% | 140.2 MiB/s | 287.2 KiB |  00m00s
[ 39/171] Installing libzstd-0:1.5.7-1. 100% | 263.4 MiB/s | 809.1 KiB |  00m00s
[ 40/171] Installing elfutils-libelf-0: 100% | 291.6 MiB/s |   1.2 MiB |  00m00s
[ 41/171] Installing sqlite-libs-0:3.50 100% | 252.7 MiB/s |   1.5 MiB |  00m00s
[ 42/171] Installing gnupg2-gpgconf-0:2 100% |  18.9 MiB/s | 252.1 KiB |  00m00s
[ 43/171] Installing libattr-0:2.5.2-5. 100% |  27.4 MiB/s |  28.1 KiB |  00m00s
[ 44/171] Installing libacl-0:2.3.2-3.f 100% |  38.2 MiB/s |  39.2 KiB |  00m00s
[ 45/171] Installing libtasn1-0:4.20.0- 100% | 173.9 MiB/s | 178.1 KiB |  00m00s
[ 46/171] Installing libunistring-0:1.1 100% | 287.8 MiB/s |   1.7 MiB |  00m00s
[ 47/171] Installing libidn2-0:2.3.8-1. 100% |  26.0 MiB/s | 558.7 KiB |  00m00s
[ 48/171] Installing crypto-policies-0: 100% |  16.8 MiB/s | 172.0 KiB |  00m00s
[ 49/171] Installing dwz-0:0.16-1.fc43. 100% |  18.8 MiB/s | 288.5 KiB |  00m00s
[ 50/171] Installing gnupg2-verify-0:2. 100% |  26.3 MiB/s | 349.9 KiB |  00m00s
[ 51/171] Installing mpfr-0:4.2.2-1.fc4 100% | 202.7 MiB/s | 830.4 KiB |  00m00s
[ 52/171] Installing gawk-0:5.3.2-1.fc4 100% |  82.5 MiB/s |   1.8 MiB |  00m00s
[ 53/171] Installing libksba-0:1.6.7-3. 100% | 197.8 MiB/s | 405.1 KiB |  00m00s
[ 54/171] Installing unzip-0:6.0-66.fc4 100% |  25.6 MiB/s | 393.8 KiB |  00m00s
[ 55/171] Installing file-libs-0:5.46-5 100% | 474.3 MiB/s |  11.9 MiB |  00m00s
[ 56/171] Installing file-0:5.46-5.fc43 100% |   7.6 MiB/s | 101.7 KiB |  00m00s
[ 57/171] Installing pcre2-0:10.45-1.fc 100% | 227.6 MiB/s | 699.1 KiB |  00m00s
[ 58/171] Installing grep-0:3.12-1.fc43 100% |  50.1 MiB/s |   1.0 MiB |  00m00s
[ 59/171] Installing xz-1:5.8.1-1.fc43. 100% |  57.9 MiB/s |   1.3 MiB |  00m00s
[ 60/171] Installing libcap-ng-0:0.8.5- 100% |  69.2 MiB/s |  70.8 KiB |  00m00s
[ 61/171] Installing audit-libs-0:4.1.0 100% | 124.2 MiB/s | 381.5 KiB |  00m00s
[ 62/171] Installing libsmartcols-0:2.4 100% | 177.4 MiB/s | 181.6 KiB |  00m00s
[ 63/171] Installing libsepol-0:3.9-1.f 100% | 267.9 MiB/s | 822.9 KiB |  00m00s
[ 64/171] Installing libselinux-0:3.9-1 100% |  94.9 MiB/s | 194.3 KiB |  00m00s
[ 65/171] Installing findutils-1:4.10.0 100% |  89.2 MiB/s |   1.9 MiB |  00m00s
[ 66/171] Installing sed-0:4.9-4.fc42.x 100% |  44.5 MiB/s | 865.5 KiB |  00m00s
[ 67/171] Installing libmount-0:2.41.1- 100% | 182.5 MiB/s | 373.8 KiB |  00m00s
[ 68/171] Installing lz4-libs-0:1.10.0- 100% | 154.7 MiB/s | 158.5 KiB |  00m00s
[ 69/171] Installing lua-libs-0:5.4.8-1 100% | 137.7 MiB/s | 282.0 KiB |  00m00s
[ 70/171] Installing libffi-0:3.5.1-1.f 100% |  83.0 MiB/s |  85.0 KiB |  00m00s
[ 71/171] Installing p11-kit-0:0.25.5-8 100% |  84.0 MiB/s |   2.2 MiB |  00m00s
[ 72/171] Installing json-c-0:0.18-4.fc 100% |  82.0 MiB/s |  84.0 KiB |  00m00s
[ 73/171] Installing libeconf-0:0.7.9-1 100% |  65.0 MiB/s |  66.5 KiB |  00m00s
[ 74/171] Installing pam-libs-0:1.7.1-2 100% |  63.1 MiB/s | 129.2 KiB |  00m00s
[ 75/171] Installing libcap-0:2.76-1.fc 100% |  14.9 MiB/s | 214.3 KiB |  00m00s
[ 76/171] Installing systemd-libs-0:257 100% | 248.0 MiB/s |   2.2 MiB |  00m00s
[ 77/171] Installing alternatives-0:1.3 100% |   4.8 MiB/s |  63.8 KiB |  00m00s
[ 78/171] Installing p11-kit-trust-0:0. 100% |  12.5 MiB/s | 397.1 KiB |  00m00s
[ 79/171] Installing util-linux-core-0: 100% |  61.6 MiB/s |   1.5 MiB |  00m00s
[ 80/171] Installing libusb1-0:1.0.28-2 100% |  84.3 MiB/s | 172.7 KiB |  00m00s
[ 81/171] Installing systemd-standalone 100% |  20.9 MiB/s | 277.8 KiB |  00m00s
[ 82/171] Installing zstd-0:1.5.7-1.fc4 100% |  95.0 MiB/s |   1.7 MiB |  00m00s
[ 83/171] Installing tar-2:1.35-5.fc42. 100% | 118.5 MiB/s |   3.0 MiB |  00m00s
[ 84/171] Installing libsemanage-0:3.9- 100% | 151.5 MiB/s | 310.2 KiB |  00m00s
[ 85/171] Installing zip-0:3.0-43.fc42. 100% |  45.7 MiB/s | 702.4 KiB |  00m00s
[ 86/171] Installing gnupg2-keyboxd-0:2 100% |  12.4 MiB/s | 202.7 KiB |  00m00s
[ 87/171] Installing libpsl-0:0.21.5-5. 100% |  75.7 MiB/s |  77.5 KiB |  00m00s
[ 88/171] Installing liblastlog2-0:2.41 100% |   2.2 MiB/s |  35.9 KiB |  00m00s
[ 89/171] Installing libfdisk-0:2.41.1- 100% | 124.2 MiB/s | 381.5 KiB |  00m00s
[ 90/171] Installing nettle-0:3.10.1-1. 100% | 193.8 MiB/s | 793.6 KiB |  00m00s
[ 91/171] Installing gnutls-0:3.8.10-1. 100% | 240.0 MiB/s |   3.8 MiB |  00m00s
[ 92/171] Installing libxml2-0:2.12.10- 100% |  85.2 MiB/s |   1.7 MiB |  00m00s
[ 93/171] Installing bzip2-0:1.0.8-20.f 100% |   7.8 MiB/s | 103.8 KiB |  00m00s
[ 94/171] Installing add-determinism-0: 100% | 117.4 MiB/s |   2.5 MiB |  00m00s
[ 95/171] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 96/171] Installing cpio-0:2.15-2.fc41 100% |  57.9 MiB/s |   1.1 MiB |  00m00s
[ 97/171] Installing diffutils-0:3.12-2 100% |  74.3 MiB/s |   1.6 MiB |  00m00s
[ 98/171] Installing ed-0:1.22-1.fc43.x 100% |  11.2 MiB/s | 149.4 KiB |  00m00s
[ 99/171] Installing patch-0:2.8-1.fc43 100% |  15.9 MiB/s | 228.3 KiB |  00m00s
[100/171] Installing libgomp-0:15.1.1-2 100% | 175.9 MiB/s | 540.5 KiB |  00m00s
[101/171] Installing libtool-ltdl-0:2.5 100% |  69.6 MiB/s |  71.2 KiB |  00m00s
[102/171] Installing gdbm-libs-1:1.23-9 100% | 128.5 MiB/s | 131.6 KiB |  00m00s
[103/171] Installing cyrus-sasl-lib-0:2 100% | 109.7 MiB/s |   2.3 MiB |  00m00s
[104/171] Installing jansson-0:2.14-2.f 100% |  92.2 MiB/s |  94.4 KiB |  00m00s
[105/171] Installing libpkgconf-0:2.3.0 100% |  77.4 MiB/s |  79.2 KiB |  00m00s
[106/171] Installing pkgconf-0:2.3.0-2. 100% |   6.8 MiB/s |  91.0 KiB |  00m00s
[107/171] Installing pkgconf-pkg-config 100% | 147.8 KiB/s |   1.8 KiB |  00m00s
[108/171] Installing xxhash-libs-0:0.8. 100% |  89.4 MiB/s |  91.6 KiB |  00m00s
[109/171] Installing libnghttp2-0:1.66. 100% | 159.5 MiB/s | 163.3 KiB |  00m00s
[110/171] Installing keyutils-libs-0:1. 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[111/171] Installing libcom_err-0:1.47. 100% |  62.7 MiB/s |  64.2 KiB |  00m00s
[112/171] Installing libverto-0:0.3.2-1 100% |  26.6 MiB/s |  27.2 KiB |  00m00s
[113/171] Installing libbrotli-0:1.1.0- 100% | 204.0 MiB/s | 835.6 KiB |  00m00s
[114/171] Installing filesystem-srpm-ma 100% |  38.0 MiB/s |  38.9 KiB |  00m00s
[115/171] Installing elfutils-default-y 100% | 145.9 KiB/s |   2.0 KiB |  00m00s
[116/171] Installing elfutils-libs-0:0. 100% | 167.3 MiB/s | 685.2 KiB |  00m00s
[117/171] Installing rust-srpm-macros-0 100% |   5.4 MiB/s |   5.6 KiB |  00m00s
[118/171] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[119/171] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[120/171] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[121/171] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[122/171] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[123/171] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[124/171] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[125/171] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[126/171] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[127/171] Installing coreutils-common-0 100% | 245.5 MiB/s |  11.3 MiB |  00m00s
[128/171] Installing openssl-libs-1:3.5 100% | 318.0 MiB/s |   8.9 MiB |  00m00s
[129/171] Installing coreutils-0:9.7-4. 100% | 102.7 MiB/s |   5.4 MiB |  00m00s
[130/171] Installing ca-certificates-0: 100% |   1.2 MiB/s |   2.4 MiB |  00m02s
[131/171] Installing libarchive-0:3.8.1 100% | 155.1 MiB/s | 953.1 KiB |  00m00s
[132/171] Installing krb5-libs-0:1.21.3 100% |  81.9 MiB/s |   2.3 MiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-7.fc43.x86_64                  
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-7.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.   
>>>                                                                             
[133/171] Installing tpm2-tss-0:4.1.3-7 100% | 174.2 MiB/s |   1.6 MiB |  00m00s
[134/171] Installing ima-evm-utils-libs 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[135/171] Installing gnupg2-gpg-agent-0 100% |  20.0 MiB/s | 675.4 KiB |  00m00s
[136/171] Installing libssh-0:0.11.2-1. 100% | 138.9 MiB/s | 568.8 KiB |  00m00s
[137/171] Installing gzip-0:1.13-3.fc42 100% |  24.3 MiB/s | 398.4 KiB |  00m00s
[138/171] Installing rpm-sequoia-0:1.9. 100% | 275.4 MiB/s |   2.5 MiB |  00m00s
[139/171] Installing rpm-libs-0:5.99.91 100% | 228.3 MiB/s | 935.3 KiB |  00m00s
[140/171] Installing libfsverity-0:1.6- 100% |  32.7 MiB/s |  33.5 KiB |  00m00s
[141/171] Installing libevent-0:2.1.12- 100% | 221.4 MiB/s | 906.9 KiB |  00m00s
[142/171] Installing openldap-0:2.6.10- 100% | 161.0 MiB/s | 659.6 KiB |  00m00s
[143/171] Installing libcurl-0:8.15.0-1 100% | 220.8 MiB/s | 904.3 KiB |  00m00s
[144/171] Installing elfutils-debuginfo 100% |   6.0 MiB/s |  86.2 KiB |  00m00s
[145/171] Installing elfutils-0:0.193-2 100% | 127.1 MiB/s |   2.9 MiB |  00m00s
[146/171] Installing binutils-0:2.44.90 100% | 238.2 MiB/s |  26.4 MiB |  00m00s
[147/171] Installing gdb-minimal-0:16.3 100% | 240.9 MiB/s |  13.2 MiB |  00m00s
[148/171] Installing debugedit-0:5.2-1. 100% |  14.0 MiB/s | 200.5 KiB |  00m00s
[149/171] Installing curl-0:8.15.0-1.fc 100% |  13.7 MiB/s | 476.3 KiB |  00m00s
[150/171] Installing rpm-0:5.99.91-1.fc 100% |  44.5 MiB/s |   2.5 MiB |  00m00s
[151/171] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.1 KiB |  00m00s
[152/171] Installing java-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[153/171] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[154/171] Installing tree-sitter-srpm-m 100% |   9.0 MiB/s |   9.3 KiB |  00m00s
[155/171] Installing zig-srpm-macros-0: 100% |   1.6 MiB/s |   1.7 KiB |  00m00s
[156/171] Installing gnupg2-dirmngr-0:2 100% |  19.6 MiB/s | 621.1 KiB |  00m00s
[157/171] Installing gnupg2-0:2.4.8-2.f 100% | 168.0 MiB/s |   6.6 MiB |  00m00s
[158/171] Installing rpm-sign-libs-0:5. 100% |  39.6 MiB/s |  40.6 KiB |  00m00s
[159/171] Installing rpm-build-libs-0:5 100% | 131.5 MiB/s | 269.2 KiB |  00m00s
[160/171] Installing gpgverify-0:2.2-2. 100% |   9.2 MiB/s |   9.4 KiB |  00m00s
[161/171] Installing rpm-build-0:5.99.9 100% |  18.2 MiB/s | 298.4 KiB |  00m00s
[162/171] Installing pyproject-srpm-mac 100% |   2.4 MiB/s |   2.5 KiB |  00m00s
[163/171] Installing redhat-rpm-config- 100% |  45.9 MiB/s | 188.1 KiB |  00m00s
[164/171] Installing forge-srpm-macros- 100% |  39.3 MiB/s |  40.3 KiB |  00m00s
[165/171] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[166/171] Installing go-srpm-macros-0:3 100% |  61.3 MiB/s |  62.7 KiB |  00m00s
[167/171] Installing python-srpm-macros 100% |  51.6 MiB/s |  52.8 KiB |  00m00s
[168/171] Installing which-0:2.23-2.fc4 100% |   5.2 MiB/s |  85.7 KiB |  00m00s
[169/171] Installing util-linux-0:2.41. 100% |  62.6 MiB/s |   3.6 MiB |  00m00s
[170/171] Installing shadow-utils-2:4.1 100% |  84.5 MiB/s |   4.0 MiB |  00m00s
[171/171] Installing info-0:7.2-4.fc43. 100% | 133.2 KiB/s | 354.3 KiB |  00m03s
Warning: skipped OpenPGP checks for 1 package from repository: copr_base
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.6.0-1.fc43.x86_64
alternatives-1.33-1.fc43.x86_64
ansible-srpm-macros-1-17.1.fc42.noarch
audit-libs-4.1.0-1.fc43.x86_64
bash-5.3.0-1.fc43.x86_64
binutils-2.44.90-2.fc43.x86_64
build-reproducibility-srpm-macros-0.6.0-1.fc43.noarch
bzip2-1.0.8-20.fc42.x86_64
bzip2-libs-1.0.8-20.fc42.x86_64
ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch
coreutils-9.7-4.fc43.x86_64
coreutils-common-9.7-4.fc43.x86_64
cpio-2.15-2.fc41.x86_64
crypto-policies-20250714-1.gitcd6043a.fc43.noarch
curl-8.15.0-1.fc43.x86_64
cyrus-sasl-lib-2.1.28-30.fc42.x86_64
debugedit-5.2-1.fc43.x86_64
diffutils-3.12-2.fc43.x86_64
dwz-0.16-1.fc43.x86_64
ed-1.22-1.fc43.x86_64
efi-srpm-macros-6-3.fc43.noarch
elfutils-0.193-2.fc43.x86_64
elfutils-debuginfod-client-0.193-2.fc43.x86_64
elfutils-default-yama-scope-0.193-2.fc43.noarch
elfutils-libelf-0.193-2.fc43.x86_64
elfutils-libs-0.193-2.fc43.x86_64
fedora-gpg-keys-43-0.2.noarch
fedora-release-43-0.19.noarch
fedora-release-common-43-0.19.noarch
fedora-release-identity-basic-43-0.19.noarch
fedora-repos-43-0.2.noarch
fedora-repos-rawhide-43-0.2.noarch
file-5.46-5.fc43.x86_64
file-libs-5.46-5.fc43.x86_64
filesystem-3.18-44.fc43.x86_64
filesystem-srpm-macros-3.18-44.fc43.noarch
findutils-4.10.0-5.fc42.x86_64
fonts-srpm-macros-2.0.5-22.fc43.noarch
forge-srpm-macros-0.4.0-2.fc42.noarch
fpc-srpm-macros-1.3-14.fc42.noarch
gawk-5.3.2-1.fc43.x86_64
gdb-minimal-16.3-3.fc43.x86_64
gdbm-libs-1.23-9.fc42.x86_64
ghc-srpm-macros-1.9.2-2.fc42.noarch
glibc-2.41.9000-23.fc43.x86_64
glibc-common-2.41.9000-23.fc43.x86_64
glibc-gconv-extra-2.41.9000-23.fc43.x86_64
glibc-minimal-langpack-2.41.9000-23.fc43.x86_64
gmp-6.3.0-3.fc43.x86_64
gnat-srpm-macros-6-7.fc42.noarch
gnupg2-2.4.8-2.fc43.x86_64
gnupg2-dirmngr-2.4.8-2.fc43.x86_64
gnupg2-gpg-agent-2.4.8-2.fc43.x86_64
gnupg2-gpgconf-2.4.8-2.fc43.x86_64
gnupg2-keyboxd-2.4.8-2.fc43.x86_64
gnupg2-verify-2.4.8-2.fc43.x86_64
gnutls-3.8.10-1.fc43.x86_64
go-srpm-macros-3.7.0-1.fc43.noarch
gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b
gpg-pubkey-b0f4950458f69e1150c6c5edc8ac4916105ef944-65ca83d1
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-2.fc43.noarch
grep-3.12-1.fc43.x86_64
gzip-1.13-3.fc42.x86_64
ima-evm-utils-libs-1.6.2-5.fc43.x86_64
info-7.2-4.fc43.x86_64
jansson-2.14-2.fc42.x86_64
java-srpm-macros-1-6.fc43.noarch
json-c-0.18-4.fc43.x86_64
kernel-srpm-macros-1.0-25.fc42.noarch
keyutils-libs-1.6.3-5.fc42.x86_64
krb5-libs-1.21.3-6.fc43.x86_64
libacl-2.3.2-3.fc42.x86_64
libarchive-3.8.1-2.fc43.x86_64
libassuan-2.5.7-3.fc42.x86_64
libattr-2.5.2-5.fc42.x86_64
libblkid-2.41.1-11.fc43.x86_64
libbrotli-1.1.0-7.fc43.x86_64
libcap-2.76-1.fc43.x86_64
libcap-ng-0.8.5-5.fc43.x86_64
libcom_err-1.47.3-1.fc43.x86_64
libcurl-8.15.0-1.fc43.x86_64
libeconf-0.7.9-1.fc43.x86_64
libevent-2.1.12-15.fc42.x86_64
libfdisk-2.41.1-11.fc43.x86_64
libffi-3.5.1-1.fc43.x86_64
libfsverity-1.6-2.fc42.x86_64
libgcc-15.1.1-2.fc43.x86_64
libgcrypt-1.11.1-1.fc43.x86_64
libgomp-15.1.1-2.fc43.x86_64
libgpg-error-1.55-1.fc43.x86_64
libidn2-2.3.8-1.fc43.x86_64
libksba-1.6.7-3.fc42.x86_64
liblastlog2-2.41.1-11.fc43.x86_64
libmount-2.41.1-11.fc43.x86_64
libnghttp2-1.66.0-1.fc43.x86_64
libpkgconf-2.3.0-2.fc42.x86_64
libpsl-0.21.5-5.fc42.x86_64
libselinux-3.9-1.fc43.x86_64
libsemanage-3.9-1.fc43.x86_64
libsepol-3.9-1.fc43.x86_64
libsmartcols-2.41.1-11.fc43.x86_64
libssh-0.11.2-1.fc43.x86_64
libssh-config-0.11.2-1.fc43.noarch
libstdc++-15.1.1-2.fc43.x86_64
libtasn1-4.20.0-1.fc43.x86_64
libtool-ltdl-2.5.4-5.fc43.x86_64
libunistring-1.1-9.fc42.x86_64
libusb1-1.0.28-2.fc43.x86_64
libuuid-2.41.1-11.fc43.x86_64
libverto-0.3.2-10.fc42.x86_64
libxcrypt-4.4.38-7.fc43.x86_64
libxml2-2.12.10-2.fc43.x86_64
libzstd-1.5.7-1.fc43.x86_64
lua-libs-5.4.8-1.fc43.x86_64
lua-srpm-macros-1-15.fc42.noarch
lz4-libs-1.10.0-2.fc42.x86_64
mpfr-4.2.2-1.fc43.x86_64
ncurses-base-6.5-6.20250614.fc43.noarch
ncurses-libs-6.5-6.20250614.fc43.x86_64
nettle-3.10.1-1.fc43.x86_64
npth-1.8-2.fc42.x86_64
ocaml-srpm-macros-10-4.fc42.noarch
openblas-srpm-macros-2-19.fc42.noarch
openldap-2.6.10-2.fc43.x86_64
openssl-libs-3.5.1-1.fc43.x86_64
p11-kit-0.25.5-8.fc43.x86_64
p11-kit-trust-0.25.5-8.fc43.x86_64
package-notes-srpm-macros-0.5-13.fc42.noarch
pam-libs-1.7.1-2.fc43.x86_64
patch-2.8-1.fc43.x86_64
pcre2-10.45-1.fc43.x86_64
pcre2-syntax-10.45-1.fc43.noarch
perl-srpm-macros-1-59.fc43.noarch
pkgconf-2.3.0-2.fc42.x86_64
pkgconf-m4-2.3.0-2.fc42.noarch
pkgconf-pkg-config-2.3.0-2.fc42.x86_64
popt-1.19-8.fc42.x86_64
publicsuffix-list-dafsa-20250616-1.fc43.noarch
pyproject-srpm-macros-1.18.3-1.fc43.noarch
python-srpm-macros-3.14-3.fc43.noarch
qt5-srpm-macros-5.15.17-1.fc43.noarch
qt6-srpm-macros-6.9.1-1.fc43.noarch
readline-8.3-1.fc43.x86_64
redhat-rpm-config-343-7.fc43.noarch
rpm-5.99.91-1.fc43.x86_64
rpm-build-5.99.91-1.fc43.x86_64
rpm-build-libs-5.99.91-1.fc43.x86_64
rpm-libs-5.99.91-1.fc43.x86_64
rpm-sequoia-1.9.0-1.fc43.x86_64
rpm-sign-libs-5.99.91-1.fc43.x86_64
rust-srpm-macros-26.3-4.fc42.noarch
sed-4.9-4.fc42.x86_64
setup-2.15.0-25.fc43.noarch
shadow-utils-4.18.0-1.fc43.x86_64
sqlite-libs-3.50.2-1.fc43.x86_64
systemd-libs-257.7-1.fc43.x86_64
systemd-standalone-sysusers-257.7-1.fc43.x86_64
tar-1.35-5.fc42.x86_64
tpm2-tss-4.1.3-7.fc43.x86_64
tree-sitter-srpm-macros-0.4.1-1.fc43.noarch
unzip-6.0-66.fc42.x86_64
util-linux-2.41.1-11.fc43.x86_64
util-linux-core-2.41.1-11.fc43.x86_64
which-2.23-2.fc43.x86_64
xxhash-libs-0.8.3-2.fc42.x86_64
xz-5.8.1-1.fc43.x86_64
xz-libs-5.8.1-1.fc43.x86_64
zig-srpm-macros-1-4.fc42.noarch
zip-3.0-43.fc42.x86_64
zlib-ng-compat-2.2.4-2.fc43.x86_64
zstd-1.5.7-1.fc43.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.fc43.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_64-1753433315.726432/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-1qsyy_sr/percolator/percolator.spec) Config(child) 1 minutes 7 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.fc43.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1753433315.726432/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1753433315.726432/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_64-1753433315.726432/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-5.99.91-1.fc43.x86_64
  rpm-sequoia-1.9.0-1.fc43.x86_64
  dnf5-5.2.15.0-3.fc43.x86_64
  dnf5-plugins-5.2.15.0-3.fc43.x86_64
Finish: chroot init
Start: build phase for percolator-3.08-1.fc43.src.rpm
Start: build setup for percolator-3.08-1.fc43.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.fc43.src.rpm
Updating and loading repositories:
 Copr repository                        100% |  34.2 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 325.3 KiB/s |  27.0 KiB |  00m00s
Repositories loaded.
Package                    Arch   Version              Repository      Size
Installing:
 boost-devel               x86_64 1.83.0-13.fc43       fedora     143.0 MiB
 boost-static              x86_64 1.83.0-13.fc43       fedora      33.7 MiB
 bzip2-devel               x86_64 1.0.8-20.fc42        fedora     309.8 KiB
 cmake                     x86_64 3.31.6-3.fc43        copr_base   34.5 MiB
 eigen3-devel              noarch 3.4.0-17.fc43        copr_base    8.4 MiB
 gcc                       x86_64 15.1.1-2.fc43        fedora     111.1 MiB
 gcc-c++                   x86_64 15.1.1-2.fc43        fedora      41.3 MiB
 gtest-devel               x86_64 1.15.2-3.fc43        copr_base    1.0 MiB
 libtirpc-devel            x86_64 1.3.6-1.rc3.fc42.2   fedora     251.6 KiB
 make                      x86_64 1:4.4.1-10.fc42      fedora       1.8 MiB
 python3-devel             x86_64 3.14.0~rc1-1.fc43    fedora       1.9 MiB
 sqlite-devel              x86_64 3.50.2-1.fc43        fedora     684.1 KiB
 tokyocabinet-devel        x86_64 1.4.48-27.fc42       fedora     460.2 KiB
 xerces-c-devel            x86_64 3.3.0-7.fc43         copr_base    4.1 MiB
 xsd                       x86_64 4.1.0-0.17.a11.fc42  fedora       5.0 MiB
 zlib-ng-compat-devel      x86_64 2.2.4-2.fc43         copr_base  107.0 KiB
Installing dependencies:
 annobin-docs              noarch 12.98-1.fc43         fedora      98.9 KiB
 annobin-plugin-gcc        x86_64 12.98-1.fc43         fedora       1.0 MiB
 boost                     x86_64 1.83.0-13.fc43       fedora       1.3 KiB
 boost-atomic              x86_64 1.83.0-13.fc43       fedora      20.9 KiB
 boost-chrono              x86_64 1.83.0-13.fc43       fedora      37.5 KiB
 boost-container           x86_64 1.83.0-13.fc43       fedora      65.4 KiB
 boost-context             x86_64 1.83.0-13.fc43       fedora      12.4 KiB
 boost-contract            x86_64 1.83.0-13.fc43       fedora      99.1 KiB
 boost-coroutine           x86_64 1.83.0-13.fc43       fedora      21.1 KiB
 boost-date-time           x86_64 1.83.0-13.fc43       fedora      12.2 KiB
 boost-fiber               x86_64 1.83.0-13.fc43       fedora      78.7 KiB
 boost-filesystem          x86_64 1.83.0-13.fc43       fedora     143.6 KiB
 boost-graph               x86_64 1.83.0-13.fc43       fedora     363.1 KiB
 boost-iostreams           x86_64 1.83.0-13.fc43       fedora      90.6 KiB
 boost-json                x86_64 1.83.0-13.fc43       fedora     337.1 KiB
 boost-locale              x86_64 1.83.0-13.fc43       fedora     617.7 KiB
 boost-log                 x86_64 1.83.0-13.fc43       fedora       1.5 MiB
 boost-math                x86_64 1.83.0-13.fc43       fedora     642.6 KiB
 boost-nowide              x86_64 1.83.0-13.fc43       fedora      20.8 KiB
 boost-numpy3              x86_64 1.83.0-13.fc43       fedora      57.6 KiB
 boost-program-options     x86_64 1.83.0-13.fc43       fedora     280.8 KiB
 boost-python3             x86_64 1.83.0-13.fc43       fedora     258.2 KiB
 boost-random              x86_64 1.83.0-13.fc43       fedora      29.6 KiB
 boost-regex               x86_64 1.83.0-13.fc43       fedora     291.1 KiB
 boost-serialization       x86_64 1.83.0-13.fc43       fedora     441.6 KiB
 boost-stacktrace          x86_64 1.83.0-13.fc43       fedora      59.8 KiB
 boost-system              x86_64 1.83.0-13.fc43       fedora      12.2 KiB
 boost-test                x86_64 1.83.0-13.fc43       fedora     647.2 KiB
 boost-thread              x86_64 1.83.0-13.fc43       fedora     132.7 KiB
 boost-timer               x86_64 1.83.0-13.fc43       fedora      21.0 KiB
 boost-type_erasure        x86_64 1.83.0-13.fc43       fedora      54.1 KiB
 boost-wave                x86_64 1.83.0-13.fc43       fedora     860.3 KiB
 cmake-data                noarch 3.31.6-3.fc43        copr_base    8.5 MiB
 cmake-filesystem          x86_64 3.31.6-3.fc43        copr_base    0.0   B
 cmake-rpm-macros          noarch 3.31.6-3.fc43        copr_base    7.7 KiB
 cpp                       x86_64 15.1.1-2.fc43        fedora      37.9 MiB
 emacs-filesystem          noarch 1:30.0-4.fc42        fedora       0.0   B
 expat                     x86_64 2.7.1-1.fc43         fedora     294.2 KiB
 flexiblas                 x86_64 3.4.5-2.fc43         copr_base   50.4 KiB
 flexiblas-netlib          x86_64 3.4.5-2.fc43         copr_base   10.9 MiB
 flexiblas-openblas-openmp x86_64 3.4.5-2.fc43         copr_base   39.2 KiB
 gcc-plugin-annobin        x86_64 15.1.1-2.fc43        fedora      57.2 KiB
 glibc-devel               x86_64 2.41.9000-23.fc43    fedora       2.3 MiB
 gmock                     x86_64 1.15.2-3.fc43        copr_base  131.0 KiB
 gtest                     x86_64 1.15.2-3.fc43        copr_base  501.7 KiB
 jsoncpp                   x86_64 1.9.6-1.fc43         copr_base  261.6 KiB
 kernel-headers            x86_64 6.16.0-0.rc7.58.fc43 fedora       6.7 MiB
 libcutl                   x86_64 1.10.0-32.fc42       fedora       1.1 MiB
 libgfortran               x86_64 15.1.1-2.fc43        fedora       3.3 MiB
 libicu                    x86_64 76.1-4.fc42          fedora      36.3 MiB
 libicu-devel              x86_64 76.1-4.fc42          fedora       5.0 MiB
 libmpc                    x86_64 1.3.1-7.fc42         fedora     164.5 KiB
 libquadmath               x86_64 15.1.1-2.fc43        fedora     317.9 KiB
 libquadmath-devel         x86_64 15.1.1-2.fc43        fedora      22.1 KiB
 libstdc++-devel           x86_64 15.1.1-2.fc43        fedora      16.1 MiB
 libtirpc                  x86_64 1.3.6-1.rc3.fc42.2   fedora     199.0 KiB
 libuv                     x86_64 1:1.51.0-1.fc43      fedora     570.2 KiB
 libxcrypt-devel           x86_64 4.4.38-7.fc43        fedora      30.8 KiB
 mpdecimal                 x86_64 4.0.1-1.fc43         fedora     217.2 KiB
 ninja-build               x86_64 1.13.1-1.fc43        fedora     480.7 KiB
 openblas                  x86_64 0.3.29-1.fc42        fedora     111.7 KiB
 openblas-openmp           x86_64 0.3.29-1.fc42        fedora      43.7 MiB
 pyproject-rpm-macros      noarch 1.18.3-1.fc43        fedora     114.5 KiB
 python-pip-wheel          noarch 25.1.1-13.fc43       fedora       1.2 MiB
 python-rpm-macros         noarch 3.14-3.fc43          fedora      22.8 KiB
 python3                   x86_64 3.14.0~rc1-1.fc43    fedora      28.9 KiB
 python3-libs              x86_64 3.14.0~rc1-1.fc43    fedora      42.9 MiB
 python3-numpy             x86_64 1:2.3.1-1.fc43       fedora      41.1 MiB
 python3-numpy-f2py        x86_64 1:2.3.1-1.fc43       fedora       2.1 MiB
 python3-packaging         noarch 25.0-3.fc43          fedora     607.5 KiB
 python3-rpm-generators    noarch 14-12.fc42           fedora      81.7 KiB
 python3-rpm-macros        noarch 3.14-3.fc43          fedora       6.5 KiB
 rhash                     x86_64 1.4.5-2.fc42         fedora     351.0 KiB
 sqlite                    x86_64 3.50.2-1.fc43        fedora       1.8 MiB
 tokyocabinet              x86_64 1.4.48-27.fc42       fedora       1.5 MiB
 tzdata                    noarch 2025b-1.fc43         fedora       1.6 MiB
 vim-filesystem            noarch 2:9.1.1537-2.fc43    fedora      40.0   B
 xerces-c                  x86_64 3.3.0-7.fc43         copr_base    3.8 MiB

Transaction Summary:
 Installing:        94 packages

Total size of inbound packages is 159 MiB. Need to download 159 MiB.
After this operation, 668 MiB extra will be used (install 668 MiB, remove 0 B).
[ 1/94] make-1:4.4.1-10.fc42.x86_64     100% |   1.7 MiB/s | 587.0 KiB |  00m00s
[ 2/94] xsd-0:4.1.0-0.17.a11.fc42.x86_6 100% |   3.4 MiB/s |   1.2 MiB |  00m00s
[ 3/94] boost-static-0:1.83.0-13.fc43.x 100% |  19.2 MiB/s |   3.2 MiB |  00m00s
[ 4/94] bzip2-devel-0:1.0.8-20.fc42.x86 100% |   2.2 MiB/s | 213.7 KiB |  00m00s
[ 5/94] boost-devel-0:1.83.0-13.fc43.x8 100% |  26.0 MiB/s |  14.2 MiB |  00m01s
[ 6/94] cmake-0:3.31.6-3.fc43.x86_64    100% |  34.3 MiB/s |  12.2 MiB |  00m00s
[ 7/94] eigen3-devel-0:3.4.0-17.fc43.no 100% |  10.7 MiB/s |   1.1 MiB |  00m00s
[ 8/94] gtest-devel-0:1.15.2-3.fc43.x86 100% |   3.1 MiB/s | 243.8 KiB |  00m00s
[ 9/94] libtirpc-devel-0:1.3.6-1.rc3.fc 100% |   2.3 MiB/s | 125.9 KiB |  00m00s
[10/94] sqlite-devel-0:3.50.2-1.fc43.x8 100% |   2.3 MiB/s | 152.4 KiB |  00m00s
[11/94] tokyocabinet-devel-0:1.4.48-27. 100% |   1.5 MiB/s |  88.8 KiB |  00m00s
[12/94] xerces-c-devel-0:3.3.0-7.fc43.x 100% |  11.6 MiB/s | 438.9 KiB |  00m00s
[13/94] python3-devel-0:3.14.0~rc1-1.fc 100% |   8.8 MiB/s | 434.5 KiB |  00m00s
[14/94] gcc-c++-0:15.1.1-2.fc43.x86_64  100% |  39.4 MiB/s |  15.2 MiB |  00m00s
[15/94] gcc-0:15.1.1-2.fc43.x86_64      100% |  28.1 MiB/s |  39.4 MiB |  00m01s
[16/94] zlib-ng-compat-devel-0:2.2.4-2. 100% | 579.5 KiB/s |  38.8 KiB |  00m00s
[17/94] libmpc-0:1.3.1-7.fc42.x86_64    100% |   1.3 MiB/s |  70.9 KiB |  00m00s
[18/94] libcutl-0:1.10.0-32.fc42.x86_64 100% |   5.4 MiB/s | 340.5 KiB |  00m00s
[19/94] boost-0:1.83.0-13.fc43.x86_64   100% | 251.5 KiB/s |  12.1 KiB |  00m00s
[20/94] boost-numpy3-0:1.83.0-13.fc43.x 100% | 460.2 KiB/s |  28.1 KiB |  00m00s
[21/94] libicu-devel-0:76.1-4.fc42.x86_ 100% |   8.9 MiB/s | 793.6 KiB |  00m00s
[22/94] libquadmath-devel-0:15.1.1-2.fc 100% | 644.5 KiB/s |  40.6 KiB |  00m00s
[23/94] expat-0:2.7.1-1.fc43.x86_64     100% |   3.0 MiB/s | 115.9 KiB |  00m00s
[24/94] rhash-0:1.4.5-2.fc42.x86_64     100% |   3.8 MiB/s | 198.7 KiB |  00m00s
[25/94] cpp-0:15.1.1-2.fc43.x86_64      100% |  42.6 MiB/s |  12.9 MiB |  00m00s
[26/94] gmock-0:1.15.2-3.fc43.x86_64    100% |   1.8 MiB/s |  61.5 KiB |  00m00s
[27/94] gtest-0:1.15.2-3.fc43.x86_64    100% |   3.4 MiB/s | 185.5 KiB |  00m00s
[28/94] libtirpc-0:1.3.6-1.rc3.fc42.2.x 100% |   2.0 MiB/s |  95.5 KiB |  00m00s
[29/94] sqlite-0:3.50.2-1.fc43.x86_64   100% |  12.4 MiB/s | 925.3 KiB |  00m00s
[30/94] tokyocabinet-0:1.4.48-27.fc42.x 100% |   9.0 MiB/s | 518.8 KiB |  00m00s
[31/94] boost-atomic-0:1.83.0-13.fc43.x 100% | 372.1 KiB/s |  17.9 KiB |  00m00s
[32/94] xerces-c-0:3.3.0-7.fc43.x86_64  100% |   7.5 MiB/s |   1.0 MiB |  00m00s
[33/94] boost-container-0:1.83.0-13.fc4 100% | 929.0 KiB/s |  38.1 KiB |  00m00s
[34/94] boost-chrono-0:1.83.0-13.fc43.x 100% | 183.9 KiB/s |  24.1 KiB |  00m00s
[35/94] boost-context-0:1.83.0-13.fc43. 100% | 109.1 KiB/s |  14.8 KiB |  00m00s
[36/94] python3-libs-0:3.14.0~rc1-1.fc4 100% |  29.1 MiB/s |   9.8 MiB |  00m00s
[37/94] boost-coroutine-0:1.83.0-13.fc4 100% | 378.1 KiB/s |  18.1 KiB |  00m00s
[38/94] boost-date-time-0:1.83.0-13.fc4 100% | 378.8 KiB/s |  13.6 KiB |  00m00s
[39/94] boost-fiber-0:1.83.0-13.fc43.x8 100% | 955.1 KiB/s |  41.1 KiB |  00m00s
[40/94] boost-filesystem-0:1.83.0-13.fc 100% |   1.8 MiB/s |  68.5 KiB |  00m00s
[41/94] boost-graph-0:1.83.0-13.fc43.x8 100% |   3.3 MiB/s | 156.7 KiB |  00m00s
[42/94] boost-iostreams-0:1.83.0-13.fc4 100% | 972.6 KiB/s |  39.9 KiB |  00m00s
[43/94] boost-json-0:1.83.0-13.fc43.x86 100% |   3.0 MiB/s | 145.1 KiB |  00m00s
[44/94] boost-locale-0:1.83.0-13.fc43.x 100% |   3.8 MiB/s | 215.4 KiB |  00m00s
[45/94] boost-contract-0:1.83.0-13.fc43 100% | 139.4 KiB/s |  44.6 KiB |  00m00s
[46/94] boost-log-0:1.83.0-13.fc43.x86_ 100% |   9.3 MiB/s | 504.9 KiB |  00m00s
[47/94] boost-math-0:1.83.0-13.fc43.x86 100% |   4.2 MiB/s | 213.9 KiB |  00m00s
[48/94] boost-program-options-0:1.83.0- 100% |   2.4 MiB/s | 110.9 KiB |  00m00s
[49/94] boost-python3-0:1.83.0-13.fc43. 100% |   2.6 MiB/s |  97.4 KiB |  00m00s
[50/94] boost-random-0:1.83.0-13.fc43.x 100% | 613.2 KiB/s |  22.1 KiB |  00m00s
[51/94] boost-nowide-0:1.83.0-13.fc43.x 100% | 184.4 KiB/s |  18.6 KiB |  00m00s
[52/94] boost-regex-0:1.83.0-13.fc43.x8 100% |   2.7 MiB/s | 114.7 KiB |  00m00s
[53/94] boost-serialization-0:1.83.0-13 100% |   3.5 MiB/s | 133.7 KiB |  00m00s
[54/94] boost-system-0:1.83.0-13.fc43.x 100% | 310.1 KiB/s |  13.6 KiB |  00m00s
[55/94] boost-test-0:1.83.0-13.fc43.x86 100% |   5.1 MiB/s | 241.7 KiB |  00m00s
[56/94] boost-thread-0:1.83.0-13.fc43.x 100% |   1.6 MiB/s |  59.6 KiB |  00m00s
[57/94] boost-timer-0:1.83.0-13.fc43.x8 100% | 426.8 KiB/s |  19.6 KiB |  00m00s
[58/94] boost-stacktrace-0:1.83.0-13.fc 100% | 228.0 KiB/s |  29.2 KiB |  00m00s
[59/94] boost-type_erasure-0:1.83.0-13. 100% | 737.5 KiB/s |  31.7 KiB |  00m00s
[60/94] boost-wave-0:1.83.0-13.fc43.x86 100% |   5.8 MiB/s | 250.4 KiB |  00m00s
[61/94] mpdecimal-0:4.0.1-1.fc43.x86_64 100% |   2.2 MiB/s |  97.1 KiB |  00m00s
[62/94] python-pip-wheel-0:25.1.1-13.fc 100% |  22.3 MiB/s |   1.2 MiB |  00m00s
[63/94] tzdata-0:2025b-1.fc43.noarch    100% |  15.2 MiB/s | 714.0 KiB |  00m00s
[64/94] python3-numpy-f2py-1:2.3.1-1.fc 100% |   9.1 MiB/s | 510.5 KiB |  00m00s
[65/94] python3-0:3.14.0~rc1-1.fc43.x86 100% | 756.3 KiB/s |  27.2 KiB |  00m00s
[66/94] libicu-0:76.1-4.fc42.x86_64     100% |  39.6 MiB/s |  10.7 MiB |  00m00s
[67/94] flexiblas-0:3.4.5-2.fc43.x86_64 100% | 500.7 KiB/s |  26.5 KiB |  00m00s
[68/94] flexiblas-openblas-openmp-0:3.4 100% | 548.5 KiB/s |  17.6 KiB |  00m00s
[69/94] libgfortran-0:15.1.1-2.fc43.x86 100% |  14.8 MiB/s | 957.2 KiB |  00m00s
[70/94] flexiblas-netlib-0:3.4.5-2.fc43 100% |  19.5 MiB/s |   3.4 MiB |  00m00s
[71/94] libquadmath-0:15.1.1-2.fc43.x86 100% |   3.9 MiB/s | 198.1 KiB |  00m00s
[72/94] openblas-0:0.3.29-1.fc42.x86_64 100% |   1.0 MiB/s |  42.3 KiB |  00m00s
[73/94] openblas-openmp-0:0.3.29-1.fc42 100% |  45.9 MiB/s |   5.4 MiB |  00m00s
[74/94] libstdc++-devel-0:15.1.1-2.fc43 100% |  32.9 MiB/s |   2.9 MiB |  00m00s
[75/94] glibc-devel-0:2.41.9000-23.fc43 100% |   9.8 MiB/s | 562.4 KiB |  00m00s
[76/94] cmake-filesystem-0:3.31.6-3.fc4 100% |   1.9 MiB/s |  17.8 KiB |  00m00s
[77/94] cmake-data-0:3.31.6-3.fc43.noar 100% |  51.1 MiB/s |   1.9 MiB |  00m00s
[78/94] libxcrypt-devel-0:4.4.38-7.fc43 100% | 481.5 KiB/s |  29.4 KiB |  00m00s
[79/94] emacs-filesystem-1:30.0-4.fc42. 100% | 156.5 KiB/s |   7.4 KiB |  00m00s
[80/94] vim-filesystem-2:9.1.1537-2.fc4 100% | 257.1 KiB/s |  15.2 KiB |  00m00s
[81/94] jsoncpp-0:1.9.6-1.fc43.x86_64   100% |   5.3 MiB/s | 103.5 KiB |  00m00s
[82/94] libuv-1:1.51.0-1.fc43.x86_64    100% |   4.8 MiB/s | 266.4 KiB |  00m00s
[83/94] kernel-headers-0:6.16.0-0.rc7.5 100% |  20.8 MiB/s |   1.7 MiB |  00m00s
[84/94] gcc-plugin-annobin-0:15.1.1-2.f 100% | 940.7 KiB/s |  51.7 KiB |  00m00s
[85/94] annobin-docs-0:12.98-1.fc43.noa 100% |   1.7 MiB/s |  90.2 KiB |  00m00s
[86/94] annobin-plugin-gcc-0:12.98-1.fc 100% |   6.8 MiB/s | 997.1 KiB |  00m00s
[87/94] pyproject-rpm-macros-0:1.18.3-1 100% |   1.2 MiB/s |  44.3 KiB |  00m00s
[88/94] python-rpm-macros-0:3.14-3.fc43 100% | 460.0 KiB/s |  17.0 KiB |  00m00s
[89/94] python3-rpm-generators-0:14-12. 100% | 810.6 KiB/s |  29.2 KiB |  00m00s
[90/94] python3-rpm-macros-0:3.14-3.fc4 100% | 321.8 KiB/s |  11.6 KiB |  00m00s
[91/94] cmake-rpm-macros-0:3.31.6-3.fc4 100% |   1.9 MiB/s |  17.2 KiB |  00m00s
[92/94] python3-packaging-0:25.0-3.fc43 100% |   4.3 MiB/s | 161.4 KiB |  00m00s
[93/94] ninja-build-0:1.13.1-1.fc43.x86 100% |   3.4 MiB/s | 197.7 KiB |  00m00s
[94/94] python3-numpy-1:2.3.1-1.fc43.x8 100% |   5.5 MiB/s |   8.2 MiB |  00m02s
--------------------------------------------------------------------------------
[94/94] Total                           100% |  39.8 MiB/s | 158.8 MiB |  00m04s
Running transaction
[ 1/96] Verify package files            100% | 156.0   B/s |  94.0   B |  00m01s
[ 2/96] Prepare transaction             100% | 357.0   B/s |  94.0   B |  00m00s
[ 3/96] Installing boost-system-0:1.83. 100% |  12.9 MiB/s |  13.2 KiB |  00m00s
[ 4/96] Installing boost-chrono-0:1.83. 100% |  37.6 MiB/s |  38.5 KiB |  00m00s
[ 5/96] Installing cmake-filesystem-0:3 100% |   2.5 MiB/s |   7.6 KiB |  00m00s
[ 6/96] Installing boost-thread-0:1.83. 100% | 130.4 MiB/s | 133.5 KiB |  00m00s
[ 7/96] Installing libicu-0:76.1-4.fc42 100% | 313.2 MiB/s |  36.3 MiB |  00m00s
[ 8/96] Installing boost-regex-0:1.83.0 100% | 142.6 MiB/s | 292.1 KiB |  00m00s
[ 9/96] Installing python-rpm-macros-0: 100% |  23.0 MiB/s |  23.5 KiB |  00m00s
[10/96] Installing boost-context-0:1.83 100% |  13.1 MiB/s |  13.4 KiB |  00m00s
[11/96] Installing boost-atomic-0:1.83. 100% |  21.4 MiB/s |  21.9 KiB |  00m00s
[12/96] Installing boost-filesystem-0:1 100% | 141.3 MiB/s | 144.6 KiB |  00m00s
[13/96] Installing expat-0:2.7.1-1.fc43 100% |  18.1 MiB/s | 296.3 KiB |  00m00s
[14/96] Installing libmpc-0:1.3.1-7.fc4 100% | 162.2 MiB/s | 166.1 KiB |  00m00s
[15/96] Installing python3-rpm-macros-0 100% |   6.6 MiB/s |   6.8 KiB |  00m00s
[16/96] Installing vim-filesystem-2:9.1 100% |   2.3 MiB/s |   4.7 KiB |  00m00s
[17/96] Installing libquadmath-0:15.1.1 100% | 155.8 MiB/s | 319.2 KiB |  00m00s
[18/96] Installing libgfortran-0:15.1.1 100% | 334.3 MiB/s |   3.3 MiB |  00m00s
[19/96] Installing boost-date-time-0:1. 100% |  12.9 MiB/s |  13.2 KiB |  00m00s
[20/96] Installing boost-container-0:1. 100% |  64.9 MiB/s |  66.4 KiB |  00m00s
[21/96] Installing xerces-c-0:3.3.0-7.f 100% | 313.8 MiB/s |   3.8 MiB |  00m00s
[22/96] Installing gtest-0:1.15.2-3.fc4 100% | 163.8 MiB/s | 503.2 KiB |  00m00s
[23/96] Installing make-1:4.4.1-10.fc42 100% |  81.8 MiB/s |   1.8 MiB |  00m00s
[24/96] Installing gmock-0:1.15.2-3.fc4 100% |  64.7 MiB/s | 132.4 KiB |  00m00s
[25/96] Installing boost-json-0:1.83.0- 100% | 165.1 MiB/s | 338.1 KiB |  00m00s
[26/96] Installing boost-wave-0:1.83.0- 100% | 280.4 MiB/s | 861.3 KiB |  00m00s
[27/96] Installing pyproject-rpm-macros 100% |  56.9 MiB/s | 116.5 KiB |  00m00s
[28/96] Installing cpp-0:15.1.1-2.fc43. 100% | 280.4 MiB/s |  37.9 MiB |  00m00s
[29/96] Installing libcutl-0:1.10.0-32. 100% | 213.9 MiB/s |   1.1 MiB |  00m00s
[30/96] Installing boost-fiber-0:1.83.0 100% |  77.8 MiB/s |  79.7 KiB |  00m00s
[31/96] Installing boost-log-0:1.83.0-1 100% | 253.7 MiB/s |   1.5 MiB |  00m00s
[32/96] Installing boost-coroutine-0:1. 100% |  21.5 MiB/s |  22.1 KiB |  00m00s
[33/96] Installing boost-graph-0:1.83.0 100% | 118.5 MiB/s | 364.1 KiB |  00m00s
[34/96] Installing libicu-devel-0:76.1- 100% | 137.1 MiB/s |   5.1 MiB |  00m00s
[35/96] Installing boost-locale-0:1.83. 100% | 201.4 MiB/s | 618.7 KiB |  00m00s
[36/96] Installing boost-type_erasure-0 100% |  53.9 MiB/s |  55.2 KiB |  00m00s
[37/96] Installing boost-timer-0:1.83.0 100% |  21.5 MiB/s |  22.0 KiB |  00m00s
[38/96] Installing annobin-docs-0:12.98 100% |  32.6 MiB/s | 100.1 KiB |  00m00s
[39/96] Installing kernel-headers-0:6.1 100% | 108.4 MiB/s |   6.8 MiB |  00m00s
[40/96] Installing glibc-devel-0:2.41.9 100% |  86.7 MiB/s |   2.3 MiB |  00m00s
[41/96] Installing libxcrypt-devel-0:4. 100% |  16.2 MiB/s |  33.1 KiB |  00m00s
[42/96] Installing gcc-0:15.1.1-2.fc43. 100% | 302.9 MiB/s | 111.2 MiB |  00m00s
[43/96] Installing libquadmath-devel-0: 100% |  23.1 MiB/s |  23.6 KiB |  00m00s
[44/96] Installing libuv-1:1.51.0-1.fc4 100% | 186.5 MiB/s | 573.0 KiB |  00m00s
[45/96] Installing jsoncpp-0:1.9.6-1.fc 100% | 128.5 MiB/s | 263.1 KiB |  00m00s
[46/96] Installing emacs-filesystem-1:3 100% | 177.1 KiB/s | 544.0   B |  00m00s
[47/96] Installing libstdc++-devel-0:15 100% | 210.6 MiB/s |  16.2 MiB |  00m00s
[48/96] Installing openblas-0:0.3.29-1. 100% | 110.8 MiB/s | 113.5 KiB |  00m00s
[49/96] Installing openblas-openmp-0:0. 100% | 470.1 MiB/s |  43.7 MiB |  00m00s
[50/96] Installing flexiblas-netlib-0:3 100% | 227.4 MiB/s |  10.9 MiB |  00m00s
[51/96] Installing flexiblas-0:3.4.5-2. 100% |  50.4 MiB/s |  51.6 KiB |  00m00s
[52/96] Installing flexiblas-openblas-o 100% |   7.8 MiB/s |  40.1 KiB |  00m00s
[53/96] Installing tzdata-0:2025b-1.fc4 100% |  25.6 MiB/s |   1.9 MiB |  00m00s
[54/96] Installing python-pip-wheel-0:2 100% | 415.0 MiB/s |   1.2 MiB |  00m00s
[55/96] Installing mpdecimal-0:4.0.1-1. 100% |  30.5 MiB/s | 218.8 KiB |  00m00s
[56/96] Installing python3-libs-0:3.14. 100% | 207.1 MiB/s |  43.3 MiB |  00m00s
[57/96] Installing python3-0:3.14.0~rc1 100% |   1.9 MiB/s |  30.7 KiB |  00m00s
[58/96] Installing boost-python3-0:1.83 100% |  84.4 MiB/s | 259.2 KiB |  00m00s
[59/96] Installing python3-numpy-f2py-1 100% |  53.0 MiB/s |   2.2 MiB |  00m00s
[60/96] Installing python3-numpy-1:2.3. 100% | 222.6 MiB/s |  41.4 MiB |  00m00s
[61/96] Installing boost-numpy3-0:1.83. 100% |  57.1 MiB/s |  58.5 KiB |  00m00s
[62/96] Installing python3-packaging-0: 100% | 121.1 MiB/s | 620.0 KiB |  00m00s
[63/96] Installing python3-rpm-generato 100% |  81.0 MiB/s |  82.9 KiB |  00m00s
[64/96] Installing ninja-build-0:1.13.1 100% |  27.8 MiB/s | 483.8 KiB |  00m00s
[65/96] Installing cmake-rpm-macros-0:3 100% |   8.2 MiB/s |   8.4 KiB |  00m00s
[66/96] Installing boost-test-0:1.83.0- 100% | 211.1 MiB/s | 648.5 KiB |  00m00s
[67/96] Installing boost-stacktrace-0:1 100% |  30.1 MiB/s |  61.6 KiB |  00m00s
[68/96] Installing boost-serialization- 100% | 216.3 MiB/s | 443.1 KiB |  00m00s
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[70/96] Installing boost-program-option 100% | 137.6 MiB/s | 281.8 KiB |  00m00s
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[77/96] Installing tokyocabinet-0:1.4.4 100% |  64.8 MiB/s |   1.5 MiB |  00m00s
[78/96] Installing sqlite-0:3.50.2-1.fc 100% |  92.1 MiB/s |   1.8 MiB |  00m00s
[79/96] Installing libtirpc-0:1.3.6-1.r 100% |  98.0 MiB/s | 200.7 KiB |  00m00s
[80/96] Installing rhash-0:1.4.5-2.fc42 100% |  21.8 MiB/s | 356.4 KiB |  00m00s
[81/96] Installing cmake-0:3.31.6-3.fc4 100% | 257.5 MiB/s |  34.5 MiB |  00m00s
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Warning: skipped OpenPGP checks for 15 packages from repository: copr_base
Complete!
Finish: build setup for percolator-3.08-1.fc43.src.rpm
Start: rpmbuild percolator-3.08-1.fc43.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.MVSvyV
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.iiQVcM
+ 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 .
+ echo 'Patch #0 (percolator-unbundle_eigen_gtest.patch):'
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.ScIIF0
+ 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 -G Ninja -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 15.1.1
-- The CXX compiler identification is GNU 15.1.1
-- 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 "1.15.2")
-- 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 (1.3s)
-- Generating done (0.0s)
-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_COLOR_MAKEFILE
    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


+ 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 -j2 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'

Run Build Command(s): /usr/bin/ninja-build -v -j 2
[1/82] 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
[2/82] 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
[3/82] /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 src/dblas/CMakeFiles/dblas.dir/daxpy.c.o.d -o src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[4/82] /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/percolator_in.cxx.o -MF src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/percolator_in.cxx
[5/82] /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 src/CMakeFiles/perclibrary.dir/parser.cxx.o.d -o src/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);
      |         ^
[6/82] /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 src/CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o src/CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/serializer.cxx
[7/82] /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 src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o src/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);
      |        ^~~
[8/82] /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 src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
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[10/82] /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 src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[11/82] /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 src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[12/82] /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 src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.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/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();
      |                                ^~~~~~~~~~~
[13/82] /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 src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[14/82] /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 src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[15/82] /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 src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o src/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/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;
      |                                          ^~~~~
[16/82] /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 src/CMakeFiles/perclibrary.dir/svm.cpp.o.d -o src/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;
      |                        ^~
[17/82] /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 src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.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)
      |   ^~~~~~~~~~~
/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;
      |           ^~~~~~~~~~~
[18/82] /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 src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o src/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/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++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[19/82] /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 src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
[20/82] /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 src/CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.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/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/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()
      | ^~~~~~
[21/82] /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 src/CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[22/82] /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 src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[23/82] /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 src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[24/82] /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 src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
[25/82] /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 src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.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() :
      | ^~~~~~~~~~~
[26/82] /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 src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
/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) {
      |                     ~~^~~~~~~~~~~~
[27/82] /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 src/CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[28/82] /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 src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[29/82] /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 src/CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[30/82] /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 src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.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);
      |        ^~~
[31/82] /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 src/CMakeFiles/perclibrary.dir/Option.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[32/82] /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 src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~~~
[33/82] /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 src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o src/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);
      |        ^~~
[34/82] /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 src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[35/82] /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 src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o src/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();
      |          ^~
[36/82] /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 src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[37/82] /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 src/CMakeFiles/perclibrary.dir/Set.cpp.o.d -o src/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++) {
      |                 ~^~~~~~~~~
[38/82] /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 src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o src/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);
      |        ^~~
[39/82] /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 src/CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[40/82] /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 src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o src/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);
      |        ^~~
[41/82] /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 src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.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);
      |        ^~~
[42/82] /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 src/CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[43/82] /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 src/CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[44/82] /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 src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~
[45/82] /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 src/CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[46/82] /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 src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
[47/82] /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 src/CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
[48/82] /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 src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[49/82] /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 src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o src/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);
      |        ^~~
[50/82] /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 src/CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o src/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++)
      |                 ~^~~~~~~~~
[51/82] /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/ddot.c.o -MF src/dblas/CMakeFiles/dblas.dir/ddot.c.o.d -o src/dblas/CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[52/82] /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/dgemv.c.o -MF src/dblas/CMakeFiles/dblas.dir/dgemv.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[53/82] /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/dnrm2.c.o -MF src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[54/82] /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/dscal.c.o -MF src/dblas/CMakeFiles/dblas.dir/dscal.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[55/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[56/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[57/82] /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/__/MyException.cpp.o -MF src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[58/82] /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 src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[59/82] /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/Database.cpp.o -MF src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
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[61/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o src/picked_protein/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);
      |                             ~~~~~~^~~~~~~~~~~~
[62/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[63/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[64/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[65/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[66/82] : && /usr/bin/cmake -E rm -f src/libperclibrary.a && /usr/bin/ar qc src/libperclibrary.a  src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o src/CMakeFiles/perclibrary.dir/parser.cxx.o src/CMakeFiles/perclibrary.dir/serializer.cxx.o src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/svm.cpp.o src/CMakeFiles/perclibrary.dir/Caller.cpp.o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o src/CMakeFiles/perclibrary.dir/Globals.cpp.o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o src/CMakeFiles/perclibrary.dir/Option.cpp.o src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/Scores.cpp.o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o src/CMakeFiles/perclibrary.dir/Set.cpp.o src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/ssl.cpp.o src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o src/CMakeFiles/perclibrary.dir/Logger.cpp.o src/CMakeFiles/perclibrary.dir/MyException.cpp.o src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o src/CMakeFiles/perclibrary.dir/Timer.cpp.o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o src/CMakeFiles/perclibrary.dir/Vector.cpp.o && /usr/bin/ranlib src/libperclibrary.a && :
[67/82] /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 src/CMakeFiles/percolator.dir/main.cpp.o.d -o src/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/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)
      |   ^~~~~~~~~~~
[68/82] : && /usr/bin/cmake -E rm -f src/dblas/libdblas.a && /usr/bin/ar rcv src/dblas/libdblas.a  src/dblas/CMakeFiles/dblas.dir/daxpy.c.o src/dblas/CMakeFiles/dblas.dir/ddot.c.o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o src/dblas/CMakeFiles/dblas.dir/dscal.c.o && /usr/bin/ranlib src/dblas/libdblas.a && :
a - src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
a - src/dblas/CMakeFiles/dblas.dir/ddot.c.o
a - src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
a - src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
a - src/dblas/CMakeFiles/dblas.dir/dscal.c.o
[69/82] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
[70/82] : && /usr/bin/cmake -E rm -f src/picked_protein/libpicked_protein.a && /usr/bin/ar qc src/picked_protein/libpicked_protein.a  src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o && /usr/bin/ranlib src/picked_protein/libpicked_protein.a && :
[71/82] /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 src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o src/qvality/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);
      |        ^~~
[72/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o tests/unit_tests/percolator/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
[73/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o tests/unit_tests/percolator/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
[74/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o tests/unit_tests/percolator/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
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);
      |        ^~~
[75/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o tests/unit_tests/percolator/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/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)
      |        ^
[76/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o tests/unit_tests/percolator/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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[77/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o tests/unit_tests/percolator/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
[78/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o tests/unit_tests/percolator/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,
      |         ^~~~~~~
[79/82] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o tests/unit_tests/percolator/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);
      |        ^~~
[80/82] : && /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=src/qvality/CMakeFiles/qvality.dir/link.d src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -o src/qvality/qvality -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src src/libperclibrary.a && :
[81/82] : && /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=tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/link.d tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o tests/unit_tests/percolator/gtest_unit  /usr/lib64/libgtest_main.so.1.15.2  src/libperclibrary.a  src/dblas/libdblas.a  -lpthread  /usr/lib64/libgtest.so.1.15.2 && :
[82/82] : && /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=src/CMakeFiles/percolator.dir/link.d src/CMakeFiles/percolator.dir/main.cpp.o -o src/percolator  src/libperclibrary.a  src/dblas/libdblas.a  src/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 && :

+ 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 -G Ninja -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 15.1.1
-- The CXX compiler identification is GNU 15.1.1
-- 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 "1.15.2")
-- 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 (1.3s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_COLOR_MAKEFILE
    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


-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido
+ /usr/bin/cmake --build src/fido -j2 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'

Run Build Command(s): /usr/bin/ninja-build -v -j 2
[1/76] /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 src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[2/76] /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 src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[3/76] /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 src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[4/76] /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 src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o src/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);
      |        ^~~
[5/76] /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 src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.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/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,
      | ^~~~~~~~~~~~
[6/76] /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 src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[7/76] /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 src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[8/76] /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 src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o src/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/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;
      |                                          ^~~~~
[9/76] /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 src/CMakeFiles/perclibrary.dir/svm.cpp.o.d -o src/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;
      |                        ^~
[10/76] /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 src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.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)
      |   ^~~~~~~~~~~
/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;
      |           ^~~~~~~~~~~
[11/76] /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 src/CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.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/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/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()
      | ^~~~~~
[12/76] /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 src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o src/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/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++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[13/76] /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 src/CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[14/76] /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 src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
[15/76] /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 src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[16/76] /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 src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[17/76] /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 src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
[18/76] /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 src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.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() :
      | ^~~~~~~~~~~
[19/76] /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 src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
/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) {
      |                     ~~^~~~~~~~~~~~
[20/76] /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 src/CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[21/76] /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 src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[22/76] /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 src/CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[23/76] /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 src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.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);
      |        ^~~
[24/76] /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 src/CMakeFiles/perclibrary.dir/Option.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[25/76] /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 src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~~~
[26/76] /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 src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o src/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);
      |        ^~~
[27/76] /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 src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[28/76] /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 src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o src/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();
      |          ^~
[29/76] /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 src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[30/76] /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 src/CMakeFiles/perclibrary.dir/Set.cpp.o.d -o src/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++) {
      |                 ~^~~~~~~~~
[31/76] /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 src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o src/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);
      |        ^~~
[32/76] /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 src/CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[33/76] /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 src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o src/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);
      |        ^~~
[34/76] /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 src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.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);
      |        ^~~
[35/76] /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 src/CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[36/76] /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 src/CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[37/76] /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 src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~
[38/76] /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 src/CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[39/76] /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 src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
[40/76] /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 src/CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
[41/76] /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 src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[42/76] /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 src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o src/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);
      |        ^~~
[43/76] /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 src/CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o src/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++)
      |                 ~^~~~~~~~~
[44/76] /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 src/dblas/CMakeFiles/dblas.dir/daxpy.c.o.d -o src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[45/76] /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 src/dblas/CMakeFiles/dblas.dir/ddot.c.o.d -o src/dblas/CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[46/76] /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 src/dblas/CMakeFiles/dblas.dir/dgemv.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[47/76] /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 src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[48/76] /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 src/dblas/CMakeFiles/dblas.dir/dscal.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[49/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[50/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[51/76] /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 src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[52/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
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[54/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o src/picked_protein/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);
      |                             ~~~~~~^~~~~~~~~~~~
[55/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[56/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[57/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[58/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[59/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[60/76] : && /usr/bin/cmake -E rm -f src/libperclibrary.a && /usr/bin/ar qc src/libperclibrary.a  src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/svm.cpp.o src/CMakeFiles/perclibrary.dir/Caller.cpp.o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o src/CMakeFiles/perclibrary.dir/Globals.cpp.o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o src/CMakeFiles/perclibrary.dir/Option.cpp.o src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/Scores.cpp.o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o src/CMakeFiles/perclibrary.dir/Set.cpp.o src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/ssl.cpp.o src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o src/CMakeFiles/perclibrary.dir/Logger.cpp.o src/CMakeFiles/perclibrary.dir/MyException.cpp.o src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o src/CMakeFiles/perclibrary.dir/Timer.cpp.o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o src/CMakeFiles/perclibrary.dir/Vector.cpp.o && /usr/bin/ranlib src/libperclibrary.a && :
[61/76] /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 src/CMakeFiles/percolator.dir/main.cpp.o.d -o src/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/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)
      |   ^~~~~~~~~~~
[62/76] : && /usr/bin/cmake -E rm -f src/dblas/libdblas.a && /usr/bin/ar rcv src/dblas/libdblas.a  src/dblas/CMakeFiles/dblas.dir/daxpy.c.o src/dblas/CMakeFiles/dblas.dir/ddot.c.o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o src/dblas/CMakeFiles/dblas.dir/dscal.c.o && /usr/bin/ranlib src/dblas/libdblas.a && :
a - src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
a - src/dblas/CMakeFiles/dblas.dir/ddot.c.o
a - src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
a - src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
a - src/dblas/CMakeFiles/dblas.dir/dscal.c.o
[63/76] /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 src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o src/qvality/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);
      |        ^~~
[64/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
[65/76] : && /usr/bin/cmake -E rm -f src/picked_protein/libpicked_protein.a && /usr/bin/ar qc src/picked_protein/libpicked_protein.a  src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o && /usr/bin/ranlib src/picked_protein/libpicked_protein.a && :
[66/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o tests/unit_tests/percolator/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
[67/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o tests/unit_tests/percolator/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
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);
      |        ^~~
[68/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o tests/unit_tests/percolator/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
[69/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o tests/unit_tests/percolator/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/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)
      |        ^
[70/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o tests/unit_tests/percolator/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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[71/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o tests/unit_tests/percolator/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
[72/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o tests/unit_tests/percolator/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,
      |         ^~~~~~~
[73/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o tests/unit_tests/percolator/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);
      |        ^~~
[74/76] : && /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=src/qvality/CMakeFiles/qvality.dir/link.d src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -o src/qvality/qvality -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src src/libperclibrary.a && :
[75/76] : && /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=tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/link.d tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o tests/unit_tests/percolator/gtest_unit  /usr/lib64/libgtest_main.so.1.15.2  src/libperclibrary.a  src/dblas/libdblas.a  -lpthread  /usr/lib64/libgtest.so.1.15.2 && :
[76/76] : && /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=src/CMakeFiles/percolator.dir/link.d src/CMakeFiles/percolator.dir/main.cpp.o -o src/percolator  src/libperclibrary.a  src/dblas/libdblas.a  src/picked_protein/libpicked_protein.a  -lstdc++  /usr/lib64/libboost_filesystem.a  /usr/lib64/libboost_system.a  /usr/lib64/libboost_atomic.a && :

+ 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 -G Ninja -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 15.1.1
-- The CXX compiler identification is GNU 15.1.1
-- 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 "1.15.2")
-- 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 (1.3s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_COLOR_MAKEFILE
    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 -j2 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'

Run Build Command(s): /usr/bin/ninja-build -v -j 2
[1/76] /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 src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[2/76] /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 src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[3/76] /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 src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[4/76] /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 src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o src/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);
      |        ^~~
[5/76] /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 src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.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/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,
      | ^~~~~~~~~~~~
[6/76] /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 src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[7/76] /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 src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[8/76] /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 src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o src/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/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;
      |                                          ^~~~~
[9/76] /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 src/CMakeFiles/perclibrary.dir/svm.cpp.o.d -o src/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;
      |                        ^~
[10/76] /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 src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.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)
      |   ^~~~~~~~~~~
/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;
      |           ^~~~~~~~~~~
[11/76] /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 src/CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.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/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/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()
      | ^~~~~~
[12/76] /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 src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o src/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/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++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[13/76] /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 src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
[14/76] /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 src/CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[15/76] /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 src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[16/76] /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 src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[17/76] /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 src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
[18/76] /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 src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.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() :
      | ^~~~~~~~~~~
[19/76] /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 src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
/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) {
      |                     ~~^~~~~~~~~~~~
[20/76] /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 src/CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[21/76] /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 src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[22/76] /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 src/CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[23/76] /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 src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.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);
      |        ^~~
[24/76] /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 src/CMakeFiles/perclibrary.dir/Option.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[25/76] /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 src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~~~
[26/76] /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 src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o src/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);
      |        ^~~
[27/76] /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 src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[28/76] /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 src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o src/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();
      |          ^~
[29/76] /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 src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[30/76] /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 src/CMakeFiles/perclibrary.dir/Set.cpp.o.d -o src/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++) {
      |                 ~^~~~~~~~~
[31/76] /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 src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o src/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);
      |        ^~~
[32/76] /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 src/CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o src/CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[33/76] /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 src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o src/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);
      |        ^~~
[34/76] /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 src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.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);
      |        ^~~
[35/76] /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 src/CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[36/76] /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 src/CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o src/CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[37/76] /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 src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o src/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,
      | ^~~~~~~~~~~~~~~~~~
[38/76] /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 src/CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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/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);
      |        ^~~
[39/76] /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 src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
[40/76] /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 src/CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o src/CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
[41/76] /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 src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[42/76] /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 src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o src/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);
      |        ^~~
[43/76] /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 src/CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o src/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++)
      |                 ~^~~~~~~~~
[44/76] /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 src/dblas/CMakeFiles/dblas.dir/daxpy.c.o.d -o src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
[45/76] /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 src/dblas/CMakeFiles/dblas.dir/ddot.c.o.d -o src/dblas/CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[46/76] /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 src/dblas/CMakeFiles/dblas.dir/dgemv.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[47/76] /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 src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[48/76] /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 src/dblas/CMakeFiles/dblas.dir/dscal.c.o.d -o src/dblas/CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[49/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[50/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[51/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[52/76] /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 src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[53/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[54/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o src/picked_protein/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);
      |                             ~~~~~~^~~~~~~~~~~~
[55/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[56/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[57/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[58/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[59/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[60/76] : && /usr/bin/cmake -E rm -f src/libperclibrary.a && /usr/bin/ar qc src/libperclibrary.a  src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/svm.cpp.o src/CMakeFiles/perclibrary.dir/Caller.cpp.o src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o src/CMakeFiles/perclibrary.dir/Globals.cpp.o src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o src/CMakeFiles/perclibrary.dir/DataSet.cpp.o src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o src/CMakeFiles/perclibrary.dir/Numerical.cpp.o src/CMakeFiles/perclibrary.dir/Option.cpp.o src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/Scores.cpp.o src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o src/CMakeFiles/perclibrary.dir/Set.cpp.o src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o src/CMakeFiles/perclibrary.dir/ssl.cpp.o src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o src/CMakeFiles/perclibrary.dir/Logger.cpp.o src/CMakeFiles/perclibrary.dir/MyException.cpp.o src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o src/CMakeFiles/perclibrary.dir/Timer.cpp.o src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o src/CMakeFiles/perclibrary.dir/Vector.cpp.o && /usr/bin/ranlib src/libperclibrary.a && :
[61/76] /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 src/CMakeFiles/percolator.dir/main.cpp.o.d -o src/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/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)
      |   ^~~~~~~~~~~
[62/76] : && /usr/bin/cmake -E rm -f src/dblas/libdblas.a && /usr/bin/ar rcv src/dblas/libdblas.a  src/dblas/CMakeFiles/dblas.dir/daxpy.c.o src/dblas/CMakeFiles/dblas.dir/ddot.c.o src/dblas/CMakeFiles/dblas.dir/dgemv.c.o src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o src/dblas/CMakeFiles/dblas.dir/dscal.c.o && /usr/bin/ranlib src/dblas/libdblas.a && :
a - src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
a - src/dblas/CMakeFiles/dblas.dir/ddot.c.o
a - src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
a - src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
a - src/dblas/CMakeFiles/dblas.dir/dscal.c.o
[63/76] /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 src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o src/qvality/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);
      |        ^~~
[64/76] /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 src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
[65/76] : && /usr/bin/cmake -E rm -f src/picked_protein/libpicked_protein.a && /usr/bin/ar qc src/picked_protein/libpicked_protein.a  src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o && /usr/bin/ranlib src/picked_protein/libpicked_protein.a && :
[66/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o tests/unit_tests/percolator/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
[67/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o tests/unit_tests/percolator/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
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);
      |        ^~~
[68/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o tests/unit_tests/percolator/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
[69/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o tests/unit_tests/percolator/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/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)
      |        ^
[70/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o tests/unit_tests/percolator/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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[71/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o tests/unit_tests/percolator/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
[72/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o tests/unit_tests/percolator/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,
      |         ^~~~~~~
[73/76] /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++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o tests/unit_tests/percolator/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);
      |        ^~~
[74/76] : && /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=src/qvality/CMakeFiles/qvality.dir/link.d src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -o src/qvality/qvality -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src src/libperclibrary.a && :
[75/76] : && /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=tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/link.d tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o tests/unit_tests/percolator/gtest_unit  /usr/lib64/libgtest_main.so.1.15.2  src/libperclibrary.a  src/dblas/libdblas.a  -lpthread  /usr/lib64/libgtest.so.1.15.2 && :
[76/76] : && /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=src/CMakeFiles/percolator.dir/link.d src/CMakeFiles/percolator.dir/main.cpp.o -o src/percolator  src/libperclibrary.a  src/dblas/libdblas.a  src/picked_protein/libpicked_protein.a  -lstdc++  /usr/lib64/libboost_filesystem.a  /usr/lib64/libboost_system.a  /usr/lib64/libboost_atomic.a && :

+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.09NUNM
+ 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 -j2 --strict-build-id -m -i --build-id-seed 3.08-1.fc43 --unique-debug-suffix -3.08-1.fc43.x86_64 --unique-debug-src-base percolator-3.08-1.fc43.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.fc43.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/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 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
/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/libdblas.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libperclibrary.a: replacing with normalized version
Scanned 24 directories and 125 files,
               processed 3 inodes,
               3 modified (3 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/percolator-3.08-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ikOcHq
+ 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 -j2 -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 (18 ms)
1: [----------] 1 test from CrossValidationTest (18 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 (1 ms)
1: [----------] 7 tests from IsplineRegressionTest (4 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. (24 ms total)
1: [  PASSED  ] 29 tests.
1/1 Test #1: UnitTest_Percolator_RunAllTests ...   Passed    0.03 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.03 sec
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.08-1.fc43.x86_64
Provides: percolator = 3.08-1.fc43 percolator(x86-64) = 3.08-1.fc43
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.fc43.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.kPxJci
+ 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.KvA5Xd
+ 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.fc43
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.fc43.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.IYRhb1
+ 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.upYJDi
+ 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.fc43 percolator-static(x86-64) = 3.08-1.fc43
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.fc43.x86_64
Provides: percolator-debugsource = 3.08-1.fc43 percolator-debugsource(x86-64) = 3.08-1.fc43
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.fc43.x86_64
Provides: debuginfo(build-id) = 304f2863ae93f136bb808536408ae347d4955b61 debuginfo(build-id) = 41eb9bddf997e5728ae132d40012ba1a01f01208 percolator-debuginfo = 3.08-1.fc43 percolator-debuginfo(x86-64) = 3.08-1.fc43
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.fc43
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.08-1.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-3.08-1.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.08-1.fc43.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.08-1.fc43.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.08-1.fc43.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Ec3e06
+ 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.fc43.src.rpm
Finish: build phase for percolator-3.08-1.fc43.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1753433315.726432/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.fc43.src.rpm) Config(child) 12 minutes 14 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "x86_64"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "src"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "x86_64"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "noarch"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "x86_64"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc43",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished