Warning: Permanently added '54.159.249.64' (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/9644300-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64


Version: 1.6
PID: 35765
Logging PID: 35767
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 9644300,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '769d163186014b551be024ee0483d5c2ce0f218e',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/terjeros/gtest-1.17.0/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.08-1',
 'project_dirname': 'gtest-1.17.0',
 'project_name': 'gtest-1.17.0',
 'project_owner': 'terjeros',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/terjeros/gtest-1.17.0/fedora-rawhide-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'terjeros/gtest-1.17.0--terjeros',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'terjeros',
 'tags': [],
 'task_id': '9644300-fedora-rawhide-aarch64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/terjeros/gtest-1.17.0/percolator /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/terjeros/gtest-1.17.0/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator'...

Running: git checkout 769d163186014b551be024ee0483d5c2ce0f218e --

cmd: ['git', 'checkout', '769d163186014b551be024ee0483d5c2ce0f218e', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator
rc: 0
stdout: 
stderr: Note: switching to '769d163186014b551be024ee0483d5c2ce0f218e'.

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 769d163 automatic import of percolator

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading percolator-rel-3-08.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o percolator-rel-3-08.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/terjeros/gtest-1.17.0/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  36.7M      0 --:--:-- --:--:-- --:--:-- 36.8M
INFO: Reading stdout from command: md5sum percolator-rel-3-08.tar.gz

tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759572895.816751 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.3 starting (python version = 3.13.7, NVR = mock-6.3-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-sjl24137/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759572895.816751 -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-sjl24137/percolator/percolator.spec)  Config(fedora-rawhide-aarch64)
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-aarch64-bootstrap-1759572895.816751/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-bc30457e-5ca8-455a-945d-79103db3b95f
INFO: Checking that f19ac277ab86030eb74fc27c891801db7c16d216d06a363f19130e3962ae8eaf image matches host's architecture
INFO: Copy content of container f19ac277ab86030eb74fc27c891801db7c16d216d06a363f19130e3962ae8eaf to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1759572895.816751/root
INFO: mounting f19ac277ab86030eb74fc27c891801db7c16d216d06a363f19130e3962ae8eaf with podman image mount
INFO: image f19ac277ab86030eb74fc27c891801db7c16d216d06a363f19130e3962ae8eaf as /var/lib/containers/storage/overlay/7e6f693150e281c7568b6722f6b201623d84085f2c8f18246202ff4f2912ecf1/merged
INFO: umounting image f19ac277ab86030eb74fc27c891801db7c16d216d06a363f19130e3962ae8eaf (/var/lib/containers/storage/overlay/7e6f693150e281c7568b6722f6b201623d84085f2c8f18246202ff4f2912ecf1/merged) with podman image umount
INFO: Removing image mock-bootstrap-bc30457e-5ca8-455a-945d-79103db3b95f
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1759572895.816751/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-6.0.0-1.fc44.aarch64
  rpm-sequoia-1.9.0-2.fc43.aarch64
  dnf5-5.2.17.0-2.fc44.aarch64
  dnf5-plugins-5.2.17.0-2.fc44.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Copr repository                        100% |  84.7 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 184.1 KiB/s |  14.9 KiB |  00m00s
Repositories loaded.
Package                            Arch    Version                    Repository      Size
Installing group/module packages:
 bash                              aarch64 5.3.0-2.fc43               fedora       8.4 MiB
 bzip2                             aarch64 1.0.8-21.fc43              fedora     171.3 KiB
 coreutils                         aarch64 9.8-3.fc44                 fedora       8.2 MiB
 cpio                              aarch64 2.15-6.fc43                fedora       1.1 MiB
 diffutils                         aarch64 3.12-3.fc43                fedora       1.6 MiB
 fedora-release-common             noarch  44-0.3                     fedora      20.6 KiB
 findutils                         aarch64 1:4.10.0-6.fc43            fedora       1.9 MiB
 gawk                              aarch64 5.3.2-2.fc43               fedora       2.6 MiB
 glibc-minimal-langpack            aarch64 2.42.9000-5.fc44           fedora       0.0   B
 grep                              aarch64 3.12-2.fc43                fedora       1.0 MiB
 gzip                              aarch64 1.14-1.fc44                fedora     437.6 KiB
 info                              aarch64 7.2-6.fc43                 fedora     421.6 KiB
 patch                             aarch64 2.8-2.fc43                 fedora     262.5 KiB
 redhat-rpm-config                 noarch  343-14.fc44                fedora     183.3 KiB
 rpm-build                         aarch64 6.0.0-1.fc44               fedora     598.9 KiB
 sed                               aarch64 4.9-5.fc43                 fedora     873.2 KiB
 shadow-utils                      aarch64 2:4.18.0-3.fc43            fedora       4.4 MiB
 tar                               aarch64 2:1.35-6.fc43              fedora       3.0 MiB
 unzip                             aarch64 6.0-68.fc44                fedora     470.2 KiB
 util-linux                        aarch64 2.41.1-17.fc44             fedora       6.8 MiB
 which                             aarch64 2.23-3.fc43                fedora     123.4 KiB
 xz                                aarch64 1:5.8.1-2.fc43             fedora       1.4 MiB
Installing dependencies:
 add-determinism                   aarch64 0.7.2-2.fc44               fedora       2.0 MiB
 alternatives                      aarch64 1.33-2.fc43                fedora      90.2 KiB
 ansible-srpm-macros               noarch  1-18.1.fc43                fedora      35.7 KiB
 audit-libs                        aarch64 4.1.2-2.fc44               fedora     486.9 KiB
 binutils                          aarch64 2.45.50-4.fc44             fedora      30.9 MiB
 build-reproducibility-srpm-macros noarch  0.7.2-2.fc44               fedora       1.2 KiB
 bzip2-libs                        aarch64 1.0.8-21.fc43              fedora      72.6 KiB
 ca-certificates                   noarch  2025.2.80_v9.0.304-2.fc44  fedora       2.7 MiB
 coreutils-common                  aarch64 9.8-3.fc44                 fedora      11.1 MiB
 crypto-policies                   noarch  20250714-5.gitcd6043a.fc44 fedora     146.9 KiB
 curl                              aarch64 8.16.0-1.fc44              fedora     471.4 KiB
 cyrus-sasl-lib                    aarch64 2.1.28-33.fc44             fedora       2.4 MiB
 debugedit                         aarch64 5.2-3.fc44                 fedora     317.9 KiB
 dwz                               aarch64 0.16-2.fc43                fedora     322.6 KiB
 ed                                aarch64 1.22.2-1.fc44              fedora     156.0 KiB
 efi-srpm-macros                   noarch  6-4.fc43                   fedora      40.1 KiB
 elfutils                          aarch64 0.193-3.fc43               fedora       3.2 MiB
 elfutils-debuginfod-client        aarch64 0.193-3.fc43               fedora     143.9 KiB
 elfutils-default-yama-scope       noarch  0.193-3.fc43               fedora       1.8 KiB
 elfutils-libelf                   aarch64 0.193-3.fc43               fedora       1.2 MiB
 elfutils-libs                     aarch64 0.193-3.fc43               fedora     746.7 KiB
 fedora-gpg-keys                   noarch  44-0.1                     fedora     131.2 KiB
 fedora-release                    noarch  44-0.3                     fedora       0.0   B
 fedora-release-identity-basic     noarch  44-0.3                     fedora     664.0   B
 fedora-repos                      noarch  44-0.1                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch  44-0.1                     fedora       2.2 KiB
 file                              aarch64 5.46-8.fc44                fedora     140.2 KiB
 file-libs                         aarch64 5.46-8.fc44                fedora      11.9 MiB
 filesystem                        aarch64 3.18-50.fc43               fedora     112.0   B
 filesystem-srpm-macros            noarch  3.18-50.fc43               fedora      38.2 KiB
 fonts-srpm-macros                 noarch  1:5.0.0-1.fc44             fedora      55.8 KiB
 forge-srpm-macros                 noarch  0.4.0-3.fc43               fedora      38.9 KiB
 fpc-srpm-macros                   noarch  1.3-15.fc43                fedora     144.0   B
 gap-srpm-macros                   noarch  2-1.fc44                   fedora       2.1 KiB
 gdb-minimal                       aarch64 16.3-6.fc44                fedora      13.0 MiB
 gdbm-libs                         aarch64 1:1.23-10.fc43             fedora     233.9 KiB
 ghc-srpm-macros                   noarch  1.9.2-3.fc43               fedora     779.0   B
 glibc                             aarch64 2.42.9000-5.fc44           fedora       6.3 MiB
 glibc-common                      aarch64 2.42.9000-5.fc44           fedora       1.3 MiB
 glibc-gconv-extra                 aarch64 2.42.9000-5.fc44           fedora      18.6 MiB
 gmp                               aarch64 1:6.3.0-4.fc44             fedora     658.0 KiB
 gnat-srpm-macros                  noarch  6-8.fc43                   fedora       1.0 KiB
 gnulib-l10n                       noarch  20241231-1.fc44            fedora     655.0 KiB
 gnupg2                            aarch64 2.4.8-4.fc43               fedora       6.5 MiB
 gnupg2-dirmngr                    aarch64 2.4.8-4.fc43               fedora     646.4 KiB
 gnupg2-gpg-agent                  aarch64 2.4.8-4.fc43               fedora     847.3 KiB
 gnupg2-gpgconf                    aarch64 2.4.8-4.fc43               fedora     321.9 KiB
 gnupg2-keyboxd                    aarch64 2.4.8-4.fc43               fedora     233.3 KiB
 gnupg2-verify                     aarch64 2.4.8-4.fc43               fedora     364.4 KiB
 gnutls                            aarch64 3.8.10-5.fc44              fedora       3.7 MiB
 go-srpm-macros                    noarch  3.8.0-1.fc44               fedora      61.9 KiB
 gpgverify                         noarch  2.2-3.fc43                 fedora       8.7 KiB
 ima-evm-utils-libs                aarch64 1.6.2-6.fc43               fedora      92.7 KiB
 jansson                           aarch64 2.14-3.fc43                fedora      93.1 KiB
 java-srpm-macros                  noarch  1-7.fc43                   fedora     870.0   B
 json-c                            aarch64 0.18-7.fc43                fedora     138.7 KiB
 kernel-srpm-macros                noarch  1.0-27.fc43                fedora       1.9 KiB
 keyutils-libs                     aarch64 1.6.3-6.fc43               fedora      98.3 KiB
 krb5-libs                         aarch64 1.21.3-8.fc44              fedora       2.5 MiB
 libacl                            aarch64 2.3.2-4.fc43               fedora      68.0 KiB
 libarchive                        aarch64 3.8.1-3.fc43               fedora     975.1 KiB
 libassuan                         aarch64 2.5.7-4.fc43               fedora     215.8 KiB
 libattr                           aarch64 2.5.2-6.fc43               fedora      68.5 KiB
 libblkid                          aarch64 2.41.1-17.fc44             fedora     290.5 KiB
 libbrotli                         aarch64 1.1.0-10.fc44              fedora     909.5 KiB
 libcap                            aarch64 2.76-3.fc44                fedora     508.8 KiB
 libcap-ng                         aarch64 0.8.5-8.fc44               fedora     160.9 KiB
 libcom_err                        aarch64 1.47.3-2.fc43              fedora     111.2 KiB
 libcurl                           aarch64 8.16.0-1.fc44              fedora     915.4 KiB
 libeconf                          aarch64 0.7.9-2.fc43               fedora      81.0 KiB
 libevent                          aarch64 2.1.12-16.fc43             fedora       1.1 MiB
 libfdisk                          aarch64 2.41.1-17.fc44             fedora     418.9 KiB
 libffi                            aarch64 3.5.2-1.fc44               fedora     155.9 KiB
 libfsverity                       aarch64 1.6-3.fc43                 fedora      68.5 KiB
 libgcc                            aarch64 15.2.1-2.fc44              fedora     222.2 KiB
 libgcrypt                         aarch64 1.11.1-2.fc43              fedora       1.2 MiB
 libgomp                           aarch64 15.2.1-2.fc44              fedora     516.6 KiB
 libgpg-error                      aarch64 1.55-2.fc43                fedora     971.3 KiB
 libidn2                           aarch64 2.3.8-2.fc43               fedora     560.6 KiB
 libksba                           aarch64 1.6.7-4.fc43               fedora     398.4 KiB
 liblastlog2                       aarch64 2.41.1-17.fc44             fedora     137.9 KiB
 libmount                          aarch64 2.41.1-17.fc44             fedora     420.2 KiB
 libnghttp2                        aarch64 1.67.1-1.fc44              fedora     198.0 KiB
 libpkgconf                        aarch64 2.3.0-3.fc43               fedora     134.0 KiB
 libpsl                            aarch64 0.21.5-6.fc43              fedora     132.5 KiB
 libselinux                        aarch64 3.9-5.fc44                 fedora     201.1 KiB
 libselinux-utils                  aarch64 3.9-5.fc44                 fedora       1.3 MiB
 libsemanage                       aarch64 3.9-4.fc44                 fedora     360.1 KiB
 libsepol                          aarch64 3.9-2.fc43                 fedora     809.8 KiB
 libsmartcols                      aarch64 2.41.1-17.fc44             fedora     224.5 KiB
 libssh                            aarch64 0.11.3-1.fc44              fedora     587.0 KiB
 libssh-config                     noarch  0.11.3-1.fc44              fedora     277.0   B
 libstdc++                         aarch64 15.2.1-2.fc44              fedora       2.8 MiB
 libtasn1                          aarch64 4.20.0-2.fc43              fedora     220.4 KiB
 libtool-ltdl                      aarch64 2.5.4-7.fc43               fedora      94.0 KiB
 libunistring                      aarch64 1.1-10.fc43                fedora       1.7 MiB
 libusb1                           aarch64 1.0.29-4.fc44              fedora     178.9 KiB
 libuuid                           aarch64 2.41.1-17.fc44             fedora      69.4 KiB
 libverto                          aarch64 0.3.2-11.fc43              fedora      69.4 KiB
 libxcrypt                         aarch64 4.4.38-9.fc44              fedora     272.5 KiB
 libxml2                           aarch64 2.12.10-5.fc44             fedora       1.9 MiB
 libzstd                           aarch64 1.5.7-3.fc44               fedora     860.4 KiB
 linkdupes                         aarch64 0.7.2-2.fc44               fedora     779.4 KiB
 lua-libs                          aarch64 5.4.8-2.fc43               fedora     328.8 KiB
 lua-srpm-macros                   noarch  1-16.fc43                  fedora       1.3 KiB
 lz4-libs                          aarch64 1.10.0-3.fc43              fedora     197.4 KiB
 mpfr                              aarch64 4.2.2-2.fc43               fedora     755.5 KiB
 ncurses-base                      noarch  6.5-7.20250614.fc43        fedora     328.1 KiB
 ncurses-libs                      aarch64 6.5-7.20250614.fc43        fedora       1.2 MiB
 nettle                            aarch64 3.10.1-2.fc43              fedora     765.3 KiB
 npth                              aarch64 1.8-3.fc43                 fedora      93.5 KiB
 ocaml-srpm-macros                 noarch  11-2.fc43                  fedora       1.9 KiB
 openblas-srpm-macros              noarch  2-20.fc43                  fedora     112.0   B
 openldap                          aarch64 2.6.10-4.fc44              fedora     761.9 KiB
 openssl-libs                      aarch64 1:3.5.1-3.fc44             fedora       7.7 MiB
 p11-kit                           aarch64 0.25.8-1.fc44              fedora       2.5 MiB
 p11-kit-trust                     aarch64 0.25.8-1.fc44              fedora     530.3 KiB
 package-notes-srpm-macros         noarch  0.5-14.fc43                fedora       1.6 KiB
 pam-libs                          aarch64 1.7.1-3.fc43               fedora     223.0 KiB
 pcre2                             aarch64 10.46-1.fc44               fedora     713.6 KiB
 pcre2-syntax                      noarch  10.46-1.fc44               fedora     275.3 KiB
 perl-srpm-macros                  noarch  1-60.fc43                  fedora     861.0   B
 pkgconf                           aarch64 2.3.0-3.fc43               fedora     112.4 KiB
 pkgconf-m4                        noarch  2.3.0-3.fc43               fedora      14.4 KiB
 pkgconf-pkg-config                aarch64 2.3.0-3.fc43               fedora     990.0   B
 policycoreutils                   aarch64 3.9-5.fc44                 fedora       1.3 MiB
 popt                              aarch64 1.19-9.fc43                fedora     144.8 KiB
 publicsuffix-list-dafsa           noarch  20250616-2.fc43            fedora      69.1 KiB
 pyproject-srpm-macros             noarch  1.18.4-1.fc44              fedora       1.9 KiB
 python-srpm-macros                noarch  3.14-8.fc44                fedora      51.6 KiB
 qt5-srpm-macros                   noarch  5.15.17-2.fc43             fedora     500.0   B
 qt6-srpm-macros                   noarch  6.10.0~rc-1.fc44           fedora     464.0   B
 readline                          aarch64 8.3-2.fc43                 fedora     563.8 KiB
 rpm                               aarch64 6.0.0-1.fc44               fedora       3.4 MiB
 rpm-build-libs                    aarch64 6.0.0-1.fc44               fedora     264.1 KiB
 rpm-libs                          aarch64 6.0.0-1.fc44               fedora     995.5 KiB
 rpm-plugin-selinux                aarch64 6.0.0-1.fc44               fedora      68.0 KiB
 rpm-sequoia                       aarch64 1.9.0-2.fc43               fedora       2.3 MiB
 rpm-sign-libs                     aarch64 6.0.0-1.fc44               fedora      67.8 KiB
 rust-srpm-macros                  noarch  26.4-1.fc44                fedora       4.8 KiB
 selinux-policy                    noarch  42.11-2.fc44               fedora      31.9 KiB
 selinux-policy-targeted           noarch  42.11-2.fc44               fedora      18.7 MiB
 setup                             noarch  2.15.0-26.fc43             fedora     725.0 KiB
 sqlite-libs                       aarch64 3.50.4-1.fc44              fedora       1.5 MiB
 systemd-libs                      aarch64 258-1.fc44                 fedora       2.4 MiB
 systemd-standalone-sysusers       aarch64 258-1.fc44                 fedora     329.6 KiB
 tpm2-tss                          aarch64 4.1.3-8.fc43               fedora       2.1 MiB
 tree-sitter-srpm-macros           noarch  0.4.2-1.fc43               fedora       8.3 KiB
 util-linux-core                   aarch64 2.41.1-17.fc44             fedora       2.4 MiB
 xxhash-libs                       aarch64 0.8.3-3.fc43               fedora      86.0 KiB
 xz-libs                           aarch64 1:5.8.1-2.fc43             fedora     201.5 KiB
 zig-srpm-macros                   noarch  1-5.fc43                   fedora       1.1 KiB
 zip                               aarch64 3.0-44.fc43                fedora     762.5 KiB
 zlib-ng-compat                    aarch64 2.2.5-2.fc44               fedora     133.4 KiB
 zstd                              aarch64 1.5.7-3.fc44               fedora     574.0 KiB
Installing groups:
 Buildsystem building group                                                               

Transaction Summary:
 Installing:       177 packages

Total size of inbound packages is 65 MiB. Need to download 0 B.
After this operation, 247 MiB extra will be used (install 247 MiB, remove 0 B).
[  1/177] tar-2:1.35-6.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  2/177] bzip2-0:1.0.8-21.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  3/177] redhat-rpm-config-0:343-14.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  4/177] rpm-build-0:6.0.0-1.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  5/177] unzip-0:6.0-68.fc44.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  6/177] cpio-0:2.15-6.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  7/177] which-0:2.23-3.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  8/177] bash-0:5.3.0-2.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[  9/177] coreutils-0:9.8-3.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 10/177] grep-0:3.12-2.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 11/177] patch-0:2.8-2.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 12/177] sed-0:4.9-5.fc43.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 13/177] shadow-utils-2:4.18.0-3.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 14/177] util-linux-0:2.41.1-17.fc44.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 15/177] diffutils-0:3.12-3.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 16/177] fedora-release-common-0:44-0. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 17/177] findutils-1:4.10.0-6.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 18/177] gawk-0:5.3.2-2.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 19/177] glibc-minimal-langpack-0:2.42 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 20/177] gzip-0:1.14-1.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 21/177] info-0:7.2-6.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 22/177] xz-1:5.8.1-2.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 23/177] glibc-0:2.42.9000-5.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 24/177] libacl-0:2.3.2-4.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 25/177] libselinux-0:3.9-5.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 26/177] bzip2-libs-0:1.0.8-21.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 27/177] ansible-srpm-macros-0:1-18.1. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 28/177] build-reproducibility-srpm-ma 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 29/177] dwz-0:0.16-2.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 30/177] efi-srpm-macros-0:6-4.fc43.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 31/177] file-0:5.46-8.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 32/177] filesystem-srpm-macros-0:3.18 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 33/177] fonts-srpm-macros-1:5.0.0-1.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 34/177] forge-srpm-macros-0:0.4.0-3.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 35/177] fpc-srpm-macros-0:1.3-15.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 36/177] gap-srpm-macros-0:2-1.fc44.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 37/177] ghc-srpm-macros-0:1.9.2-3.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 38/177] gnat-srpm-macros-0:6-8.fc43.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 39/177] go-srpm-macros-0:3.8.0-1.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 40/177] java-srpm-macros-0:1-7.fc43.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 41/177] kernel-srpm-macros-0:1.0-27.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 42/177] lua-srpm-macros-0:1-16.fc43.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 43/177] ocaml-srpm-macros-0:11-2.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 44/177] openblas-srpm-macros-0:2-20.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 45/177] package-notes-srpm-macros-0:0 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 46/177] perl-srpm-macros-0:1-60.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 47/177] pyproject-srpm-macros-0:1.18. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 48/177] python-srpm-macros-0:3.14-8.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 49/177] qt5-srpm-macros-0:5.15.17-2.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 50/177] qt6-srpm-macros-0:6.10.0~rc-1 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 51/177] rpm-0:6.0.0-1.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 52/177] rust-srpm-macros-0:26.4-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 53/177] tree-sitter-srpm-macros-0:0.4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 54/177] zig-srpm-macros-0:1-5.fc43.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 55/177] zip-0:3.0-44.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 56/177] binutils-0:2.45.50-4.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 57/177] debugedit-0:5.2-3.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 58/177] elfutils-0:0.193-3.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 59/177] elfutils-libelf-0:0.193-3.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 60/177] libarchive-0:3.8.1-3.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 61/177] libgcc-0:15.2.1-2.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 62/177] libstdc++-0:15.2.1-2.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 63/177] pkgconf-pkg-config-0:2.3.0-3. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 64/177] popt-0:1.19-9.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 65/177] readline-0:8.3-2.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 66/177] rpm-build-libs-0:6.0.0-1.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 67/177] rpm-libs-0:6.0.0-1.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 68/177] zstd-0:1.5.7-3.fc44.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 69/177] filesystem-0:3.18-50.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 70/177] ncurses-libs-0:6.5-7.20250614 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 71/177] coreutils-common-0:9.8-3.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 72/177] gmp-1:6.3.0-4.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 73/177] libattr-0:2.5.2-6.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 74/177] libcap-0:2.76-3.fc44.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 75/177] openssl-libs-1:3.5.1-3.fc44.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 76/177] systemd-libs-0:258-1.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 77/177] pcre2-0:10.46-1.fc44.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 78/177] ed-0:1.22.2-1.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 79/177] audit-libs-0:4.1.2-2.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 80/177] libeconf-0:0.7.9-2.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 81/177] libsemanage-0:3.9-4.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 82/177] libxcrypt-0:4.4.38-9.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 83/177] pam-libs-0:1.7.1-3.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 84/177] setup-0:2.15.0-26.fc43.noarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 85/177] libblkid-0:2.41.1-17.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 86/177] libcap-ng-0:0.8.5-8.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 87/177] libfdisk-0:2.41.1-17.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 88/177] liblastlog2-0:2.41.1-17.fc44. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 89/177] libmount-0:2.41.1-17.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 90/177] libsmartcols-0:2.41.1-17.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 91/177] libuuid-0:2.41.1-17.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 92/177] util-linux-core-0:2.41.1-17.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 93/177] zlib-ng-compat-0:2.2.5-2.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 94/177] fedora-repos-0:44-0.1.noarch  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 95/177] mpfr-0:4.2.2-2.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 96/177] glibc-common-0:2.42.9000-5.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 97/177] xz-libs-1:5.8.1-2.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 98/177] glibc-gconv-extra-0:2.42.9000 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 99/177] libsepol-0:3.9-2.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[100/177] add-determinism-0:0.7.2-2.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[101/177] linkdupes-0:0.7.2-2.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[102/177] file-libs-0:5.46-8.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[103/177] curl-0:8.16.0-1.fc44.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[104/177] alternatives-0:1.33-2.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[105/177] elfutils-debuginfod-client-0: 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[106/177] jansson-0:2.14-3.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[107/177] elfutils-libs-0:0.193-3.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[108/177] libzstd-0:1.5.7-3.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[109/177] libxml2-0:2.12.10-5.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[110/177] lz4-libs-0:1.10.0-3.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[111/177] pkgconf-0:2.3.0-3.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[112/177] pkgconf-m4-0:2.3.0-3.fc43.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[113/177] libgomp-0:15.2.1-2.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[114/177] lua-libs-0:5.4.8-2.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[115/177] rpm-sign-libs-0:6.0.0-1.fc44. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[116/177] rpm-sequoia-0:1.9.0-2.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[117/177] sqlite-libs-0:3.50.4-1.fc44.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[118/177] ncurses-base-0:6.5-7.20250614 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[119/177] gnulib-l10n-0:20241231-1.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[120/177] ca-certificates-0:2025.2.80_v 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[121/177] crypto-policies-0:20250714-5. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[122/177] pcre2-syntax-0:10.46-1.fc44.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[123/177] fedora-gpg-keys-0:44-0.1.noar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[124/177] fedora-repos-rawhide-0:44-0.1 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[125/177] json-c-0:0.18-7.fc43.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[126/177] elfutils-default-yama-scope-0 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[127/177] libpkgconf-0:2.3.0-3.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[128/177] gnupg2-0:2.4.8-4.fc43.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[129/177] ima-evm-utils-libs-0:1.6.2-6. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[130/177] libfsverity-0:1.6-3.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[131/177] libffi-0:3.5.2-1.fc44.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[132/177] p11-kit-0:0.25.8-1.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[133/177] p11-kit-trust-0:0.25.8-1.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[134/177] gpgverify-0:2.2-3.fc43.noarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[135/177] gnupg2-dirmngr-0:2.4.8-4.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[136/177] gnupg2-gpg-agent-0:2.4.8-4.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[137/177] gnupg2-gpgconf-0:2.4.8-4.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[138/177] gnupg2-keyboxd-0:2.4.8-4.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[139/177] gnupg2-verify-0:2.4.8-4.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[140/177] libassuan-0:2.5.7-4.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[141/177] libgcrypt-0:1.11.1-2.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[142/177] libgpg-error-0:1.55-2.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[143/177] npth-0:1.8-3.fc43.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[144/177] tpm2-tss-0:4.1.3-8.fc43.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[145/177] libtasn1-0:4.20.0-2.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[146/177] gnutls-0:3.8.10-5.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[147/177] libksba-0:1.6.7-4.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[148/177] openldap-0:2.6.10-4.fc44.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[149/177] libusb1-0:1.0.29-4.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[150/177] libidn2-0:2.3.8-2.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[151/177] libunistring-0:1.1-10.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[152/177] nettle-0:3.10.1-2.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[153/177] cyrus-sasl-lib-0:2.1.28-33.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[154/177] libevent-0:2.1.12-16.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[155/177] libtool-ltdl-0:2.5.4-7.fc43.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[156/177] gdbm-libs-1:1.23-10.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[157/177] fedora-release-0:44-0.3.noarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[158/177] systemd-standalone-sysusers-0 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[159/177] gdb-minimal-0:16.3-6.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[160/177] xxhash-libs-0:0.8.3-3.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[161/177] fedora-release-identity-basic 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[162/177] libcurl-0:8.16.0-1.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[163/177] krb5-libs-0:1.21.3-8.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[164/177] libbrotli-0:1.1.0-10.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[165/177] libnghttp2-0:1.67.1-1.fc44.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[166/177] libpsl-0:0.21.5-6.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[167/177] libssh-0:0.11.3-1.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[168/177] keyutils-libs-0:1.6.3-6.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[169/177] libcom_err-0:1.47.3-2.fc43.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[170/177] libverto-0:0.3.2-11.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[171/177] publicsuffix-list-dafsa-0:202 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[172/177] libssh-config-0:0.11.3-1.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[173/177] selinux-policy-targeted-0:42. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[174/177] policycoreutils-0:3.9-5.fc44. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[175/177] selinux-policy-0:42.11-2.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[176/177] libselinux-utils-0:3.9-5.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[177/177] rpm-plugin-selinux-0:6.0.0-1. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
--------------------------------------------------------------------------------
[177/177] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
Importing OpenPGP key 0xF577861E:
 UserID     : "Fedora (45) <fedora-45-primary@fedoraproject.org>"
 Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary
The key was successfully imported.
[  1/179] Verify package files          100% | 753.0   B/s | 177.0   B |  00m00s
[  2/179] Prepare transaction           100% |   2.2 KiB/s | 177.0   B |  00m00s
[  3/179] Installing libgcc-0:15.2.1-2. 100% | 109.3 MiB/s | 223.9 KiB |  00m00s
[  4/179] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/179] Installing publicsuffix-list- 100% |  68.2 MiB/s |  69.8 KiB |  00m00s
[  6/179] Installing fedora-release-ide 100% |   0.0   B/s | 920.0   B |  00m00s
[  7/179] Installing fedora-repos-rawhi 100% |   2.4 MiB/s |   2.4 KiB |  00m00s
[  8/179] Installing fedora-gpg-keys-0: 100% |  29.1 MiB/s | 179.0 KiB |  00m00s
[  9/179] Installing fedora-repos-0:44- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/179] Installing fedora-release-com 100% |  24.3 MiB/s |  24.9 KiB |  00m00s
[ 11/179] Installing fedora-release-0:4 100% |  15.1 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch                   
>>> Finished sysusers scriptlet: setup-0:2.15.0-26.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.                           
>>>                                                                             
[ 12/179] Installing setup-0:2.15.0-26. 100% |  37.6 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew                               
[ 13/179] Installing filesystem-0:3.18- 100% |   1.9 MiB/s | 212.8 KiB |  00m00s
[ 14/179] Installing pcre2-syntax-0:10. 100% | 135.6 MiB/s | 277.8 KiB |  00m00s
[ 15/179] Installing gnulib-l10n-0:2024 100% | 129.3 MiB/s | 661.9 KiB |  00m00s
[ 16/179] Installing coreutils-common-0 100% | 310.4 MiB/s |  11.2 MiB |  00m00s
[ 17/179] Installing ncurses-base-0:6.5 100% |  57.5 MiB/s | 353.5 KiB |  00m00s
[ 18/179] Installing bash-0:5.3.0-2.fc4 100% | 210.7 MiB/s |   8.4 MiB |  00m00s
[ 19/179] Installing glibc-common-0:2.4 100% |  60.2 MiB/s |   1.3 MiB |  00m00s
[ 20/179] Installing glibc-gconv-extra- 100% | 397.1 MiB/s |  18.7 MiB |  00m00s
[ 21/179] Installing glibc-0:2.42.9000- 100% | 149.6 MiB/s |   6.3 MiB |  00m00s
[ 22/179] Installing ncurses-libs-0:6.5 100% | 249.5 MiB/s |   1.2 MiB |  00m00s
[ 23/179] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 24/179] Installing zlib-ng-compat-0:2 100% | 131.1 MiB/s | 134.2 KiB |  00m00s
[ 25/179] Installing bzip2-libs-0:1.0.8 100% |  72.0 MiB/s |  73.8 KiB |  00m00s
[ 26/179] Installing libgpg-error-0:1.5 100% |  47.7 MiB/s | 977.1 KiB |  00m00s
[ 27/179] Installing libstdc++-0:15.2.1 100% | 315.1 MiB/s |   2.8 MiB |  00m00s
[ 28/179] Installing libassuan-0:2.5.7- 100% | 212.6 MiB/s | 217.7 KiB |  00m00s
[ 29/179] Installing libgcrypt-0:1.11.1 100% | 298.7 MiB/s |   1.2 MiB |  00m00s
[ 30/179] Installing readline-0:8.3-2.f 100% | 276.3 MiB/s | 565.9 KiB |  00m00s
[ 31/179] Installing gmp-1:6.3.0-4.fc44 100% | 214.9 MiB/s | 660.2 KiB |  00m00s
[ 32/179] Installing libuuid-0:2.41.1-1 100% |  68.8 MiB/s |  70.4 KiB |  00m00s
[ 33/179] Installing xz-libs-1:5.8.1-2. 100% | 197.9 MiB/s | 202.6 KiB |  00m00s
[ 34/179] Installing popt-0:1.19-9.fc43 100% |  49.3 MiB/s | 151.4 KiB |  00m00s
[ 35/179] Installing libzstd-0:1.5.7-3. 100% | 280.5 MiB/s | 861.7 KiB |  00m00s
[ 36/179] Installing elfutils-libelf-0: 100% | 297.5 MiB/s |   1.2 MiB |  00m00s
[ 37/179] Installing npth-0:1.8-3.fc43. 100% |  92.4 MiB/s |  94.6 KiB |  00m00s
[ 38/179] Installing libblkid-0:2.41.1- 100% | 284.8 MiB/s | 291.6 KiB |  00m00s
[ 39/179] Installing libxcrypt-0:4.4.38 100% | 134.4 MiB/s | 275.2 KiB |  00m00s
[ 40/179] Installing libsepol-0:3.9-2.f 100% | 263.9 MiB/s | 810.8 KiB |  00m00s
[ 41/179] Installing sqlite-libs-0:3.50 100% | 250.2 MiB/s |   1.5 MiB |  00m00s
[ 42/179] Installing gnupg2-gpgconf-0:2 100% |  18.6 MiB/s | 324.0 KiB |  00m00s
[ 43/179] Installing libattr-0:2.5.2-6. 100% |  67.8 MiB/s |  69.4 KiB |  00m00s
[ 44/179] Installing libacl-0:2.3.2-4.f 100% |  67.2 MiB/s |  68.8 KiB |  00m00s
[ 45/179] Installing pcre2-0:10.46-1.fc 100% | 232.7 MiB/s | 715.0 KiB |  00m00s
[ 46/179] Installing libselinux-0:3.9-5 100% | 197.6 MiB/s | 202.4 KiB |  00m00s
[ 47/179] Installing grep-0:3.12-2.fc43 100% |  47.2 MiB/s |   1.0 MiB |  00m00s
[ 48/179] Installing sed-0:4.9-5.fc43.a 100% |  41.0 MiB/s | 881.4 KiB |  00m00s
[ 49/179] Installing findutils-1:4.10.0 100% |  80.0 MiB/s |   1.9 MiB |  00m00s
[ 50/179] Installing libtasn1-0:4.20.0- 100% | 217.0 MiB/s | 222.2 KiB |  00m00s
[ 51/179] Installing libunistring-0:1.1 100% | 291.0 MiB/s |   1.7 MiB |  00m00s
[ 52/179] Installing libidn2-0:2.3.8-2. 100% |  50.3 MiB/s | 566.7 KiB |  00m00s
[ 53/179] Installing crypto-policies-0: 100% |  21.0 MiB/s | 172.0 KiB |  00m00s
[ 54/179] Installing xz-1:5.8.1-2.fc43. 100% |  56.5 MiB/s |   1.4 MiB |  00m00s
[ 55/179] Installing libmount-0:2.41.1- 100% | 205.7 MiB/s | 421.2 KiB |  00m00s
[ 56/179] Installing gnupg2-verify-0:2. 100% |  21.0 MiB/s | 365.8 KiB |  00m00s
[ 57/179] Installing dwz-0:0.16-2.fc43. 100% |  18.6 MiB/s | 324.0 KiB |  00m00s
[ 58/179] Installing mpfr-0:4.2.2-2.fc4 100% | 246.5 MiB/s | 757.2 KiB |  00m00s
[ 59/179] Installing gawk-0:5.3.2-2.fc4 100% | 103.3 MiB/s |   2.6 MiB |  00m00s
[ 60/179] Installing libksba-0:1.6.7-4. 100% | 195.8 MiB/s | 401.0 KiB |  00m00s
[ 61/179] Installing unzip-0:6.0-68.fc4 100% |  25.7 MiB/s | 473.8 KiB |  00m00s
[ 62/179] Installing file-libs-0:5.46-8 100% | 565.7 MiB/s |  11.9 MiB |  00m00s
[ 63/179] Installing file-0:5.46-8.fc44 100% |   8.1 MiB/s | 141.7 KiB |  00m00s
[ 64/179] Installing diffutils-0:3.12-3 100% |  73.8 MiB/s |   1.6 MiB |  00m00s
[ 65/179] Installing libeconf-0:0.7.9-2 100% |  80.7 MiB/s |  82.6 KiB |  00m00s
[ 66/179] Installing libcap-ng-0:0.8.5- 100% | 159.0 MiB/s | 162.8 KiB |  00m00s
[ 67/179] Installing audit-libs-0:4.1.2 100% | 239.1 MiB/s | 489.6 KiB |  00m00s
[ 68/179] Installing pam-libs-0:1.7.1-3 100% | 220.1 MiB/s | 225.4 KiB |  00m00s
[ 69/179] Installing libcap-0:2.76-3.fc 100% |  27.9 MiB/s | 513.9 KiB |  00m00s
[ 70/179] Installing systemd-libs-0:258 100% | 300.0 MiB/s |   2.4 MiB |  00m00s
[ 71/179] Installing libsemanage-0:3.9- 100% | 176.7 MiB/s | 361.9 KiB |  00m00s
[ 72/179] Installing libsmartcols-0:2.4 100% | 220.3 MiB/s | 225.5 KiB |  00m00s
[ 73/179] Installing alternatives-0:1.3 100% |   5.6 MiB/s |  91.8 KiB |  00m00s
[ 74/179] Installing lua-libs-0:5.4.8-2 100% | 161.2 MiB/s | 330.0 KiB |  00m00s
[ 75/179] Installing json-c-0:0.18-7.fc 100% | 136.7 MiB/s | 139.9 KiB |  00m00s
[ 76/179] Installing libffi-0:3.5.2-1.f 100% | 153.6 MiB/s | 157.3 KiB |  00m00s
[ 77/179] Installing p11-kit-0:0.25.8-1 100% |  93.1 MiB/s |   2.5 MiB |  00m00s
[ 78/179] Installing p11-kit-trust-0:0. 100% |  20.0 MiB/s | 532.0 KiB |  00m00s
[ 79/179] Installing openssl-libs-1:3.5 100% | 307.8 MiB/s |   7.7 MiB |  00m00s
[ 80/179] Installing coreutils-0:9.8-3. 100% | 175.1 MiB/s |   8.2 MiB |  00m00s
[ 81/179] Installing ca-certificates-0: 100% |   1.5 MiB/s |   2.5 MiB |  00m02s
[ 82/179] Installing gzip-0:1.14-1.fc44 100% |  21.6 MiB/s | 443.2 KiB |  00m00s
[ 83/179] Installing rpm-sequoia-0:1.9. 100% | 287.9 MiB/s |   2.3 MiB |  00m00s
[ 84/179] Installing libfsverity-0:1.6- 100% |  67.8 MiB/s |  69.4 KiB |  00m00s
[ 85/179] Installing libevent-0:2.1.12- 100% | 271.3 MiB/s |   1.1 MiB |  00m00s
[ 86/179] Installing util-linux-core-0: 100% |  98.6 MiB/s |   2.5 MiB |  00m00s
[ 87/179] Installing libusb1-0:1.0.29-4 100% |  17.6 MiB/s | 180.6 KiB |  00m00s
>>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.aarch64                 
>>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.aarch64                
>>> Scriptlet output:                                                           
>>> Creating group 'tss' with GID 59.                                           
>>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59.   
>>>                                                                             
[ 88/179] Installing tpm2-tss-0:4.1.3-8 100% | 239.9 MiB/s |   2.2 MiB |  00m00s
[ 89/179] Installing ima-evm-utils-libs 100% |  91.8 MiB/s |  94.0 KiB |  00m00s
[ 90/179] Installing gnupg2-gpg-agent-0 100% |  29.7 MiB/s | 851.2 KiB |  00m00s
[ 91/179] Installing systemd-standalone 100% |  17.9 MiB/s | 330.1 KiB |  00m00s
[ 92/179] Installing rpm-libs-0:6.0.0-1 100% | 243.4 MiB/s | 997.0 KiB |  00m00s
[ 93/179] Installing zip-0:3.0-44.fc43. 100% |  39.4 MiB/s | 766.4 KiB |  00m00s
[ 94/179] Installing gnupg2-keyboxd-0:2 100% |  32.7 MiB/s | 234.6 KiB |  00m00s
[ 95/179] Installing libpsl-0:0.21.5-6. 100% | 130.5 MiB/s | 133.6 KiB |  00m00s
[ 96/179] Installing tar-2:1.35-6.fc43. 100% | 103.6 MiB/s |   3.0 MiB |  00m00s
[ 97/179] Installing linkdupes-0:0.7.2- 100% |  40.1 MiB/s | 780.8 KiB |  00m00s
[ 98/179] Installing libselinux-utils-0 100% |  64.7 MiB/s |   1.4 MiB |  00m00s
[ 99/179] Installing liblastlog2-0:2.41 100% |  19.5 MiB/s | 140.1 KiB |  00m00s
[100/179] Installing libfdisk-0:2.41.1- 100% | 136.7 MiB/s | 419.9 KiB |  00m00s
[101/179] Installing util-linux-0:2.41. 100% | 127.0 MiB/s |   6.9 MiB |  00m00s
[102/179] Installing policycoreutils-0: 100% |  36.0 MiB/s |   1.3 MiB |  00m00s
[103/179] Installing selinux-policy-0:4 100% |   1.3 MiB/s |  33.5 KiB |  00m00s
[104/179] Installing selinux-policy-tar 100% | 129.6 MiB/s |  14.9 MiB |  00m00s
[105/179] Installing zstd-0:1.5.7-3.fc4 100% |  26.9 MiB/s | 577.6 KiB |  00m00s
[106/179] Installing libxml2-0:2.12.10- 100% |  82.2 MiB/s |   1.9 MiB |  00m00s
[107/179] Installing nettle-0:3.10.1-2. 100% | 187.6 MiB/s | 768.4 KiB |  00m00s
[108/179] Installing gnutls-0:3.8.10-5. 100% | 307.9 MiB/s |   3.7 MiB |  00m00s
[109/179] Installing bzip2-0:1.0.8-21.f 100% |  10.1 MiB/s | 175.8 KiB |  00m00s
[110/179] Installing add-determinism-0: 100% |  90.0 MiB/s |   2.0 MiB |  00m00s
[111/179] Installing build-reproducibil 100% |   1.5 MiB/s |   1.5 KiB |  00m00s
[112/179] Installing cpio-0:2.15-6.fc43 100% |  52.2 MiB/s |   1.1 MiB |  00m00s
[113/179] Installing ed-0:1.22.2-1.fc44 100% |   9.1 MiB/s | 158.3 KiB |  00m00s
[114/179] Installing patch-0:2.8-2.fc43 100% |  15.2 MiB/s | 264.1 KiB |  00m00s
[115/179] Installing jansson-0:2.14-3.f 100% |  92.3 MiB/s |  94.5 KiB |  00m00s
[116/179] Installing lz4-libs-0:1.10.0- 100% | 193.9 MiB/s | 198.5 KiB |  00m00s
[117/179] Installing libarchive-0:3.8.1 100% | 238.5 MiB/s | 977.0 KiB |  00m00s
[118/179] Installing libgomp-0:15.2.1-2 100% | 252.9 MiB/s | 518.0 KiB |  00m00s
[119/179] Installing libpkgconf-0:2.3.0 100% | 132.0 MiB/s | 135.1 KiB |  00m00s
[120/179] Installing pkgconf-0:2.3.0-3. 100% |   6.6 MiB/s | 114.9 KiB |  00m00s
[121/179] Installing libtool-ltdl-0:2.5 100% |  92.9 MiB/s |  95.1 KiB |  00m00s
[122/179] Installing gdbm-libs-1:1.23-1 100% | 230.1 MiB/s | 235.6 KiB |  00m00s
[123/179] Installing cyrus-sasl-lib-0:2 100% | 100.7 MiB/s |   2.4 MiB |  00m00s
[124/179] Installing openldap-0:2.6.10- 100% | 186.9 MiB/s | 765.6 KiB |  00m00s
[125/179] Installing gnupg2-dirmngr-0:2 100% |  24.4 MiB/s | 649.1 KiB |  00m00s
[126/179] Installing gnupg2-0:2.4.8-4.f 100% | 167.4 MiB/s |   6.5 MiB |  00m00s
[127/179] Installing rpm-sign-libs-0:6. 100% |  66.9 MiB/s |  68.5 KiB |  00m00s
[128/179] Installing gpgverify-0:2.2-3. 100% |   9.2 MiB/s |   9.4 KiB |  00m00s
[129/179] Installing xxhash-libs-0:0.8. 100% |  85.3 MiB/s |  87.4 KiB |  00m00s
[130/179] Installing libbrotli-0:1.1.0- 100% | 222.6 MiB/s | 911.8 KiB |  00m00s
[131/179] Installing libnghttp2-0:1.67. 100% | 194.4 MiB/s | 199.1 KiB |  00m00s
[132/179] Installing keyutils-libs-0:1. 100% |  97.4 MiB/s |  99.8 KiB |  00m00s
[133/179] Installing libcom_err-0:1.47. 100% | 109.5 MiB/s | 112.2 KiB |  00m00s
[134/179] Installing libverto-0:0.3.2-1 100% |  69.5 MiB/s |  71.2 KiB |  00m00s
[135/179] Installing krb5-libs-0:1.21.3 100% | 253.3 MiB/s |   2.5 MiB |  00m00s
[136/179] Installing libssh-0:0.11.3-1. 100% | 191.8 MiB/s | 589.1 KiB |  00m00s
[137/179] Installing libcurl-0:8.16.0-1 100% | 223.8 MiB/s | 916.5 KiB |  00m00s
[138/179] Installing curl-0:8.16.0-1.fc 100% |  16.5 MiB/s | 474.2 KiB |  00m00s
[139/179] Installing rpm-0:6.0.0-1.fc44 100% |  61.2 MiB/s |   2.8 MiB |  00m00s
[140/179] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.1 KiB |  00m00s
[141/179] Installing java-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[142/179] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[143/179] Installing tree-sitter-srpm-m 100% |   9.1 MiB/s |   9.3 KiB |  00m00s
[144/179] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[145/179] Installing filesystem-srpm-ma 100% |  38.0 MiB/s |  38.9 KiB |  00m00s
[146/179] Installing elfutils-default-y 100% | 340.5 KiB/s |   2.0 KiB |  00m00s
[147/179] Installing elfutils-libs-0:0. 100% | 182.8 MiB/s | 748.5 KiB |  00m00s
[148/179] Installing elfutils-debuginfo 100% |   7.5 MiB/s | 146.2 KiB |  00m00s
[149/179] Installing binutils-0:2.45.50 100% | 286.0 MiB/s |  30.9 MiB |  00m00s
[150/179] Installing elfutils-0:0.193-3 100% | 123.2 MiB/s |   3.2 MiB |  00m00s
[151/179] Installing gdb-minimal-0:16.3 100% | 241.5 MiB/s |  13.0 MiB |  00m00s
[152/179] Installing debugedit-0:5.2-3. 100% |  17.4 MiB/s | 321.2 KiB |  00m00s
[153/179] Installing rpm-build-libs-0:6 100% | 129.4 MiB/s | 265.0 KiB |  00m00s
[154/179] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[155/179] Installing pkgconf-pkg-config 100% | 110.8 KiB/s |   1.8 KiB |  00m00s
[156/179] Installing rust-srpm-macros-0 100% |   5.4 MiB/s |   5.6 KiB |  00m00s
[157/179] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 740.0   B |  00m00s
[158/179] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[159/179] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[160/179] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[161/179] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[162/179] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.1 KiB |  00m00s
[163/179] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[164/179] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[165/179] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[166/179] Installing gap-srpm-macros-0: 100% |   0.0   B/s |   2.7 KiB |  00m00s
[167/179] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[168/179] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[169/179] Installing rpm-build-0:6.0.0- 100% |  29.7 MiB/s | 607.9 KiB |  00m00s
[170/179] Installing pyproject-srpm-mac 100% |   2.4 MiB/s |   2.5 KiB |  00m00s
[171/179] Installing redhat-rpm-config- 100% |  61.7 MiB/s | 189.5 KiB |  00m00s
[172/179] Installing forge-srpm-macros- 100% |  39.3 MiB/s |  40.3 KiB |  00m00s
[173/179] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[174/179] Installing go-srpm-macros-0:3 100% |  61.6 MiB/s |  63.0 KiB |  00m00s
[175/179] Installing python-srpm-macros 100% |  51.7 MiB/s |  52.9 KiB |  00m00s
[176/179] Installing rpm-plugin-selinux 100% |  67.4 MiB/s |  69.0 KiB |  00m00s
[177/179] Installing which-0:2.23-3.fc4 100% |   6.8 MiB/s | 125.6 KiB |  00m00s
[178/179] Installing shadow-utils-2:4.1 100% |  97.7 MiB/s |   4.5 MiB |  00m00s
[179/179] Installing info-0:7.2-6.fc43. 100% |  45.8 KiB/s | 422.0 KiB |  00m09s
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.7.2-2.fc44.aarch64
alternatives-1.33-2.fc43.aarch64
ansible-srpm-macros-1-18.1.fc43.noarch
audit-libs-4.1.2-2.fc44.aarch64
bash-5.3.0-2.fc43.aarch64
binutils-2.45.50-4.fc44.aarch64
build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch
bzip2-1.0.8-21.fc43.aarch64
bzip2-libs-1.0.8-21.fc43.aarch64
ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch
coreutils-9.8-3.fc44.aarch64
coreutils-common-9.8-3.fc44.aarch64
cpio-2.15-6.fc43.aarch64
crypto-policies-20250714-5.gitcd6043a.fc44.noarch
curl-8.16.0-1.fc44.aarch64
cyrus-sasl-lib-2.1.28-33.fc44.aarch64
debugedit-5.2-3.fc44.aarch64
diffutils-3.12-3.fc43.aarch64
dwz-0.16-2.fc43.aarch64
ed-1.22.2-1.fc44.aarch64
efi-srpm-macros-6-4.fc43.noarch
elfutils-0.193-3.fc43.aarch64
elfutils-debuginfod-client-0.193-3.fc43.aarch64
elfutils-default-yama-scope-0.193-3.fc43.noarch
elfutils-libelf-0.193-3.fc43.aarch64
elfutils-libs-0.193-3.fc43.aarch64
fedora-gpg-keys-44-0.1.noarch
fedora-release-44-0.3.noarch
fedora-release-common-44-0.3.noarch
fedora-release-identity-basic-44-0.3.noarch
fedora-repos-44-0.1.noarch
fedora-repos-rawhide-44-0.1.noarch
file-5.46-8.fc44.aarch64
file-libs-5.46-8.fc44.aarch64
filesystem-3.18-50.fc43.aarch64
filesystem-srpm-macros-3.18-50.fc43.noarch
findutils-4.10.0-6.fc43.aarch64
fonts-srpm-macros-5.0.0-1.fc44.noarch
forge-srpm-macros-0.4.0-3.fc43.noarch
fpc-srpm-macros-1.3-15.fc43.noarch
gap-srpm-macros-2-1.fc44.noarch
gawk-5.3.2-2.fc43.aarch64
gdb-minimal-16.3-6.fc44.aarch64
gdbm-libs-1.23-10.fc43.aarch64
ghc-srpm-macros-1.9.2-3.fc43.noarch
glibc-2.42.9000-5.fc44.aarch64
glibc-common-2.42.9000-5.fc44.aarch64
glibc-gconv-extra-2.42.9000-5.fc44.aarch64
glibc-minimal-langpack-2.42.9000-5.fc44.aarch64
gmp-6.3.0-4.fc44.aarch64
gnat-srpm-macros-6-8.fc43.noarch
gnulib-l10n-20241231-1.fc44.noarch
gnupg2-2.4.8-4.fc43.aarch64
gnupg2-dirmngr-2.4.8-4.fc43.aarch64
gnupg2-gpg-agent-2.4.8-4.fc43.aarch64
gnupg2-gpgconf-2.4.8-4.fc43.aarch64
gnupg2-keyboxd-2.4.8-4.fc43.aarch64
gnupg2-verify-2.4.8-4.fc43.aarch64
gnutls-3.8.10-5.fc44.aarch64
go-srpm-macros-3.8.0-1.fc44.noarch
gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b
gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-3.fc43.noarch
grep-3.12-2.fc43.aarch64
gzip-1.14-1.fc44.aarch64
ima-evm-utils-libs-1.6.2-6.fc43.aarch64
info-7.2-6.fc43.aarch64
jansson-2.14-3.fc43.aarch64
java-srpm-macros-1-7.fc43.noarch
json-c-0.18-7.fc43.aarch64
kernel-srpm-macros-1.0-27.fc43.noarch
keyutils-libs-1.6.3-6.fc43.aarch64
krb5-libs-1.21.3-8.fc44.aarch64
libacl-2.3.2-4.fc43.aarch64
libarchive-3.8.1-3.fc43.aarch64
libassuan-2.5.7-4.fc43.aarch64
libattr-2.5.2-6.fc43.aarch64
libblkid-2.41.1-17.fc44.aarch64
libbrotli-1.1.0-10.fc44.aarch64
libcap-2.76-3.fc44.aarch64
libcap-ng-0.8.5-8.fc44.aarch64
libcom_err-1.47.3-2.fc43.aarch64
libcurl-8.16.0-1.fc44.aarch64
libeconf-0.7.9-2.fc43.aarch64
libevent-2.1.12-16.fc43.aarch64
libfdisk-2.41.1-17.fc44.aarch64
libffi-3.5.2-1.fc44.aarch64
libfsverity-1.6-3.fc43.aarch64
libgcc-15.2.1-2.fc44.aarch64
libgcrypt-1.11.1-2.fc43.aarch64
libgomp-15.2.1-2.fc44.aarch64
libgpg-error-1.55-2.fc43.aarch64
libidn2-2.3.8-2.fc43.aarch64
libksba-1.6.7-4.fc43.aarch64
liblastlog2-2.41.1-17.fc44.aarch64
libmount-2.41.1-17.fc44.aarch64
libnghttp2-1.67.1-1.fc44.aarch64
libpkgconf-2.3.0-3.fc43.aarch64
libpsl-0.21.5-6.fc43.aarch64
libselinux-3.9-5.fc44.aarch64
libselinux-utils-3.9-5.fc44.aarch64
libsemanage-3.9-4.fc44.aarch64
libsepol-3.9-2.fc43.aarch64
libsmartcols-2.41.1-17.fc44.aarch64
libssh-0.11.3-1.fc44.aarch64
libssh-config-0.11.3-1.fc44.noarch
libstdc++-15.2.1-2.fc44.aarch64
libtasn1-4.20.0-2.fc43.aarch64
libtool-ltdl-2.5.4-7.fc43.aarch64
libunistring-1.1-10.fc43.aarch64
libusb1-1.0.29-4.fc44.aarch64
libuuid-2.41.1-17.fc44.aarch64
libverto-0.3.2-11.fc43.aarch64
libxcrypt-4.4.38-9.fc44.aarch64
libxml2-2.12.10-5.fc44.aarch64
libzstd-1.5.7-3.fc44.aarch64
linkdupes-0.7.2-2.fc44.aarch64
lua-libs-5.4.8-2.fc43.aarch64
lua-srpm-macros-1-16.fc43.noarch
lz4-libs-1.10.0-3.fc43.aarch64
mpfr-4.2.2-2.fc43.aarch64
ncurses-base-6.5-7.20250614.fc43.noarch
ncurses-libs-6.5-7.20250614.fc43.aarch64
nettle-3.10.1-2.fc43.aarch64
npth-1.8-3.fc43.aarch64
ocaml-srpm-macros-11-2.fc43.noarch
openblas-srpm-macros-2-20.fc43.noarch
openldap-2.6.10-4.fc44.aarch64
openssl-libs-3.5.1-3.fc44.aarch64
p11-kit-0.25.8-1.fc44.aarch64
p11-kit-trust-0.25.8-1.fc44.aarch64
package-notes-srpm-macros-0.5-14.fc43.noarch
pam-libs-1.7.1-3.fc43.aarch64
patch-2.8-2.fc43.aarch64
pcre2-10.46-1.fc44.aarch64
pcre2-syntax-10.46-1.fc44.noarch
perl-srpm-macros-1-60.fc43.noarch
pkgconf-2.3.0-3.fc43.aarch64
pkgconf-m4-2.3.0-3.fc43.noarch
pkgconf-pkg-config-2.3.0-3.fc43.aarch64
policycoreutils-3.9-5.fc44.aarch64
popt-1.19-9.fc43.aarch64
publicsuffix-list-dafsa-20250616-2.fc43.noarch
pyproject-srpm-macros-1.18.4-1.fc44.noarch
python-srpm-macros-3.14-8.fc44.noarch
qt5-srpm-macros-5.15.17-2.fc43.noarch
qt6-srpm-macros-6.10.0~rc-1.fc44.noarch
readline-8.3-2.fc43.aarch64
redhat-rpm-config-343-14.fc44.noarch
rpm-6.0.0-1.fc44.aarch64
rpm-build-6.0.0-1.fc44.aarch64
rpm-build-libs-6.0.0-1.fc44.aarch64
rpm-libs-6.0.0-1.fc44.aarch64
rpm-plugin-selinux-6.0.0-1.fc44.aarch64
rpm-sequoia-1.9.0-2.fc43.aarch64
rpm-sign-libs-6.0.0-1.fc44.aarch64
rust-srpm-macros-26.4-1.fc44.noarch
sed-4.9-5.fc43.aarch64
selinux-policy-42.11-2.fc44.noarch
selinux-policy-targeted-42.11-2.fc44.noarch
setup-2.15.0-26.fc43.noarch
shadow-utils-4.18.0-3.fc43.aarch64
sqlite-libs-3.50.4-1.fc44.aarch64
systemd-libs-258-1.fc44.aarch64
systemd-standalone-sysusers-258-1.fc44.aarch64
tar-1.35-6.fc43.aarch64
tpm2-tss-4.1.3-8.fc43.aarch64
tree-sitter-srpm-macros-0.4.2-1.fc43.noarch
unzip-6.0-68.fc44.aarch64
util-linux-2.41.1-17.fc44.aarch64
util-linux-core-2.41.1-17.fc44.aarch64
which-2.23-3.fc43.aarch64
xxhash-libs-0.8.3-3.fc43.aarch64
xz-5.8.1-2.fc43.aarch64
xz-libs-5.8.1-2.fc43.aarch64
zig-srpm-macros-1-5.fc43.noarch
zip-3.0-44.fc43.aarch64
zlib-ng-compat-2.2.5-2.fc44.aarch64
zstd-1.5.7-3.fc44.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1753228800
Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1759572895.816751/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-sjl24137/percolator/percolator.spec) Config(child) 0 minutes 25 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/percolator-3.08-1.fc44.src.rpm)  Config(fedora-rawhide-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1759572895.816751/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1759572895.816751/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1759572895.816751/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-6.0.0-1.fc44.aarch64
  rpm-sequoia-1.9.0-2.fc43.aarch64
  dnf5-5.2.17.0-2.fc44.aarch64
  dnf5-plugins-5.2.17.0-2.fc44.aarch64
Finish: chroot init
Start: build phase for percolator-3.08-1.fc44.src.rpm
Start: build setup for percolator-3.08-1.fc44.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1753228800
Wrote: /builddir/build/SRPMS/percolator-3.08-1.fc44.src.rpm
Updating and loading repositories:
 Copr repository                        100% | 101.7 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 188.8 KiB/s |  14.9 KiB |  00m00s
Repositories loaded.
Package                    Arch    Version             Repository      Size
Installing:
 boost-devel               aarch64 1.83.0-17.fc44      fedora     143.0 MiB
 boost-static              aarch64 1.83.0-17.fc44      fedora     384.6 MiB
 bzip2-devel               aarch64 1.0.8-21.fc43       fedora     309.8 KiB
 cmake                     aarch64 3.31.6-4.fc43       fedora      29.7 MiB
 eigen3-devel              noarch  3.4.0-18.fc43       fedora       8.4 MiB
 gcc                       aarch64 15.2.1-2.fc44       fedora      99.5 MiB
 gcc-c++                   aarch64 15.2.1-2.fc44       fedora      38.9 MiB
 gtest-devel               aarch64 1.17.0-1.fc44       copr_base    1.1 MiB
 libtirpc-devel            aarch64 1.3.7-0.fc44        fedora     251.6 KiB
 make                      aarch64 1:4.4.1-11.fc43     fedora       1.8 MiB
 python3-devel             aarch64 3.14.0~rc3-1.fc44   fedora       1.9 MiB
 sqlite-devel              aarch64 3.50.4-1.fc44       fedora     684.1 KiB
 tokyocabinet-devel        aarch64 1.4.48-28.fc43      fedora     460.2 KiB
 xerces-c-devel            aarch64 3.3.0-8.fc43        fedora       4.1 MiB
 xsd                       aarch64 4.1.0-0.18.a11.fc43 fedora       4.7 MiB
 zlib-ng-compat-devel      aarch64 2.2.5-2.fc44        fedora     107.0 KiB
Installing dependencies:
 annobin-docs              noarch  12.99-1.fc43        fedora      98.9 KiB
 annobin-plugin-gcc        aarch64 12.99-1.fc43        fedora       1.0 MiB
 boost                     aarch64 1.83.0-17.fc44      fedora       1.3 KiB
 boost-atomic              aarch64 1.83.0-17.fc44      fedora      68.8 KiB
 boost-chrono              aarch64 1.83.0-17.fc44      fedora      69.4 KiB
 boost-container           aarch64 1.83.0-17.fc44      fedora      69.4 KiB
 boost-context             aarch64 1.83.0-17.fc44      fedora      68.3 KiB
 boost-contract            aarch64 1.83.0-17.fc44      fedora     134.7 KiB
 boost-coroutine           aarch64 1.83.0-17.fc44      fedora      69.1 KiB
 boost-date-time           aarch64 1.83.0-17.fc44      fedora      68.2 KiB
 boost-fiber               aarch64 1.83.0-17.fc44      fedora     134.4 KiB
 boost-filesystem          aarch64 1.83.0-17.fc44      fedora     134.8 KiB
 boost-graph               aarch64 1.83.0-17.fc44      fedora     334.0 KiB
 boost-iostreams           aarch64 1.83.0-17.fc44      fedora     134.2 KiB
 boost-json                aarch64 1.83.0-17.fc44      fedora     328.4 KiB
 boost-locale              aarch64 1.83.0-17.fc44      fedora     594.6 KiB
 boost-log                 aarch64 1.83.0-17.fc44      fedora       1.5 MiB
 boost-math                aarch64 1.83.0-17.fc44      fedora     862.2 KiB
 boost-nowide              aarch64 1.83.0-17.fc44      fedora      68.8 KiB
 boost-numpy3              aarch64 1.83.0-17.fc44      fedora      69.4 KiB
 boost-program-options     aarch64 1.83.0-17.fc44      fedora     267.4 KiB
 boost-python3             aarch64 1.83.0-17.fc44      fedora     268.3 KiB
 boost-random              aarch64 1.83.0-17.fc44      fedora      69.5 KiB
 boost-regex               aarch64 1.83.0-17.fc44      fedora     266.3 KiB
 boost-serialization       aarch64 1.83.0-17.fc44      fedora     467.4 KiB
 boost-stacktrace          aarch64 1.83.0-17.fc44      fedora     203.7 KiB
 boost-system              aarch64 1.83.0-17.fc44      fedora      68.2 KiB
 boost-test                aarch64 1.83.0-17.fc44      fedora     728.4 KiB
 boost-thread              aarch64 1.83.0-17.fc44      fedora     136.3 KiB
 boost-timer               aarch64 1.83.0-17.fc44      fedora      69.0 KiB
 boost-type_erasure        aarch64 1.83.0-17.fc44      fedora      70.1 KiB
 boost-wave                aarch64 1.83.0-17.fc44      fedora     854.2 KiB
 cmake-data                noarch  3.31.6-4.fc43       fedora       8.5 MiB
 cmake-filesystem          aarch64 3.31.6-4.fc43       fedora       0.0   B
 cmake-rpm-macros          noarch  3.31.6-4.fc43       fedora       7.7 KiB
 cpp                       aarch64 15.2.1-2.fc44       fedora      35.5 MiB
 emacs-filesystem          noarch  1:30.0-5.fc43       fedora       0.0   B
 expat                     aarch64 2.7.2-1.fc44        fedora     358.6 KiB
 flexiblas                 aarch64 3.4.5-5.fc44        fedora      50.4 KiB
 flexiblas-netlib          aarch64 3.4.5-5.fc44        fedora       9.3 MiB
 flexiblas-openblas-openmp aarch64 3.4.5-5.fc44        fedora      67.3 KiB
 gcc-plugin-annobin        aarch64 15.2.1-2.fc44       fedora      69.2 KiB
 glibc-devel               aarch64 2.42.9000-5.fc44    fedora       2.3 MiB
 gmock                     aarch64 1.17.0-1.fc44       copr_base  202.1 KiB
 gtest                     aarch64 1.17.0-1.fc44       copr_base  526.3 KiB
 jsoncpp                   aarch64 1.9.6-2.fc43        fedora     271.8 KiB
 kernel-headers            aarch64 6.17.0-63.fc44      fedora       6.6 MiB
 libasan                   aarch64 15.2.1-2.fc44       fedora       1.5 MiB
 libatomic                 aarch64 15.2.1-2.fc44       fedora      68.8 KiB
 libcutl                   aarch64 1.10.0-33.fc43      fedora       1.0 MiB
 libgfortran               aarch64 15.2.1-2.fc44       fedora       1.7 MiB
 libicu                    aarch64 77.1-1.fc43         fedora      36.5 MiB
 libicu-devel              aarch64 77.1-1.fc43         fedora       5.1 MiB
 libmpc                    aarch64 1.3.1-8.fc43        fedora     152.7 KiB
 libstdc++-devel           aarch64 15.2.1-2.fc44       fedora      36.4 MiB
 libtirpc                  aarch64 1.3.7-0.fc44        fedora     210.6 KiB
 libubsan                  aarch64 15.2.1-2.fc44       fedora     475.5 KiB
 libuv                     aarch64 1:1.51.0-2.fc43     fedora     605.4 KiB
 libxcrypt-devel           aarch64 4.4.38-9.fc44       fedora      30.8 KiB
 mpdecimal                 aarch64 4.0.1-2.fc43        fedora     281.2 KiB
 openblas                  aarch64 0.3.29-2.fc43       fedora     111.7 KiB
 openblas-openmp           aarch64 0.3.29-2.fc43       fedora      20.4 MiB
 pyproject-rpm-macros      noarch  1.18.4-1.fc44       fedora     114.9 KiB
 python-pip-wheel          noarch  25.2-4.fc44         fedora       1.2 MiB
 python-rpm-macros         noarch  3.14-8.fc44         fedora      27.6 KiB
 python3                   aarch64 3.14.0~rc3-1.fc44   fedora      84.9 KiB
 python3-libs              aarch64 3.14.0~rc3-1.fc44   fedora      44.9 MiB
 python3-numpy             aarch64 1:2.3.3-2.fc44      fedora      35.2 MiB
 python3-numpy-f2py        aarch64 1:2.3.3-2.fc44      fedora       2.1 MiB
 python3-packaging         noarch  25.0-7.fc44         fedora     607.4 KiB
 python3-rpm-generators    noarch  14-13.fc43          fedora      81.7 KiB
 python3-rpm-macros        noarch  3.14-8.fc44         fedora       6.5 KiB
 rhash                     aarch64 1.4.5-3.fc43        fedora     394.8 KiB
 sqlite                    aarch64 3.50.4-1.fc44       fedora       1.9 MiB
 tokyocabinet              aarch64 1.4.48-28.fc43      fedora       2.0 MiB
 tzdata                    noarch  2025b-3.fc43        fedora       1.6 MiB
 vim-filesystem            noarch  2:9.1.1818-1.fc44   fedora      40.0   B
 xerces-c                  aarch64 3.3.0-8.fc43        fedora       3.7 MiB

Transaction Summary:
 Installing:        94 packages

Total size of inbound packages is 194 MiB. Need to download 86 MiB.
After this operation, 990 MiB extra will be used (install 990 MiB, remove 0 B).
[ 1/94] bzip2-devel-0:1.0.8-21.fc43.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 2/94] cmake-0:3.31.6-4.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 3/94] gcc-0:15.2.1-2.fc44.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 4/94] gcc-c++-0:15.2.1-2.fc44.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 5/94] make-1:4.4.1-11.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 6/94] zlib-ng-compat-devel-0:2.2.5-2. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 7/94] gtest-devel-0:1.17.0-1.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 8/94] libicu-devel-0:77.1-1.fc43.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[ 9/94] cmake-data-0:3.31.6-4.fc43.noar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[10/94] cmake-filesystem-0:3.31.6-4.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[11/94] expat-0:2.7.2-1.fc44.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[12/94] jsoncpp-0:1.9.6-2.fc43.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[13/94] libuv-1:1.51.0-2.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[14/94] rhash-0:1.4.5-3.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[15/94] cpp-0:15.2.1-2.fc44.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[16/94] glibc-devel-0:2.42.9000-5.fc44. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[17/94] libasan-0:15.2.1-2.fc44.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[18/94] libatomic-0:15.2.1-2.fc44.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[19/94] libmpc-0:1.3.1-8.fc43.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[20/94] libubsan-0:15.2.1-2.fc44.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[21/94] libstdc++-devel-0:15.2.1-2.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[22/94] libtirpc-0:1.3.7-0.fc44.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[23/94] python3-0:3.14.0~rc3-1.fc44.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[24/94] python3-libs-0:3.14.0~rc3-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[25/94] gmock-0:1.17.0-1.fc44.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[26/94] gtest-0:1.17.0-1.fc44.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[27/94] libicu-0:77.1-1.fc43.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[28/94] emacs-filesystem-1:30.0-5.fc43. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[29/94] vim-filesystem-2:9.1.1818-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[30/94] kernel-headers-0:6.17.0-63.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[31/94] libxcrypt-devel-0:4.4.38-9.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[32/94] mpdecimal-0:4.0.1-2.fc43.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[33/94] python-pip-wheel-0:25.2-4.fc44. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[34/94] tzdata-0:2025b-3.fc43.noarch    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[35/94] annobin-plugin-gcc-0:12.99-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[36/94] gcc-plugin-annobin-0:15.2.1-2.f 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[37/94] annobin-docs-0:12.99-1.fc43.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[38/94] cmake-rpm-macros-0:3.31.6-4.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[39/94] python3-packaging-0:25.0-7.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                          
[40/94] eigen3-devel-0:3.4.0-18.fc43.no 100% |  42.1 MiB/s |   1.2 MiB |  00m00s
[41/94] libtirpc-devel-0:1.3.7-0.fc44.a 100% |  15.3 MiB/s | 125.7 KiB |  00m00s
[42/94] sqlite-devel-0:3.50.4-1.fc44.aa 100% |  29.7 MiB/s | 151.9 KiB |  00m00s
[43/94] boost-devel-0:1.83.0-17.fc44.aa 100% | 168.6 MiB/s |  14.2 MiB |  00m00s
[44/94] tokyocabinet-devel-0:1.4.48-28. 100% |   1.2 MiB/s |  88.6 KiB |  00m00s
[45/94] python3-devel-0:3.14.0~rc3-1.fc 100% |  70.8 MiB/s | 434.8 KiB |  00m00s
[46/94] xsd-0:4.1.0-0.18.a11.fc43.aarch 100% |  10.0 MiB/s |   1.0 MiB |  00m00s
[47/94] xerces-c-devel-0:3.3.0-8.fc43.a 100% |   3.6 MiB/s | 513.3 KiB |  00m00s
[48/94] boost-0:1.83.0-17.fc44.aarch64  100% |   3.8 MiB/s |  11.8 KiB |  00m00s
[49/94] boost-numpy3-0:1.83.0-17.fc44.a 100% |   8.7 MiB/s |  26.8 KiB |  00m00s
[50/94] sqlite-0:3.50.4-1.fc44.aarch64  100% | 125.8 MiB/s | 901.4 KiB |  00m00s
[51/94] tokyocabinet-0:1.4.48-28.fc43.a 100% |  14.1 MiB/s | 506.2 KiB |  00m00s
[52/94] xerces-c-0:3.3.0-8.fc43.aarch64 100% |  16.4 MiB/s | 939.0 KiB |  00m00s
[53/94] boost-atomic-0:1.83.0-17.fc44.a 100% |   8.3 MiB/s |  17.0 KiB |  00m00s
[54/94] boost-chrono-0:1.83.0-17.fc44.a 100% |  11.2 MiB/s |  23.0 KiB |  00m00s
[55/94] boost-container-0:1.83.0-17.fc4 100% |  18.2 MiB/s |  37.3 KiB |  00m00s
[56/94] boost-context-0:1.83.0-17.fc44. 100% |   4.7 MiB/s |  14.6 KiB |  00m00s
[57/94] boost-contract-0:1.83.0-17.fc44 100% |  20.4 MiB/s |  41.8 KiB |  00m00s
[58/94] boost-coroutine-0:1.83.0-17.fc4 100% |   5.8 MiB/s |  17.9 KiB |  00m00s
[59/94] boost-date-time-0:1.83.0-17.fc4 100% |   4.4 MiB/s |  13.5 KiB |  00m00s
[60/94] boost-fiber-0:1.83.0-17.fc44.aa 100% |  19.3 MiB/s |  39.6 KiB |  00m00s
[61/94] boost-filesystem-0:1.83.0-17.fc 100% |  30.2 MiB/s |  61.9 KiB |  00m00s
[62/94] boost-graph-0:1.83.0-17.fc44.aa 100% |  34.9 MiB/s | 142.9 KiB |  00m00s
[63/94] boost-iostreams-0:1.83.0-17.fc4 100% |  18.4 MiB/s |  37.8 KiB |  00m00s
[64/94] boost-json-0:1.83.0-17.fc44.aar 100% |  34.3 MiB/s | 140.6 KiB |  00m00s
[65/94] boost-locale-0:1.83.0-17.fc44.a 100% |  47.5 MiB/s | 194.4 KiB |  00m00s
[66/94] boost-log-0:1.83.0-17.fc44.aarc 100% |  89.2 MiB/s | 456.7 KiB |  00m00s
[67/94] boost-math-0:1.83.0-17.fc44.aar 100% |  49.5 MiB/s | 253.7 KiB |  00m00s
[68/94] boost-nowide-0:1.83.0-17.fc44.a 100% |   8.9 MiB/s |  18.3 KiB |  00m00s
[69/94] boost-program-options-0:1.83.0- 100% |  25.2 MiB/s | 103.3 KiB |  00m00s
[70/94] libcutl-0:1.10.0-33.fc43.aarch6 100% |   3.1 MiB/s | 302.6 KiB |  00m00s
[71/94] boost-python3-0:1.83.0-17.fc44. 100% |  21.8 MiB/s |  89.3 KiB |  00m00s
[72/94] boost-random-0:1.83.0-17.fc44.a 100% |  10.6 MiB/s |  21.7 KiB |  00m00s
[73/94] boost-regex-0:1.83.0-17.fc44.aa 100% |  26.7 MiB/s | 109.2 KiB |  00m00s
[74/94] boost-serialization-0:1.83.0-17 100% |  30.0 MiB/s | 122.7 KiB |  00m00s
[75/94] boost-stacktrace-0:1.83.0-17.fc 100% |  13.6 MiB/s |  27.8 KiB |  00m00s
[76/94] boost-system-0:1.83.0-17.fc44.a 100% |   6.6 MiB/s |  13.4 KiB |  00m00s
[77/94] boost-test-0:1.83.0-17.fc44.aar 100% |  43.2 MiB/s | 221.3 KiB |  00m00s
[78/94] boost-thread-0:1.83.0-17.fc44.a 100% |  18.5 MiB/s |  56.9 KiB |  00m00s
[79/94] boost-timer-0:1.83.0-17.fc44.aa 100% |   6.2 MiB/s |  19.1 KiB |  00m00s
[80/94] boost-type_erasure-0:1.83.0-17. 100% |   9.6 MiB/s |  29.4 KiB |  00m00s
[81/94] boost-wave-0:1.83.0-17.fc44.aar 100% |  55.9 MiB/s | 229.1 KiB |  00m00s
[82/94] boost-static-0:1.83.0-17.fc44.a 100% | 114.3 MiB/s |  48.9 MiB |  00m00s
[83/94] flexiblas-netlib-0:3.4.5-5.fc44 100% |  46.8 MiB/s |   2.9 MiB |  00m00s
[84/94] flexiblas-0:3.4.5-5.fc44.aarch6 100% |   8.5 MiB/s |  26.0 KiB |  00m00s
[85/94] python3-numpy-f2py-1:2.3.3-2.fc 100% |  29.3 MiB/s | 510.5 KiB |  00m00s
[86/94] flexiblas-openblas-openmp-0:3.4 100% |   5.3 MiB/s |  16.3 KiB |  00m00s
[87/94] libgfortran-0:15.2.1-2.fc44.aar 100% |  65.8 MiB/s | 471.8 KiB |  00m00s
[88/94] openblas-0:0.3.29-2.fc43.aarch6 100% |   6.9 MiB/s |  42.2 KiB |  00m00s
[89/94] pyproject-rpm-macros-0:1.18.4-1 100% |   8.8 MiB/s |  44.9 KiB |  00m00s
[90/94] python-rpm-macros-0:3.14-8.fc44 100% |   6.3 MiB/s |  19.5 KiB |  00m00s
[91/94] openblas-openmp-0:0.3.29-2.fc43 100% | 149.0 MiB/s |   3.9 MiB |  00m00s
[92/94] python3-rpm-generators-0:14-13. 100% |   7.0 MiB/s |  28.5 KiB |  00m00s
[93/94] python3-rpm-macros-0:3.14-8.fc4 100% |   5.9 MiB/s |  12.0 KiB |  00m00s
[94/94] python3-numpy-1:2.3.3-2.fc44.aa 100% |  34.9 MiB/s |   6.8 MiB |  00m00s
--------------------------------------------------------------------------------
[94/94] Total                           100% | 128.6 MiB/s |  86.3 MiB |  00m01s
Running transaction
[ 1/96] Verify package files            100% | 154.0   B/s |  94.0   B |  00m01s
[ 2/96] Prepare transaction             100% | 456.0   B/s |  94.0   B |  00m00s
[ 3/96] Installing boost-system-0:1.83. 100% |  67.6 MiB/s |  69.2 KiB |  00m00s
[ 4/96] Installing boost-chrono-0:1.83. 100% |  68.7 MiB/s |  70.4 KiB |  00m00s
[ 5/96] Installing cmake-filesystem-0:3 100% |   3.7 MiB/s |   7.6 KiB |  00m00s
[ 6/96] Installing boost-thread-0:1.83. 100% | 134.1 MiB/s | 137.3 KiB |  00m00s
[ 7/96] Installing libicu-0:77.1-1.fc43 100% | 347.9 MiB/s |  36.5 MiB |  00m00s
[ 8/96] Installing boost-regex-0:1.83.0 100% | 130.5 MiB/s | 267.3 KiB |  00m00s
[ 9/96] Installing python-rpm-macros-0: 100% |  27.8 MiB/s |  28.5 KiB |  00m00s
[10/96] Installing boost-context-0:1.83 100% |  67.7 MiB/s |  69.4 KiB |  00m00s
[11/96] Installing boost-atomic-0:1.83. 100% |  68.2 MiB/s |  69.8 KiB |  00m00s
[12/96] Installing boost-filesystem-0:1 100% | 132.6 MiB/s | 135.8 KiB |  00m00s
[13/96] Installing libmpc-0:1.3.1-8.fc4 100% | 150.6 MiB/s | 154.2 KiB |  00m00s
[14/96] Installing expat-0:2.7.2-1.fc44 100% |  18.5 MiB/s | 360.6 KiB |  00m00s
[15/96] Installing python3-rpm-macros-0 100% |   6.6 MiB/s |   6.8 KiB |  00m00s
[16/96] Installing libgfortran-0:15.2.1 100% | 342.3 MiB/s |   1.7 MiB |  00m00s
[17/96] Installing boost-date-time-0:1. 100% |  67.6 MiB/s |  69.3 KiB |  00m00s
[18/96] Installing boost-container-0:1. 100% |  68.8 MiB/s |  70.4 KiB |  00m00s
[19/96] Installing gtest-0:1.17.0-1.fc4 100% | 257.7 MiB/s | 527.7 KiB |  00m00s
[20/96] Installing xerces-c-0:3.3.0-8.f 100% | 367.1 MiB/s |   3.7 MiB |  00m00s
[21/96] Installing make-1:4.4.1-11.fc43 100% |  77.1 MiB/s |   1.9 MiB |  00m00s
[22/96] Installing gmock-0:1.17.0-1.fc4 100% | 198.7 MiB/s | 203.5 KiB |  00m00s
[23/96] Installing boost-json-0:1.83.0- 100% | 160.8 MiB/s | 329.4 KiB |  00m00s
[24/96] Installing boost-wave-0:1.83.0- 100% | 278.4 MiB/s | 855.2 KiB |  00m00s
[25/96] Installing pyproject-rpm-macros 100% | 114.1 MiB/s | 116.8 KiB |  00m00s
[26/96] Installing libcutl-0:1.10.0-33. 100% | 255.2 MiB/s |   1.0 MiB |  00m00s
[27/96] Installing cpp-0:15.2.1-2.fc44. 100% | 279.3 MiB/s |  35.5 MiB |  00m00s
[28/96] Installing boost-fiber-0:1.83.0 100% | 132.2 MiB/s | 135.4 KiB |  00m00s
[29/96] Installing boost-log-0:1.83.0-1 100% | 297.6 MiB/s |   1.5 MiB |  00m00s
[30/96] Installing boost-coroutine-0:1. 100% |  68.4 MiB/s |  70.1 KiB |  00m00s
[31/96] Installing boost-graph-0:1.83.0 100% | 163.6 MiB/s | 335.0 KiB |  00m00s
[32/96] Installing libicu-devel-0:77.1- 100% | 146.8 MiB/s |   5.1 MiB |  00m00s
[33/96] Installing boost-locale-0:1.83. 100% | 193.9 MiB/s | 595.6 KiB |  00m00s
[34/96] Installing boost-type_erasure-0 100% |  69.3 MiB/s |  70.9 KiB |  00m00s
[35/96] Installing boost-timer-0:1.83.0 100% |  68.3 MiB/s |  70.0 KiB |  00m00s
[36/96] Installing annobin-docs-0:12.99 100% |  97.7 MiB/s | 100.1 KiB |  00m00s
[37/96] Installing openblas-0:0.3.29-2. 100% | 110.8 MiB/s | 113.5 KiB |  00m00s
[38/96] Installing openblas-openmp-0:0. 100% | 433.8 MiB/s |  20.4 MiB |  00m00s
[39/96] Installing flexiblas-netlib-0:3 100% | 210.8 MiB/s |   9.3 MiB |  00m00s
[40/96] Installing flexiblas-0:3.4.5-5. 100% |  50.4 MiB/s |  51.6 KiB |  00m00s
[41/96] Installing flexiblas-openblas-o 100% |  13.3 MiB/s |  68.2 KiB |  00m00s
[42/96] Installing tzdata-0:2025b-3.fc4 100% |  37.1 MiB/s |   1.9 MiB |  00m00s
[43/96] Installing python-pip-wheel-0:2 100% | 393.3 MiB/s |   1.2 MiB |  00m00s
[44/96] Installing mpdecimal-0:4.0.1-2. 100% |  39.4 MiB/s | 282.7 KiB |  00m00s
[45/96] Installing python3-libs-0:3.14. 100% | 261.6 MiB/s |  45.3 MiB |  00m00s
[46/96] Installing python3-0:3.14.0~rc3 100% |   4.7 MiB/s |  86.7 KiB |  00m00s
[47/96] Installing boost-python3-0:1.83 100% | 131.5 MiB/s | 269.3 KiB |  00m00s
[48/96] Installing python3-numpy-f2py-1 100% |  60.3 MiB/s |   2.2 MiB |  00m00s
[49/96] Installing python3-numpy-1:2.3. 100% | 248.1 MiB/s |  35.5 MiB |  00m00s
[50/96] Installing cmake-rpm-macros-0:3 100% |   8.1 MiB/s |   8.3 KiB |  00m00s
[51/96] Installing boost-numpy3-0:1.83. 100% |  68.7 MiB/s |  70.4 KiB |  00m00s
[52/96] Installing python3-packaging-0: 100% | 151.3 MiB/s | 619.9 KiB |  00m00s
[53/96] Installing python3-rpm-generato 100% |  27.0 MiB/s |  82.9 KiB |  00m00s
[54/96] Installing kernel-headers-0:6.1 100% | 137.9 MiB/s |   6.8 MiB |  00m00s
[55/96] Installing glibc-devel-0:2.42.9 100% | 110.6 MiB/s |   2.3 MiB |  00m00s
[56/96] Installing libxcrypt-devel-0:4. 100% |  32.3 MiB/s |  33.1 KiB |  00m00s
[57/96] Installing vim-filesystem-2:9.1 100% |   4.6 MiB/s |   4.7 KiB |  00m00s
[58/96] Installing emacs-filesystem-1:3 100% |   0.0   B/s | 544.0   B |  00m00s
[59/96] Installing boost-test-0:1.83.0- 100% | 237.6 MiB/s | 729.9 KiB |  00m00s
[60/96] Installing boost-stacktrace-0:1 100% | 200.8 MiB/s | 205.6 KiB |  00m00s
[61/96] Installing boost-serialization- 100% | 228.9 MiB/s | 468.9 KiB |  00m00s
[62/96] Installing boost-random-0:1.83. 100% |  68.8 MiB/s |  70.5 KiB |  00m00s
[63/96] Installing boost-program-option 100% | 262.1 MiB/s | 268.4 KiB |  00m00s
[64/96] Installing boost-nowide-0:1.83. 100% |  68.2 MiB/s |  69.8 KiB |  00m00s
[65/96] Installing boost-math-0:1.83.0- 100% | 281.7 MiB/s | 865.5 KiB |  00m00s
[66/96] Installing boost-iostreams-0:1. 100% | 132.0 MiB/s | 135.2 KiB |  00m00s
[67/96] Installing boost-contract-0:1.8 100% | 132.5 MiB/s | 135.7 KiB |  00m00s
[68/96] Installing boost-0:1.83.0-17.fc 100% |  45.2 KiB/s |   1.7 KiB |  00m00s
[69/96] Installing boost-devel-0:1.83.0 100% | 191.3 MiB/s | 145.8 MiB |  00m01s
[70/96] Installing tokyocabinet-0:1.4.4 100% |  79.1 MiB/s |   2.0 MiB |  00m00s
[71/96] Installing sqlite-0:3.50.4-1.fc 100% |  77.8 MiB/s |   1.9 MiB |  00m00s
[72/96] Installing libtirpc-0:1.3.7-0.f 100% |  51.9 MiB/s | 212.4 KiB |  00m00s
[73/96] Installing libstdc++-devel-0:15 100% | 380.8 MiB/s |  36.6 MiB |  00m00s
[74/96] Installing libubsan-0:15.2.1-2. 100% | 232.6 MiB/s | 476.3 KiB |  00m00s
[75/96] Installing libatomic-0:15.2.1-2 100% |  68.0 MiB/s |  69.6 KiB |  00m00s
[76/96] Installing libasan-0:15.2.1-2.f 100% | 256.8 MiB/s |   1.5 MiB |  00m00s
[77/96] Installing gcc-0:15.2.1-2.fc44. 100% | 326.2 MiB/s |  99.5 MiB |  00m00s
[78/96] Installing rhash-0:1.4.5-3.fc43 100% |  18.6 MiB/s | 400.1 KiB |  00m00s
[79/96] Installing libuv-1:1.51.0-2.fc4 100% | 198.0 MiB/s | 608.2 KiB |  00m00s
[80/96] Installing jsoncpp-0:1.9.6-2.fc 100% | 133.5 MiB/s | 273.3 KiB |  00m00s
[81/96] Installing cmake-0:3.31.6-4.fc4 100% | 272.2 MiB/s |  29.7 MiB |  00m00s
[82/96] Installing cmake-data-0:3.31.6- 100% |  72.5 MiB/s |   9.1 MiB |  00m00s
[83/96] Installing gcc-c++-0:15.2.1-2.f 100% | 281.6 MiB/s |  38.9 MiB |  00m00s
[84/96] Installing annobin-plugin-gcc-0 100% |  62.4 MiB/s |   1.0 MiB |  00m00s
[85/96] Installing gcc-plugin-annobin-0 100% |   4.1 MiB/s |  70.8 KiB |  00m00s
[86/96] Installing libtirpc-devel-0:1.3 100% |  64.2 MiB/s | 263.1 KiB |  00m00s
[87/96] Installing sqlite-devel-0:3.50. 100% | 334.4 MiB/s | 684.8 KiB |  00m00s
[88/96] Installing tokyocabinet-devel-0 100% | 226.2 MiB/s | 463.3 KiB |  00m00s
[89/96] Installing boost-static-0:1.83. 100% | 494.4 MiB/s | 384.6 MiB |  00m01s
[90/96] Installing python3-devel-0:3.14 100% |  60.3 MiB/s |   2.0 MiB |  00m00s
[91/96] Installing xsd-0:4.1.0-0.18.a11 100% | 134.0 MiB/s |   4.7 MiB |  00m00s
[92/96] Installing gtest-devel-0:1.17.0 100% | 152.1 MiB/s |   1.1 MiB |  00m00s
[93/96] Installing xerces-c-devel-0:3.3 100% | 183.1 MiB/s |   4.2 MiB |  00m00s
[94/96] Installing eigen3-devel-0:3.4.0 100% | 217.1 MiB/s |   8.5 MiB |  00m00s
[95/96] Installing zlib-ng-compat-devel 100% | 106.0 MiB/s | 108.5 KiB |  00m00s
[96/96] Installing bzip2-devel-0:1.0.8- 100% |   1.8 MiB/s | 310.7 KiB |  00m00s
Warning: skipped OpenPGP checks for 3 packages from repository: copr_base
Complete!
Finish: build setup for percolator-3.08-1.fc44.src.rpm
Start: rpmbuild percolator-3.08-1.fc44.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1753228800
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.jOoKcG
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ddskGa
+ 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.BSQZ5K
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ mkdir -p percolator
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -S . -B redhat-linux-build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -B percolator -S ./ -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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=aarch64
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = aarch64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.3.0
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Locating CodeSynthesis library with XSDDIR set to 
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from                  : /usr/lib64/libtirpc.so
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.7s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_INSTALL_FULL_SBINDIR
    CMAKE_INSTALL_SBINDIR
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd
+ /usr/bin/cmake --build percolator -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/CMakeFiles/generate_xsd.dir/build.make src/CMakeFiles/generate_xsd.dir/depend
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/generate_xsd.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/CMakeFiles/generate_xsd.dir/build.make src/CMakeFiles/generate_xsd.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[  2%] Generating percolator_in.* from XSD
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
[  3%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
[  4%] Generating percolator_out.* from XSD
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --std c++11 --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/xml/percolator_in.xsd
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
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
[  5%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[  7%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[  7%] Built target generate_xsd
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[  8%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/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 CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/percolator_in.cxx
[  9%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[ 11%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[ 13%] Linking C static library libdblas.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1
a - CMakeFiles/dblas.dir/daxpy.c.o
a - CMakeFiles/dblas.dir/ddot.c.o
a - CMakeFiles/dblas.dir/dgemv.c.o
a - CMakeFiles/dblas.dir/dnrm2.c.o
a - CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ranlib libdblas.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 13%] Built target dblas
[ 14%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 16%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/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_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/percolator_out.cxx
[ 17%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:109:35: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
  109 |   std::unique_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                   ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:104:22: warning:   ‘xercesc_3_3::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  104 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:147:1: warning:   when initialized here [-Wreorder]
  147 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx: In member function ‘std::unique_ptr<xercesc_3_3::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:182:14: warning: unused variable ‘n’ [-Wunused-variable]
  182 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/parser.cxx:174:9: warning: unused variable ‘i’ [-Wunused-variable]
  174 |     int i(1);
      |         ^
[ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[ 20%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/serializer.cxx
[ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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);
      |        ^~~
[ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
[ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[ 29%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp:17:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
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();
      |                                ^~~~~~~~~~~
[ 35%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 35%] Built target picked_protein
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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;
      |                                          ^~~~~
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  122 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable]
  118 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  168 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable]
  157 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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()
      | ^~~~~~
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
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)
      |   ^~~~~~~~~~~
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
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);
      |        ^~~
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.h:16,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:39:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
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);
      |        ^~~
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
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,
      | ^~~~~~~~~~~~~~~~~~
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o
/usr/bin/ranlib libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 84%] Built target perclibrary
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 88%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
[ 88%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
[ 88%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
[ 89%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -DXSD_CXX11 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 90%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
[ 91%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[ 92%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
[ 95%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/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)
      |        ^
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);
      |        ^~~
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[ 97%] Built target qvality
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[100%] Built target gtest_unit
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a /usr/lib64/libxerces-c.so /usr/lib64/libtirpc.so -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
[100%] Built target percolator
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/CMakeFiles 0

+ mkdir -p src/fido
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -S . -B percolator -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -B src/fido -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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=aarch64 -DBUILD_TESTING:BOOL=ON
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = OFF
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = aarch64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.7s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_INSTALL_FULL_SBINDIR
    CMAKE_INSTALL_SBINDIR
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR
    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 -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[  3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
[  3%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
[  5%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
[  5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[  6%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[  7%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[  9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 13%] Linking C static library libdblas.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1
a - CMakeFiles/dblas.dir/daxpy.c.o
a - CMakeFiles/dblas.dir/ddot.c.o
a - CMakeFiles/dblas.dir/dgemv.c.o
a - CMakeFiles/dblas.dir/dnrm2.c.o
a - CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ranlib libdblas.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 13%] Built target dblas
[ 14%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[ 17%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
[ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
[ 19%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 22%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
[ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp:17:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
[ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportUniquePeptides_’ will be initialized after [-Wreorder]
  119 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:120:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  120 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:112:22: warning:   ‘bool XMLInterface::printExpMass_’ [-Wreorder]
  112 |   bool printDecoys_, printExpMass_;
      |                      ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:59:1: warning:   when initialized here [-Wreorder]
   59 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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;
      |                                          ^~~~~
[ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 32%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
[ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 36%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
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)
      |   ^~~~~~~~~~~
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 36%] Built target picked_protein
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
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;
      |           ^~~~~~~~~~~
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder]
  102 |       useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_;
      |       ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   86 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
   98 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:24,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
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);
      |        ^~~
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.h:16,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:39:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp:9:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o
/usr/bin/ranlib libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 82%] Built target perclibrary
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 84%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
[ 85%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
[ 86%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
[ 88%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 89%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
[ 90%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[ 92%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[ 98%] Built target qvality
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);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[100%] Built target percolator
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
[100%] Built target gtest_unit
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/fido/CMakeFiles 0

+ mkdir -p src/converters
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -S . -B src/fido -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -B src/converters -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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=aarch64 -DBUILD_TESTING:BOOL=ON
-- The C compiler identification is GNU 15.2.1
-- The CXX compiler identification is GNU 15.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = OFF
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = aarch64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0") found components: filesystem system
-- Finding GoogleTest...
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.17.0")
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70.0")
-- Configuring done (1.7s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

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


-- Build files have been written to: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/cmake --build src/converters -j4 --verbose
Change Dir: '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'

Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j4
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 -B/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/CMakeFiles /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters//CMakeFiles/progress.marks
/usr/bin/gmake  -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas/CMakeFiles/dblas.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/dblas/CMakeFiles/dblas.dir/build.make src/dblas/CMakeFiles/dblas.dir/build
/usr/bin/gmake  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[  2%] Building C object src/dblas/CMakeFiles/dblas.dir/daxpy.c.o
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
[  3%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
[  5%] Building C object src/dblas/CMakeFiles/dblas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/daxpy.c.o -MF CMakeFiles/dblas.dir/daxpy.c.o.d -o CMakeFiles/dblas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/daxpy.c
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/ddot.c.o -MF CMakeFiles/dblas.dir/ddot.c.o.d -o CMakeFiles/dblas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/ddot.c
[  6%] Building C object src/dblas/CMakeFiles/dblas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dgemv.c.o -MF CMakeFiles/dblas.dir/dgemv.c.o.d -o CMakeFiles/dblas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dgemv.c
[  7%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[  9%] Building C object src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dnrm2.c.o -MF CMakeFiles/dblas.dir/dnrm2.c.o.d -o CMakeFiles/dblas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dnrm2.c
[ 10%] Building C object src/dblas/CMakeFiles/dblas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/dblas/CMakeFiles/dblas.dir/dscal.c.o -MF CMakeFiles/dblas.dir/dscal.c.o.d -o CMakeFiles/dblas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/dblas/dscal.c
[ 11%] Linking C static library libdblas.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -P CMakeFiles/dblas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/dblas && /usr/bin/cmake -E cmake_link_script CMakeFiles/dblas.dir/link.txt --verbose=1
a - CMakeFiles/dblas.dir/daxpy.c.o
a - CMakeFiles/dblas.dir/ddot.c.o
a - CMakeFiles/dblas.dir/dgemv.c.o
a - CMakeFiles/dblas.dir/dnrm2.c.o
a - CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ar rcv libdblas.a CMakeFiles/dblas.dir/daxpy.c.o CMakeFiles/dblas.dir/ddot.c.o CMakeFiles/dblas.dir/dgemv.c.o CMakeFiles/dblas.dir/dnrm2.c.o CMakeFiles/dblas.dir/dscal.c.o
/usr/bin/ranlib libdblas.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 11%] Built target dblas
[ 13%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MassHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ResultHolder.cpp
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Database.cpp
[ 19%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PSMDescription.cpp
[ 21%] Building CXX object src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -MF CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o.d -o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.cpp:17:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:986:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  986 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Peptide.cpp:977:35: note: length computed here
  977 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
[ 23%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideConstraint.cpp
[ 25%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp
[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp
[ 27%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PeptideSrc.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
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;
      |                                          ^~~~~
[ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/PickedProteinCaller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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,
      | ^~~~~~~~~~~~
[ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/Protein.cpp
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/StdvNormalizer.cpp
[ 32%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein/ProteinPeptideIterator.cpp
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp
[ 35%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:38,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -MF CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o.d -o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:102:7: warning: ‘Caller::useCompositionMatch_’ will be initialized after [-Wreorder]
  102 |       useCompositionMatch_, useIrlsPep_, useInterpolatingPep_, usePavaPep_;
      |       ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:86:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   86 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:100:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.h:98:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
   98 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Caller.cpp:42:1: warning:   when initialized here [-Wreorder]
   42 | Caller::Caller()
      | ^~~~~~
[ 39%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 39%] Built target picked_protein
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Enzyme.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:10:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/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)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::sortScorePerPeptide()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:122:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  122 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:118:11: warning: unused variable ‘composition’ [-Wunused-variable]
  118 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp: In member function ‘int CompositionSorter::inCompositionCompetition(Scores&, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:168:13: warning: unused variable ‘peptide’ [-Wunused-variable]
  168 |       auto& peptide = peptideToScores.first;
      |             ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CompositionSorter.cpp:157:11: warning: unused variable ‘composition’ [-Wunused-variable]
  157 |     auto& composition = compositionToPeptides.first;
      |           ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool, double, unsigned int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:114:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  114 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.h:102:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
  102 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:27:1: warning:   when initialized here [-Wreorder]
   27 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘void CrossValidation::initializeGridSearch(double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  154 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(const Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/CrossValidation.cpp:344:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CandidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  344 |   for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Globals.cpp
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/NoNormalizer.cpp
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Normalizer.cpp
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/UniNormalizer.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -MF CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o.d -o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp: In static member function ‘static std::string TabFileValidator::getLongestCommonPrefix(std::vector<std::__cxx11::basic_string<char> >)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TabFileValidator.cpp:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  103 |     for (int k = 1; k < numStrings; ++k) {
      |                     ~~^~~~~~~~~~~~
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureNames.cpp
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.cpp
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Numerical.cpp.o -MF CMakeFiles/perclibrary.dir/Numerical.cpp.o.d -o CMakeFiles/perclibrary.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Numerical.cpp
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);
      |        ^~~
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Option.cpp
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinFDRestimator.cpp
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:161:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  161 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.cpp:165:10: warning: unused variable ‘RT’ [-Wunused-variable]
  165 |   double RT = pPSM->getRetentionTime();
      |          ^~
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PseudoRandom.cpp
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Set.cpp.o -MF CMakeFiles/perclibrary.dir/Set.cpp.o.d -o CMakeFiles/perclibrary.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:31:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp
In file included from /usr/include/eigen3/Eigen/Core:214,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/IsotonicPEP.h:16,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.cpp:39:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:172:
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/usr/include/eigen3/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ssl.cpp
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.cpp
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedMatrix.cpp
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);
      |        ^~~
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);
      |        ^~~
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Logger.cpp
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/MyException.cpp
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinScoreHolder.cpp
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp
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,
      | ^~~~~~~~~~~~~~~~~~
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/FeatureMemoryPool.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Timer.cpp
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*, std::string&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PickedProteinInterface.cpp:167:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  167 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/TmpDir.cpp
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/perclibrary.dir/Vector.cpp.o -MF CMakeFiles/perclibrary.dir/Vector.cpp.o.d -o CMakeFiles/perclibrary.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:385:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  385 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:395:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  395 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:533:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  533 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:545:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:548:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  548 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.cpp:562:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  562 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/IsotonicPEP.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CompositionSorter.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/TabFileValidator.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Numerical.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/ScoreHolder.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/Set.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o CMakeFiles/perclibrary.dir/Vector.cpp.o
/usr/bin/ranlib libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 82%] Built target perclibrary
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08 /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/gmake  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
/usr/bin/gmake  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
gmake[2]: Entering directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 84%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
[ 85%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/. -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++14 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp
[ 86%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
[ 88%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/./Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 89%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
[ 90%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
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)
      |   ^~~~~~~~~~~
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);
      |        ^~~
[ 92%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_IsplineRegression.cpp
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src -I/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src -isystem /usr/include/eigen3 -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -std=c++17 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/src  ../libperclibrary.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[ 98%] Built target qvality
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);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Scores.h:37,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:40:3: warning:   when initialized here [-Wreorder]
   40 |   ScoreHolder()
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h: In constructor ‘ScoreHolder::ScoreHolder(double, LabelType, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:38:13: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   38 |   LabelType label;
      |             ^~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:37:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   37 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ScoreHolder.h:47:3: warning:   when initialized here [-Wreorder]
   47 |   ScoreHolder(const double s, const LabelType l, PSMDescription* psm = NULL)
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h: At global scope:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Array.h:171:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
  171 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/Set.h:13:8: note:   by ‘void Set::add(int)’
   13 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:143:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  143 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a dblas/libdblas.a picked_protein/libpicked_protein.a -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[100%] Built target percolator
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Isrc -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -I/usr/include/eigen3 -O3 -DNDEBUG -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes   -ltirpc -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_IsplineRegression.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  /usr/lib64/libgtest_main.so.1.17.0 ../../../src/libperclibrary.a ../../../src/dblas/libdblas.a -lpthread /usr/lib64/libgtest.so.1.17.0
gmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
[100%] Built target gtest_unit
gmake[1]: Leaving directory '/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/src/converters/CMakeFiles 0

+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.T1gRH2
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-08
+ DESTDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ /usr/bin/cmake --install percolator
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/percolator
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/qvality
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/./bin/gtest_unit
+ DESTDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT
+ /usr/bin/cmake --install src/converters
-- Install configuration: "Release"
-- Up-to-date: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Up-to-date: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/percolator
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/qvality
-- Installing: /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/./bin/gtest_unit
+ mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/fido/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/libperclibrary.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./src/converters/src/dblas/libdblas.a /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator
+ rm -f /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.08-1.fc44 --unique-debug-suffix -3.08-1.fc44.aarch64 --unique-debug-src-base percolator-3.08-1.fc44.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08
find-debuginfo: starting
Extracting debug info from 5 files
DWARF-compressing 2 files
sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.08-1.fc44.aarch64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-det --brp -j4 /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libdblas.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libpicked_protein.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/lib64/percolator/libperclibrary.a: replacing with normalized version
Scanned 27 directories and 125 files,
    processed 3 inodes,
    3 modified (3 replaced + 0 rewritten),
    0 unsupported format, 0 errors
+ /usr/bin/linkdupes --brp /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr
Scanned 26 directories and 125 files,
    considered 125 files, read 0 files, linked 0 files, 0 errors
    sum of sizes of linked files: 0 bytes
Reading /builddir/build/BUILD/percolator-3.08-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.iCp5Th
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules  '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-08
+ /usr/bin/ctest --test-dir percolator --output-on-failure --force-new-ctest-process -j4 -VV
Internal ctest changing into directory: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
UpdateCTestConfiguration  from :/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/DartConfiguration.tcl
UpdateCTestConfiguration  from :/builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/DartConfiguration.tcl
Test project /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
    Start 1: UnitTest_Percolator_RunAllTests

1: Test command: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator/gtest_unit
1: Working Directory: /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/percolator/tests/unit_tests/percolator
1: Test timeout computed to be: 10000000
1: [==========] Running 29 tests from 8 test suites.
1: [----------] Global test environment set-up.
1: [----------] 1 test from CrossValidationTest
1: [ RUN      ] CrossValidationTest.doStepTest
1: [       OK ] CrossValidationTest.doStepTest (15 ms)
1: [----------] 1 test from CrossValidationTest (15 ms total)
1: 
1: [----------] 2 tests from ScoreHolderTest
1: [ RUN      ] ScoreHolderTest.CheckOrderingFunctions
1: 3
1: 4
1: 1
1: 2
1: 5
1: [       OK ] ScoreHolderTest.CheckOrderingFunctions (0 ms)
1: [ RUN      ] ScoreHolderTest.CheckUniquenessFilter
1: [       OK ] ScoreHolderTest.CheckUniquenessFilter (0 ms)
1: [----------] 2 tests from ScoreHolderTest (0 ms total)
1: 
1: [----------] 2 tests from ScoresTest
1: [ RUN      ] ScoresTest.CheckPopulating
1: [       OK ] ScoresTest.CheckPopulating (0 ms)
1: [ RUN      ] ScoresTest.CheckPopulatingEmpty
1: [       OK ] ScoresTest.CheckPopulatingEmpty (0 ms)
1: [----------] 2 tests from ScoresTest (0 ms total)
1: 
1: [----------] 7 tests from IsplineRegressionTest
1: [ RUN      ] IsplineRegressionTest.CubicIsplineBasicBehavior
1: [       OK ] IsplineRegressionTest.CubicIsplineBasicBehavior (0 ms)
1: [ RUN      ] IsplineRegressionTest.MonotonicityFitY
1: [       OK ] IsplineRegressionTest.MonotonicityFitY (0 ms)
1: [ RUN      ] IsplineRegressionTest.FitXYBinaryInputs
1: [       OK ] IsplineRegressionTest.FitXYBinaryInputs (0 ms)
1: [ RUN      ] IsplineRegressionTest.FitXYBinaryInputsLarge
1: [       OK ] IsplineRegressionTest.FitXYBinaryInputsLarge (1 ms)
1: [ RUN      ] IsplineRegressionTest.HandlesConstantInput
1: [       OK ] IsplineRegressionTest.HandlesConstantInput (0 ms)
1: [ RUN      ] IsplineRegressionTest.SmallDatasetUniformKnots
1: [       OK ] IsplineRegressionTest.SmallDatasetUniformKnots (0 ms)
1: [ RUN      ] IsplineRegressionTest.LargeDatasetAdaptiveKnots
1: [       OK ] IsplineRegressionTest.LargeDatasetAdaptiveKnots (0 ms)
1: [----------] 7 tests from IsplineRegressionTest (1 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 (2 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 (3 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. (22 ms total)
1: [  PASSED  ] 29 tests.
1/1 Test #1: UnitTest_Percolator_RunAllTests ...   Passed    0.02 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.03 sec
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.08-1.fc44.aarch64
Provides: percolator = 3.08-1.fc44 percolator(aarch-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.08-1.fc44.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hxf3d5
+ 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.ZGZ4iz
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/license.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.08-1.fc44.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.RuRjXF
+ 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.mL2xbS
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ cd percolator-rel-3-08
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.08-build/percolator-rel-3-08/license.txt /builddir/build/BUILD/percolator-3.08-build/BUILDROOT/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.08-1.fc44 percolator-static(aarch-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.08-1.fc44.aarch64
Provides: percolator-debugsource = 3.08-1.fc44 percolator-debugsource(aarch-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.08-1.fc44.aarch64
Provides: debuginfo(build-id) = 1e4d223e833806a5532750767baa1539d6996d3d debuginfo(build-id) = 2363778ac5c4278493b6c800794f087101c63bba percolator-debuginfo = 3.08-1.fc44 percolator-debuginfo(aarch-64) = 3.08-1.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(aarch-64) = 3.08-1.fc44
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/percolator-3.08-build/BUILDROOT
Wrote: /builddir/build/RPMS/percolator-debugsource-3.08-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.08-1.fc44.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.08-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.08-1.fc44.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.08-1.fc44.aarch64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.72Xqvv
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.08-build
+ test -d /builddir/build/BUILD/percolator-3.08-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/percolator-3.08-build
+ rm -rf /builddir/build/BUILD/percolator-3.08-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.08-1.fc44.src.rpm
Finish: build phase for percolator-3.08-1.fc44.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1759572895.816751/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.08-1.fc44.src.rpm) Config(child) 7 minutes 18 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "noarch"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "src"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "aarch64"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.08",
            "release": "1.fc44",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished