Warning: Permanently added '150.240.0.87' (ED25519) to the list of known hosts.
You can reproduce this build on your computer by running:
sudo dnf install copr-rpmbuild
/usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6951371-fedora-rawhide-s390x --chroot fedora-rawhide-s390x
Version: 0.70
PID: 6359
Logging PID: 6360
Task:
{'appstream': False,
'background': True,
'build_id': 6951371,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-s390x',
'enable_net': False,
'fedora_review': False,
'git_hash': '459667f54114258382b26a28cd3991104da93c93',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'percolator',
'package_version': '3.06.04-3',
'project_dirname': 'openblas-0.3.23',
'project_name': 'openblas-0.3.23',
'project_owner': 'psimovec',
'repo_priority': None,
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-rawhide-s390x/',
'id': 'copr_base',
'name': 'Copr repository',
'priority': None},
{'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/',
'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch',
'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}],
'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/releng',
'source_json': {},
'source_type': None,
'submitter': 'https://src.fedoraproject.org/user/releng',
'tags': [],
'task_id': '6951371-fedora-rawhide-s390x',
'timeout': 18000,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator'...
Running: git checkout 459667f54114258382b26a28cd3991104da93c93 --
cmd: ['git', 'checkout', '459667f54114258382b26a28cd3991104da93c93', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator
rc: 0
stdout:
stderr: Note: switching to '459667f54114258382b26a28cd3991104da93c93'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at 459667f automatic import of percolator
Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator
rc: 0
stdout:
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading percolator-rel-3-06-04.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o percolator-rel-3-06-04.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23/percolator/percolator-rel-3-06-04.tar.gz/md5/e49b456754b0ee11706ca799cf511582/percolator-rel-3-06-04.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 5157k 100 5157k 0 0 998k 0 0:00:05 0:00:05 --:--:-- 1330k
INFO: Reading stdout from command: md5sum percolator-rel-3-06-04.tar.gz
INFO: Downloading yeast-01.sqt.tar.gz
INFO: Calling: curl -H Pragma: -o yeast-01.sqt.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23/percolator/yeast-01.sqt.tar.gz/md5/81e1997e1c1c193cbfcd4eb54c706af9/yeast-01.sqt.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 47.9M 100 47.9M 0 0 9514k 0 0:00:05 0:00:05 --:--:-- 11.3M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706218334.596559 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706218334.596559 -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-qqj151hc/percolator/percolator.spec) Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.4
INFO: Mock Version: 5.4
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1706218334.596559/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1706218334.596559/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/d461972510f88b0855c43f6555f325d7f314c193e953ac80e44f3492891ebb1a/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/d461972510f88b0855c43f6555f325d7f314c193e953ac80e44f3492891ebb1a/merged) with podman image umount
INFO: Using 'dnf' instead of 'dnf5' for bootstrap chroot
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf5 tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 3.8 MB/s | 21 MB 00:05
Additional repo http_kojipkgs_fedoraproject_org 138 MB/s | 68 MB 00:00
fedora 52 MB/s | 65 MB 00:01
Last metadata expiration check: 0:00:10 ago on Thu Jan 25 21:33:08 2024.
Dependencies resolved.
=========================================================================================================
Package Arch Version Repository Size
=========================================================================================================
Installing:
dnf5 s390x 5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 542 k
dnf5-plugins s390x 5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 328 k
Installing dependencies:
fmt s390x 10.2.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 129 k
libdnf5 s390x 5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 927 k
libdnf5-cli s390x 5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 225 k
sdbus-cpp s390x 1.4.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103 k
Transaction Summary
=========================================================================================================
Install 6 Packages
Total download size: 2.2 M
Installed size: 6.1 M
Downloading Packages:
(1/6): dnf5-5.1.11-1.fc40.s390x.rpm 4.3 MB/s | 542 kB 00:00
(2/6): fmt-10.2.1-1.fc40.s390x.rpm 1.0 MB/s | 129 kB 00:00
(3/6): dnf5-plugins-5.1.11-1.fc40.s390x.rpm 2.5 MB/s | 328 kB 00:00
(4/6): libdnf5-5.1.11-1.fc40.s390x.rpm 116 MB/s | 927 kB 00:00
(5/6): libdnf5-cli-5.1.11-1.fc40.s390x.rpm 32 MB/s | 225 kB 00:00
(6/6): sdbus-cpp-1.4.0-1.fc40.s390x.rpm 21 MB/s | 103 kB 00:00
--------------------------------------------------------------------------------
Total 16 MB/s | 2.2 MB 00:00
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : fmt-10.2.1-1.fc40.s390x 1/6
Installing : libdnf5-5.1.11-1.fc40.s390x 2/6
Installing : libdnf5-cli-5.1.11-1.fc40.s390x 3/6
Installing : dnf5-5.1.11-1.fc40.s390x 4/6
Installing : sdbus-cpp-1.4.0-1.fc40.s390x 5/6
Installing : dnf5-plugins-5.1.11-1.fc40.s390x 6/6
Running scriptlet: dnf5-plugins-5.1.11-1.fc40.s390x 6/6
Installed:
dnf5-5.1.11-1.fc40.s390x dnf5-plugins-5.1.11-1.fc40.s390x
fmt-10.2.1-1.fc40.s390x libdnf5-5.1.11-1.fc40.s390x
libdnf5-cli-5.1.11-1.fc40.s390x sdbus-cpp-1.4.0-1.fc40.s390x
Complete!
INFO: Switching package manager from dnf to the dnf5 (direct choice)
Finish(bootstrap): installing dnf5 tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1706218334.596559/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.19.1-2.fc40.s390x
rpm-sequoia-1.5.0-2.fc40.s390x
python3-dnf-4.18.2-1.fc40.noarch
yum-4.18.2-1.fc40.noarch
dnf5-5.1.11-1.fc40.s390x
dnf5-plugins-5.1.11-1.fc40.s390x
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
fedora 100% | 3.3 MiB/s | 18.8 MiB | 00m06s
Copr repository 100% | 641.7 KiB/s | 3.7 MiB | 00m06s
Additional repo http_kojipkgs_fedorapr 100% | 3.1 MiB/s | 16.1 MiB | 00m05s
Repositories loaded.
Package Arch Version Repository Size
Installing group/module packages:
bash s390x 5.2.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.3 MiB
bzip2 s390x 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 99.2 KiB
coreutils s390x 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.2 MiB
cpio s390x 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB
diffutils s390x 3.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB
fedora-release-common noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19.1 KiB
findutils s390x 1:4.9.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB
gawk s390x 5.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB
glibc-minimal-langpack s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B
grep s390x 3.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB
gzip s390x 1.12-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 383.7 KiB
info s390x 7.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 405.1 KiB
patch s390x 2.7.6-22.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274.3 KiB
redhat-rpm-config noarch 280-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183.2 KiB
rpm-build s390x 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 180.2 KiB
sed s390x 4.8-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 809.6 KiB
shadow-utils s390x 2:4.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.0 MiB
tar s390x 2:1.35-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 MiB
unzip s390x 6.0-62.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 414.1 KiB
util-linux s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.5 MiB
which s390x 2.21-40.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83.9 KiB
xz s390x 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB
Installing dependencies:
alternatives s390x 1.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 66.1 KiB
ansible-srpm-macros noarch 1-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 35.7 KiB
audit-libs s390x 4.0-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.8 KiB
authselect s390x 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 156.3 KiB
authselect-libs s390x 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 989.2 KiB
basesystem noarch 11-18.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B
binutils s390x 2.41-30.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25.9 MiB
binutils-gold s390x 2.41-30.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 MiB
bzip2-libs s390x 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 88.5 KiB
ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.3 MiB
coreutils-common s390x 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11.4 MiB
cracklib s390x 2.9.11-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 250.0 KiB
crypto-policies noarch 20231204-1.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 149.3 KiB
curl s390x 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 826.2 KiB
cyrus-sasl-lib s390x 2.1.28-17.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.4 MiB
debugedit s390x 5.0-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 202.5 KiB
dwz s390x 0.15-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 314.6 KiB
ed s390x 1.20-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 150.2 KiB
efi-srpm-macros noarch 5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40.1 KiB
elfutils s390x 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 MiB
elfutils-debuginfod-client s390x 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 64.4 KiB
elfutils-default-yama-scope noarch 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 KiB
elfutils-libelf s390x 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB
elfutils-libs s390x 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 734.1 KiB
fedora-gpg-keys noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 123.2 KiB
fedora-release noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B
fedora-release-identity-basic noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 694.0 B
fedora-repos noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.9 KiB
fedora-repos-rawhide noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 KiB
file s390x 5.45-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103.3 KiB
file-libs s390x 5.45-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.9 MiB
filesystem s390x 3.18-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 106.0 B
fonts-srpm-macros noarch 1:2.0.5-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 55.3 KiB
forge-srpm-macros noarch 0.2.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37.4 KiB
fpc-srpm-macros noarch 1.3-8.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144.0 B
gdb-minimal s390x 14.1-6.fc40 copr_base 12.5 MiB
gdbm s390x 1:1.23-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 483.9 KiB
gdbm-libs s390x 1:1.23-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 133.4 KiB
ghc-srpm-macros noarch 1.6.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 369.0 B
glibc s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.4 MiB
glibc-common s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB
glibc-gconv-extra s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.7 MiB
gmp s390x 1:6.2.1-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 765.1 KiB
gnat-srpm-macros noarch 6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 KiB
go-srpm-macros noarch 3.3.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 60.6 KiB
jansson s390x 2.13.1-7.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 92.1 KiB
kernel-srpm-macros noarch 1.0-20.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB
keyutils-libs s390x 1.6.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 54.2 KiB
krb5-libs s390x 1.21.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.4 MiB
libacl s390x 2.3.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43.8 KiB
libarchive s390x 3.7.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB
libattr s390x 2.5.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28.3 KiB
libblkid s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 256.9 KiB
libbrotli s390x 1.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 917.1 KiB
libcap s390x 2.69-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 231.1 KiB
libcap-ng s390x 0.8.4-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 76.7 KiB
libcom_err s390x 1.47.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 67.0 KiB
libcurl s390x 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 820.5 KiB
libeconf s390x 0.5.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 55.8 KiB
libevent s390x 2.1.12-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 938.7 KiB
libfdisk s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 390.9 KiB
libffi s390x 3.4.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 65.1 KiB
libgcc s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 173.2 KiB
libgomp s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 527.6 KiB
libidn2 s390x 2.3.4-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 322.9 KiB
libmount s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 368.1 KiB
libnghttp2 s390x 1.59.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 173.9 KiB
libnsl2 s390x 2.0.0-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 61.7 KiB
libpkgconf s390x 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85.8 KiB
libpsl s390x 0.21.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 80.3 KiB
libpwquality s390x 1.4.5-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 420.9 KiB
libselinux s390x 3.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 188.9 KiB
libsemanage s390x 3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 301.3 KiB
libsepol s390x 3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 842.2 KiB
libsmartcols s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 152.0 KiB
libssh s390x 0.10.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 529.0 KiB
libssh-config noarch 0.10.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 277.0 B
libstdc++ s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.1 MiB
libtasn1 s390x 4.19.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 187.5 KiB
libtirpc s390x 1.3.4-1.rc1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 214.6 KiB
libunistring s390x 1.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB
libutempter s390x 1.2.1-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 57.3 KiB
libuuid s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37.3 KiB
libverto s390x 0.3.2-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29.2 KiB
libxcrypt s390x 4.4.36-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274.7 KiB
libxml2 s390x 2.12.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 MiB
libzstd s390x 1.5.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 859.8 KiB
lua-libs s390x 5.4.6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 324.9 KiB
lua-srpm-macros noarch 1-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 KiB
lz4-libs s390x 1.9.4-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 169.2 KiB
mpfr s390x 4.2.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 698.8 KiB
ncurses-base noarch 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.2 KiB
ncurses-libs s390x 6.4-9.20240113.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB
ocaml-srpm-macros noarch 9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 KiB
openblas-srpm-macros noarch 2-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 104.0 B
openldap s390x 2.6.6-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 669.0 KiB
openssl-libs s390x 1:3.1.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.6 MiB
p11-kit s390x 0.25.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.5 MiB
p11-kit-trust s390x 0.25.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 467.2 KiB
package-notes-srpm-macros noarch 0.5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 KiB
pam s390x 1.6.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.7 MiB
pam-libs s390x 1.6.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 130.4 KiB
pcre2 s390x 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 657.2 KiB
pcre2-syntax noarch 10.42-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 235.1 KiB
perl-srpm-macros noarch 1-51.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0 B
pkgconf s390x 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83.6 KiB
pkgconf-m4 noarch 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13.9 KiB
pkgconf-pkg-config s390x 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 988.0 B
popt s390x 1.19-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144.6 KiB
publicsuffix-list-dafsa noarch 20240107-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 67.5 KiB
pyproject-srpm-macros noarch 1.11.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 KiB
python-srpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 50.1 KiB
qt5-srpm-macros noarch 5.15.12-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 492.0 B
qt6-srpm-macros noarch 6.6.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0 B
readline s390x 8.2-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 556.8 KiB
rpm s390x 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 MiB
rpm-build-libs s390x 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 206.2 KiB
rpm-libs s390x 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 809.6 KiB
rpm-sequoia s390x 1.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 MiB
rust-srpm-macros noarch 25.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.1 KiB
setup noarch 2.14.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.4 KiB
sqlite-libs s390x 3.45.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB
systemd-libs s390x 255.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.0 MiB
util-linux-core s390x 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 MiB
xxhash-libs s390x 0.8.2-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 68.0 KiB
xz-libs s390x 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 221.6 KiB
zig-srpm-macros noarch 1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 KiB
zip s390x 3.0-39.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 754.3 KiB
zlib-ng-compat s390x 2.1.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 117.4 KiB
zstd s390x 1.5.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 MiB
Installing groups:
Buildsystem building group
Transaction Summary:
Installing: 152 packages
Total size of inbound packages is 52 MiB. Need to download 52 MiB.
After this operation 179 MiB will be used (install 179 MiB, remove 0 B).
[ 1/152] bzip2-0:1.0.8-16.fc39.s390x 100% | 1.0 MiB/s | 53.2 KiB | 00m00s
[ 2/152] bash-0:5.2.26-1.fc40.s390x 100% | 33.3 MiB/s | 1.8 MiB | 00m00s
[ 3/152] diffutils-0:3.10-3.fc39.s390x 100% | 64.8 MiB/s | 398.2 KiB | 00m00s
[ 4/152] fedora-release-common-0:40-0. 100% | 5.0 MiB/s | 20.5 KiB | 00m00s
[ 5/152] cpio-0:2.15-1.fc40.s390x 100% | 14.2 MiB/s | 290.6 KiB | 00m00s
[ 6/152] findutils-1:4.9.0-6.fc40.s390 100% | 59.5 MiB/s | 487.8 KiB | 00m00s
[ 7/152] glibc-minimal-langpack-0:2.38 100% | 18.8 MiB/s | 96.4 KiB | 00m00s
[ 8/152] coreutils-0:9.4-3.fc40.s390x 100% | 14.2 MiB/s | 1.2 MiB | 00m00s
[ 9/152] gzip-0:1.12-6.fc39.s390x 100% | 23.2 MiB/s | 166.3 KiB | 00m00s
[ 10/152] grep-0:3.11-5.fc40.s390x 100% | 26.1 MiB/s | 294.1 KiB | 00m00s
[ 11/152] patch-0:2.7.6-22.fc39.s390x 100% | 21.8 MiB/s | 133.8 KiB | 00m00s
[ 12/152] info-0:7.1-1.fc40.s390x 100% | 23.8 MiB/s | 194.9 KiB | 00m00s
[ 13/152] redhat-rpm-config-0:280-1.fc4 100% | 14.7 MiB/s | 75.2 KiB | 00m00s
[ 14/152] rpm-build-0:4.19.1-2.fc40.s39 100% | 13.9 MiB/s | 71.4 KiB | 00m00s
[ 15/152] gawk-0:5.3.0-1.fc40.s390x 100% | 30.3 MiB/s | 1.1 MiB | 00m00s
[ 16/152] shadow-utils-2:4.14.0-2.fc40. 100% | 134.8 MiB/s | 1.2 MiB | 00m00s
[ 17/152] sed-0:4.8-14.fc39.s390x 100% | 29.3 MiB/s | 300.3 KiB | 00m00s
[ 18/152] unzip-0:6.0-62.fc39.s390x 100% | 27.1 MiB/s | 193.9 KiB | 00m00s
[ 19/152] tar-2:1.35-2.fc40.s390x 100% | 44.4 MiB/s | 864.7 KiB | 00m00s
[ 20/152] util-linux-0:2.39.3-2.fc40.s3 100% | 98.3 MiB/s | 1.1 MiB | 00m00s
[ 21/152] which-0:2.21-40.fc39.s390x 100% | 8.4 MiB/s | 43.2 KiB | 00m00s
[ 22/152] xz-0:5.4.5-1.fc40.s390x 100% | 47.2 MiB/s | 532.1 KiB | 00m00s
[ 23/152] glibc-common-0:2.38.9000-35.f 100% | 38.6 MiB/s | 394.9 KiB | 00m00s
[ 24/152] glibc-0:2.38.9000-35.fc40.s39 100% | 145.6 MiB/s | 1.9 MiB | 00m00s
[ 25/152] xz-libs-0:5.4.5-1.fc40.s390x 100% | 18.6 MiB/s | 114.2 KiB | 00m00s
[ 26/152] audit-libs-0:4.0-5.fc40.s390x 100% | 17.5 MiB/s | 125.1 KiB | 00m00s
[ 27/152] authselect-libs-0:1.5.0-1.fc4 100% | 25.3 MiB/s | 233.0 KiB | 00m00s
[ 28/152] glibc-gconv-extra-0:2.38.9000 100% | 83.1 MiB/s | 1.7 MiB | 00m00s
[ 29/152] libblkid-0:2.39.3-2.fc40.s390 100% | 10.7 MiB/s | 120.5 KiB | 00m00s
[ 30/152] libcap-ng-0:0.8.4-2.fc40.s390 100% | 6.4 MiB/s | 32.9 KiB | 00m00s
[ 31/152] libfdisk-0:2.39.3-2.fc40.s390 100% | 27.0 MiB/s | 165.8 KiB | 00m00s
[ 32/152] libmount-0:2.39.3-2.fc40.s390 100% | 25.8 MiB/s | 158.4 KiB | 00m00s
[ 33/152] libselinux-0:3.6-2.fc40.s390x 100% | 15.0 MiB/s | 92.2 KiB | 00m00s
[ 34/152] libsmartcols-0:2.39.3-2.fc40. 100% | 13.7 MiB/s | 69.9 KiB | 00m00s
[ 35/152] libutempter-0:1.2.1-10.fc39.s 100% | 5.1 MiB/s | 26.0 KiB | 00m00s
[ 36/152] libuuid-0:2.39.3-2.fc40.s390x 100% | 5.6 MiB/s | 28.6 KiB | 00m00s
[ 37/152] pam-0:1.6.0-1.fc40.s390x 100% | 64.0 MiB/s | 524.6 KiB | 00m00s
[ 38/152] ncurses-libs-0:6.4-9.20240113 100% | 39.3 MiB/s | 362.1 KiB | 00m00s
[ 39/152] pam-libs-0:1.6.0-1.fc40.s390x 100% | 8.1 MiB/s | 58.0 KiB | 00m00s
[ 40/152] readline-0:8.2-7.fc40.s390x 100% | 32.1 MiB/s | 230.0 KiB | 00m00s
[ 41/152] util-linux-core-0:2.39.3-2.fc 100% | 69.3 MiB/s | 496.6 KiB | 00m00s
[ 42/152] systemd-libs-0:255.2-2.fc40.s 100% | 49.5 MiB/s | 710.1 KiB | 00m00s
[ 43/152] zlib-ng-compat-0:2.1.6-1.fc40 100% | 10.7 MiB/s | 65.8 KiB | 00m00s
[ 44/152] bzip2-libs-0:1.0.8-16.fc39.s3 100% | 7.6 MiB/s | 46.4 KiB | 00m00s
[ 45/152] libgcc-0:14.0.1-0.2.fc40.s390 100% | 13.4 MiB/s | 68.4 KiB | 00m00s
[ 46/152] libacl-0:2.3.2-1.fc40.s390x 100% | 5.0 MiB/s | 25.4 KiB | 00m00s
[ 47/152] libcap-0:2.69-1.fc40.s390x 100% | 11.8 MiB/s | 84.7 KiB | 00m00s
[ 48/152] lz4-libs-0:1.9.4-4.fc39.s390x 100% | 15.8 MiB/s | 80.9 KiB | 00m00s
[ 49/152] libzstd-0:1.5.5-4.fc39.s390x 100% | 47.8 MiB/s | 342.4 KiB | 00m00s
[ 50/152] libattr-0:2.5.2-1.fc40.s390x 100% | 3.6 MiB/s | 18.3 KiB | 00m00s
[ 51/152] libeconf-0:0.5.2-1.fc40.s390x 100% | 5.2 MiB/s | 32.0 KiB | 00m00s
[ 52/152] libsemanage-0:3.6-1.fc40.s390 100% | 19.3 MiB/s | 118.6 KiB | 00m00s
[ 53/152] libxcrypt-0:4.4.36-4.fc40.s39 100% | 20.1 MiB/s | 123.5 KiB | 00m00s
[ 54/152] setup-0:2.14.5-1.fc40.noarch 100% | 28.9 MiB/s | 148.1 KiB | 00m00s
[ 55/152] debugedit-0:5.0-12.fc40.s390x 100% | 13.3 MiB/s | 81.5 KiB | 00m00s
[ 56/152] elfutils-0:0.190-4.fc40.s390x 100% | 50.7 MiB/s | 570.7 KiB | 00m00s
[ 57/152] elfutils-libelf-0:0.190-4.fc4 100% | 21.7 MiB/s | 199.8 KiB | 00m00s
[ 58/152] file-0:5.45-1.fc40.s390x 100% | 6.9 MiB/s | 49.1 KiB | 00m00s
[ 59/152] pkgconf-pkg-config-0:1.9.5-2. 100% | 1.3 MiB/s | 9.6 KiB | 00m00s
[ 60/152] binutils-0:2.41-30.fc40.s390x 100% | 212.0 MiB/s | 5.9 MiB | 00m00s
[ 61/152] popt-0:1.19-3.fc39.s390x 100% | 6.8 MiB/s | 62.2 KiB | 00m00s
[ 62/152] rpm-0:4.19.1-2.fc40.s390x 100% | 55.3 MiB/s | 509.4 KiB | 00m00s
[ 63/152] rpm-build-libs-0:4.19.1-2.fc4 100% | 19.0 MiB/s | 97.2 KiB | 00m00s
[ 64/152] rpm-libs-0:4.19.1-2.fc40.s390 100% | 52.7 MiB/s | 323.7 KiB | 00m00s
[ 65/152] libarchive-0:3.7.2-1.fc40.s39 100% | 61.4 MiB/s | 440.0 KiB | 00m00s
[ 66/152] zstd-0:1.5.5-4.fc39.s390x 100% | 49.4 MiB/s | 505.7 KiB | 00m00s
[ 67/152] ansible-srpm-macros-0:1-12.fc 100% | 5.1 MiB/s | 20.9 KiB | 00m00s
[ 68/152] dwz-0:0.15-3.fc39.s390x 100% | 23.4 MiB/s | 143.6 KiB | 00m00s
[ 69/152] efi-srpm-macros-0:5-9.fc39.no 100% | 5.4 MiB/s | 22.2 KiB | 00m00s
[ 70/152] fonts-srpm-macros-1:2.0.5-12. 100% | 6.5 MiB/s | 26.5 KiB | 00m00s
[ 71/152] fpc-srpm-macros-0:1.3-8.fc39. 100% | 1.8 MiB/s | 7.4 KiB | 00m00s
[ 72/152] ghc-srpm-macros-0:1.6.1-3.fc4 100% | 2.0 MiB/s | 8.1 KiB | 00m00s
[ 73/152] forge-srpm-macros-0:0.2.0-1.f 100% | 4.5 MiB/s | 18.5 KiB | 00m00s
[ 74/152] gnat-srpm-macros-0:6-3.fc39.n 100% | 2.2 MiB/s | 8.8 KiB | 00m00s
[ 75/152] kernel-srpm-macros-0:1.0-20.f 100% | 3.4 MiB/s | 10.5 KiB | 00m00s
[ 76/152] go-srpm-macros-0:3.3.1-1.fc40 100% | 6.8 MiB/s | 27.7 KiB | 00m00s
[ 77/152] lua-srpm-macros-0:1-9.fc39.no 100% | 2.8 MiB/s | 8.6 KiB | 00m00s
[ 78/152] ocaml-srpm-macros-0:9-1.fc40. 100% | 2.2 MiB/s | 9.0 KiB | 00m00s
[ 79/152] openblas-srpm-macros-0:2-14.f 100% | 2.5 MiB/s | 7.5 KiB | 00m00s
[ 80/152] package-notes-srpm-macros-0:0 100% | 2.7 MiB/s | 11.2 KiB | 00m00s
[ 81/152] perl-srpm-macros-0:1-51.fc39. 100% | 2.0 MiB/s | 8.0 KiB | 00m00s
[ 82/152] pyproject-srpm-macros-0:1.11. 100% | 3.6 MiB/s | 14.8 KiB | 00m00s
[ 83/152] qt6-srpm-macros-0:6.6.1-3.fc4 100% | 2.9 MiB/s | 8.8 KiB | 00m00s
[ 84/152] python-srpm-macros-0:3.12-7.f 100% | 5.8 MiB/s | 23.8 KiB | 00m00s
[ 85/152] qt5-srpm-macros-0:5.15.12-1.f 100% | 2.1 MiB/s | 8.4 KiB | 00m00s
[ 86/152] rust-srpm-macros-0:25.2-2.fc4 100% | 4.2 MiB/s | 13.0 KiB | 00m00s
[ 87/152] zig-srpm-macros-0:1-1.fc40.no 100% | 1.9 MiB/s | 8.0 KiB | 00m00s
[ 88/152] zip-0:3.0-39.fc40.s390x 100% | 46.0 MiB/s | 282.8 KiB | 00m00s
[ 89/152] pkgconf-0:1.9.5-2.fc39.s390x 100% | 8.3 MiB/s | 42.6 KiB | 00m00s
[ 90/152] pkgconf-m4-0:1.9.5-2.fc39.noa 100% | 3.4 MiB/s | 13.9 KiB | 00m00s
[ 91/152] libpkgconf-0:1.9.5-2.fc39.s39 100% | 6.2 MiB/s | 38.1 KiB | 00m00s
[ 92/152] authselect-0:1.5.0-1.fc40.s39 100% | 23.3 MiB/s | 143.4 KiB | 00m00s
[ 93/152] ed-0:1.20-1.fc40.s390x 100% | 11.6 MiB/s | 83.5 KiB | 00m00s
[ 94/152] gdbm-1:1.23-4.fc39.s390x 100% | 21.1 MiB/s | 151.4 KiB | 00m00s
[ 95/152] gdbm-libs-1:1.23-4.fc39.s390x 100% | 11.3 MiB/s | 58.0 KiB | 00m00s
[ 96/152] libnsl2-0:2.0.0-6.fc39.s390x 100% | 4.8 MiB/s | 29.6 KiB | 00m00s
[ 97/152] libpwquality-0:1.4.5-6.fc39.s 100% | 17.8 MiB/s | 109.3 KiB | 00m00s
[ 98/152] libtirpc-0:1.3.4-1.rc1.fc40.s 100% | 15.6 MiB/s | 96.1 KiB | 00m00s
[ 99/152] openssl-libs-1:3.1.4-1.fc40.s 100% | 156.0 MiB/s | 1.9 MiB | 00m00s
[100/152] crypto-policies-0:20231204-1. 100% | 13.4 MiB/s | 68.7 KiB | 00m00s
[101/152] ca-certificates-0:2023.2.62_v 100% | 84.2 MiB/s | 862.6 KiB | 00m00s
[102/152] ncurses-base-0:6.4-9.20240113 100% | 15.5 MiB/s | 63.5 KiB | 00m00s
[103/152] libcom_err-0:1.47.0-2.fc39.s3 100% | 4.2 MiB/s | 26.0 KiB | 00m00s
[104/152] libsepol-0:3.6-1.fc40.s390x 100% | 56.3 MiB/s | 345.7 KiB | 00m00s
[105/152] krb5-libs-0:1.21.2-3.fc40.s39 100% | 63.5 MiB/s | 780.5 KiB | 00m00s
[106/152] pcre2-0:10.42-2.fc40.s390x 100% | 40.7 MiB/s | 250.0 KiB | 00m00s
[107/152] cracklib-0:2.9.11-2.fc39.s390 100% | 13.6 MiB/s | 83.5 KiB | 00m00s
[108/152] keyutils-libs-0:1.6.3-1.fc40. 100% | 6.1 MiB/s | 31.3 KiB | 00m00s
[109/152] libverto-0:0.3.2-6.fc39.s390x 100% | 4.1 MiB/s | 20.8 KiB | 00m00s
[110/152] libxml2-0:2.12.4-1.fc40.s390x 100% | 57.4 MiB/s | 704.9 KiB | 00m00s
[111/152] basesystem-0:11-18.fc39.noarc 100% | 2.3 MiB/s | 7.2 KiB | 00m00s
[112/152] gmp-1:6.2.1-5.fc39.s390x 100% | 39.6 MiB/s | 324.5 KiB | 00m00s
[113/152] filesystem-0:3.18-6.fc39.s390 100% | 106.9 MiB/s | 1.1 MiB | 00m00s
[114/152] mpfr-0:4.2.1-1.fc40.s390x 100% | 36.3 MiB/s | 297.2 KiB | 00m00s
[115/152] fedora-repos-0:40-0.2.noarch 100% | 2.3 MiB/s | 9.3 KiB | 00m00s
[116/152] elfutils-libs-0:0.190-4.fc40. 100% | 44.9 MiB/s | 275.7 KiB | 00m00s
[117/152] file-libs-0:5.45-1.fc40.s390x 100% | 83.4 MiB/s | 768.8 KiB | 00m00s
[118/152] libstdc++-0:14.0.1-0.2.fc40.s 100% | 95.0 MiB/s | 973.0 KiB | 00m00s
[119/152] p11-kit-0:0.25.3-1.fc40.s390x 100% | 46.0 MiB/s | 518.6 KiB | 00m00s
[120/152] coreutils-common-0:9.4-3.fc40 100% | 132.8 MiB/s | 2.1 MiB | 00m00s
[121/152] alternatives-0:1.26-1.fc40.s3 100% | 5.7 MiB/s | 40.6 KiB | 00m00s
[122/152] p11-kit-trust-0:0.25.3-1.fc40 100% | 12.6 MiB/s | 142.1 KiB | 00m00s
[123/152] binutils-gold-0:2.41-30.fc40. 100% | 108.0 MiB/s | 995.8 KiB | 00m00s
[124/152] elfutils-debuginfod-client-0: 100% | 6.2 MiB/s | 38.2 KiB | 00m00s
[125/152] jansson-0:2.13.1-7.fc39.s390x 100% | 7.2 MiB/s | 44.1 KiB | 00m00s
[126/152] lua-libs-0:5.4.6-3.fc39.s390x 100% | 23.1 MiB/s | 141.7 KiB | 00m00s
[127/152] sqlite-libs-0:3.45.0-1.fc40.s 100% | 74.3 MiB/s | 761.0 KiB | 00m00s
[128/152] libgomp-0:14.0.1-0.2.fc40.s39 100% | 46.3 MiB/s | 331.9 KiB | 00m00s
[129/152] pcre2-syntax-0:10.42-2.fc40.n 100% | 28.0 MiB/s | 143.1 KiB | 00m00s
[130/152] libtasn1-0:4.19.0-3.fc39.s390 100% | 12.6 MiB/s | 77.2 KiB | 00m00s
[131/152] rpm-sequoia-0:1.5.0-2.fc40.s3 100% | 51.6 MiB/s | 1.0 MiB | 00m00s
[132/152] fedora-gpg-keys-0:40-0.2.noar 100% | 29.1 MiB/s | 119.4 KiB | 00m00s
[133/152] fedora-repos-rawhide-0:40-0.2 100% | 2.2 MiB/s | 8.9 KiB | 00m00s
[134/152] libffi-0:3.4.4-5.fc40.s390x 100% | 5.8 MiB/s | 35.4 KiB | 00m00s
[135/152] elfutils-default-yama-scope-0 100% | 3.1 MiB/s | 12.8 KiB | 00m00s
[136/152] fedora-release-0:40-0.29.noar 100% | 2.4 MiB/s | 10.0 KiB | 00m00s
[137/152] fedora-release-identity-basic 100% | 3.5 MiB/s | 10.8 KiB | 00m00s
[138/152] curl-0:8.5.0-2.fc40.s390x 100% | 45.5 MiB/s | 372.7 KiB | 00m00s
[139/152] libcurl-0:8.5.0-2.fc40.s390x 100% | 50.8 MiB/s | 364.2 KiB | 00m00s
[140/152] xxhash-libs-0:0.8.2-1.fc39.s3 100% | 7.2 MiB/s | 36.8 KiB | 00m00s
[141/152] libbrotli-0:1.1.0-1.fc40.s390 100% | 46.2 MiB/s | 378.5 KiB | 00m00s
[142/152] libidn2-0:2.3.4-3.fc39.s390x 100% | 15.5 MiB/s | 111.3 KiB | 00m00s
[143/152] libnghttp2-0:1.59.0-1.fc40.s3 100% | 15.5 MiB/s | 79.2 KiB | 00m00s
[144/152] libpsl-0:0.21.5-1.fc40.s390x 100% | 12.4 MiB/s | 63.7 KiB | 00m00s
[145/152] openldap-0:2.6.6-1.fc39.s390x 100% | 42.6 MiB/s | 262.0 KiB | 00m00s
[146/152] libssh-0:0.10.6-2.fc40.s390x 100% | 25.6 MiB/s | 209.3 KiB | 00m00s
[147/152] libevent-0:2.1.12-9.fc39.s390 100% | 36.2 MiB/s | 259.6 KiB | 00m00s
[148/152] cyrus-sasl-lib-0:2.1.28-17.fc 100% | 72.8 MiB/s | 820.3 KiB | 00m00s
[149/152] libssh-config-0:0.10.6-2.fc40 100% | 2.2 MiB/s | 9.1 KiB | 00m00s
[150/152] libunistring-0:1.1-5.fc40.s39 100% | 60.4 MiB/s | 556.3 KiB | 00m00s
[151/152] publicsuffix-list-dafsa-0:202 100% | 9.4 MiB/s | 58.0 KiB | 00m00s
[152/152] gdb-minimal-0:14.1-6.fc40.s39 100% | 765.8 KiB/s | 4.2 MiB | 00m06s
--------------------------------------------------------------------------------
[152/152] Total 100% | 8.6 MiB/s | 52.1 MiB | 00m06s
Running transaction
[ 1/154] Verify package files 100% | 791.0 B/s | 152.0 B | 00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-6.fc39.s390x
>>> Stop pre-transaction scriptlet: filesystem-0:3.18-6.fc39.s390x
[ 2/154] Prepare transaction 100% | 2.8 KiB/s | 152.0 B | 00m00s
[ 3/154] Installing libgcc-0:14.0.1-0. 100% | 85.4 MiB/s | 174.9 KiB | 00m00s
>>> Running post-install scriptlet: libgcc-0:14.0.1-0.2.fc40.s390x
>>> Stop post-install scriptlet: libgcc-0:14.0.1-0.2.fc40.s390x
[ 4/154] Installing crypto-policies-0: 100% | 35.5 MiB/s | 181.7 KiB | 00m00s
>>> Running post-install scriptlet: crypto-policies-0:20231204-1.git1e3a2e4.fc40
>>> Stop post-install scriptlet: crypto-policies-0:20231204-1.git1e3a2e4.fc40.no
[ 5/154] Installing fedora-release-ide 100% | 0.0 B/s | 952.0 B | 00m00s
[ 6/154] Installing fedora-gpg-keys-0: 100% | 40.9 MiB/s | 167.6 KiB | 00m00s
[ 7/154] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s
[ 8/154] Installing fedora-repos-0:40- 100% | 0.0 B/s | 5.7 KiB | 00m00s
[ 9/154] Installing fedora-release-com 100% | 22.6 MiB/s | 23.2 KiB | 00m00s
[ 10/154] Installing fedora-release-0:4 100% | 0.0 B/s | 124.0 B | 00m00s
[ 11/154] Installing setup-0:2.14.5-1.f 100% | 50.6 MiB/s | 725.8 KiB | 00m00s
>>> Running post-install scriptlet: setup-0:2.14.5-1.fc40.noarch
>>> Stop post-install scriptlet: setup-0:2.14.5-1.fc40.noarch
[ 12/154] Installing filesystem-0:3.18- 100% | 2.7 MiB/s | 212.4 KiB | 00m00s
[ 13/154] Installing basesystem-0:11-18 100% | 0.0 B/s | 124.0 B | 00m00s
[ 14/154] Installing publicsuffix-list- 100% | 0.0 B/s | 68.3 KiB | 00m00s
[ 15/154] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s
[ 16/154] Installing pcre2-syntax-0:10. 100% | 232.0 MiB/s | 237.6 KiB | 00m00s
[ 17/154] Installing coreutils-common-0 100% | 266.6 MiB/s | 11.5 MiB | 00m00s
[ 18/154] Installing ncurses-base-0:6.4 100% | 85.9 MiB/s | 351.6 KiB | 00m00s
[ 19/154] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s
[ 20/154] Installing ncurses-libs-0:6.4 100% | 177.1 MiB/s | 1.1 MiB | 00m00s
>>> Running pre-install scriptlet: glibc-0:2.38.9000-35.fc40.s390x
>>> Stop pre-install scriptlet: glibc-0:2.38.9000-35.fc40.s390x
[ 21/154] Installing glibc-0:2.38.9000- 100% | 174.8 MiB/s | 5.4 MiB | 00m00s
>>> Running post-install scriptlet: glibc-0:2.38.9000-35.fc40.s390x
>>> Stop post-install scriptlet: glibc-0:2.38.9000-35.fc40.s390x
[ 22/154] Installing bash-0:5.2.26-1.fc 100% | 278.6 MiB/s | 8.4 MiB | 00m00s
>>> Running post-install scriptlet: bash-0:5.2.26-1.fc40.s390x
>>> Stop post-install scriptlet: bash-0:5.2.26-1.fc40.s390x
[ 23/154] Installing glibc-common-0:2.3 100% | 158.4 MiB/s | 1.1 MiB | 00m00s
[ 24/154] Installing glibc-gconv-extra- 100% | 194.8 MiB/s | 7.8 MiB | 00m00s
>>> Running post-install scriptlet: glibc-gconv-extra-0:2.38.9000-35.fc40.s390x
>>> Stop post-install scriptlet: glibc-gconv-extra-0:2.38.9000-35.fc40.s390x
[ 25/154] Installing zlib-ng-compat-0:2 100% | 115.4 MiB/s | 118.2 KiB | 00m00s
[ 26/154] Installing xz-libs-0:5.4.5-1. 100% | 217.5 MiB/s | 222.7 KiB | 00m00s
[ 27/154] Installing bzip2-libs-0:1.0.8 100% | 87.5 MiB/s | 89.6 KiB | 00m00s
[ 28/154] Installing libuuid-0:2.39.3-2 100% | 0.0 B/s | 38.6 KiB | 00m00s
[ 29/154] Installing readline-0:8.2-7.f 100% | 181.9 MiB/s | 558.9 KiB | 00m00s
[ 30/154] Installing libzstd-0:1.5.5-4. 100% | 210.2 MiB/s | 861.1 KiB | 00m00s
[ 31/154] Installing elfutils-libelf-0: 100% | 249.3 MiB/s | 1.0 MiB | 00m00s
[ 32/154] Installing popt-0:1.19-3.fc39 100% | 49.2 MiB/s | 151.3 KiB | 00m00s
[ 33/154] Installing libstdc++-0:14.0.1 100% | 260.2 MiB/s | 3.1 MiB | 00m00s
[ 34/154] Installing libblkid-0:2.39.3- 100% | 251.8 MiB/s | 257.8 KiB | 00m00s
[ 35/154] Installing libattr-0:2.5.2-1. 100% | 0.0 B/s | 29.3 KiB | 00m00s
[ 36/154] Installing libacl-0:2.3.2-1.f 100% | 0.0 B/s | 44.6 KiB | 00m00s
[ 37/154] Installing libxcrypt-0:4.4.36 100% | 135.4 MiB/s | 277.4 KiB | 00m00s
[ 38/154] Installing gmp-1:6.2.1-5.fc39 100% | 249.8 MiB/s | 767.4 KiB | 00m00s
[ 39/154] Installing lz4-libs-0:1.9.4-4 100% | 166.3 MiB/s | 170.3 KiB | 00m00s
[ 40/154] Installing libeconf-0:0.5.2-1 100% | 56.1 MiB/s | 57.5 KiB | 00m00s
[ 41/154] Installing gdbm-libs-1:1.23-4 100% | 132.0 MiB/s | 135.1 KiB | 00m00s
[ 42/154] Installing mpfr-0:4.2.1-1.fc4 100% | 228.0 MiB/s | 700.3 KiB | 00m00s
[ 43/154] Installing gawk-0:5.3.0-1.fc4 100% | 201.2 MiB/s | 1.8 MiB | 00m00s
[ 44/154] Installing dwz-0:0.15-3.fc39. 100% | 308.5 MiB/s | 315.9 KiB | 00m00s
[ 45/154] Installing unzip-0:6.0-62.fc3 100% | 203.9 MiB/s | 417.6 KiB | 00m00s
[ 46/154] Installing file-libs-0:5.45-1 100% | 473.6 MiB/s | 9.9 MiB | 00m00s
[ 47/154] Installing file-0:5.45-1.fc40 100% | 102.3 MiB/s | 104.8 KiB | 00m00s
[ 48/154] Installing libcap-ng-0:0.8.4- 100% | 76.7 MiB/s | 78.5 KiB | 00m00s
[ 49/154] Installing audit-libs-0:4.0-5 100% | 160.6 MiB/s | 329.0 KiB | 00m00s
[ 50/154] Installing pam-libs-0:1.6.0-1 100% | 129.5 MiB/s | 132.6 KiB | 00m00s
[ 51/154] Installing libcap-0:2.69-1.fc 100% | 115.1 MiB/s | 235.8 KiB | 00m00s
[ 52/154] Installing systemd-libs-0:255 100% | 246.5 MiB/s | 2.0 MiB | 00m00s
[ 53/154] Installing libsmartcols-0:2.3 100% | 149.6 MiB/s | 153.2 KiB | 00m00s
[ 54/154] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 68.1 KiB | 00m00s
[ 55/154] Installing libsepol-0:3.6-1.f 100% | 274.5 MiB/s | 843.2 KiB | 00m00s
[ 56/154] Installing pcre2-0:10.42-2.fc 100% | 214.4 MiB/s | 658.6 KiB | 00m00s
[ 57/154] Installing libselinux-0:3.6-2 100% | 185.7 MiB/s | 190.1 KiB | 00m00s
[ 58/154] Installing sed-0:4.8-14.fc39. 100% | 199.6 MiB/s | 817.6 KiB | 00m00s
[ 59/154] Installing grep-0:3.11-5.fc40 100% | 202.9 MiB/s | 1.0 MiB | 00m00s
[ 60/154] Installing findutils-1:4.9.0- 100% | 135.4 MiB/s | 1.5 MiB | 00m00s
[ 61/154] Installing xz-0:5.4.5-1.fc40. 100% | 200.1 MiB/s | 2.0 MiB | 00m00s
[ 62/154] Installing libmount-0:2.39.3- 100% | 180.3 MiB/s | 369.3 KiB | 00m00s
[ 63/154] Installing alternatives-0:1.2 100% | 66.2 MiB/s | 67.8 KiB | 00m00s
[ 64/154] Installing jansson-0:2.13.1-7 100% | 91.3 MiB/s | 93.5 KiB | 00m00s
[ 65/154] Installing lua-libs-0:5.4.6-3 100% | 159.2 MiB/s | 326.1 KiB | 00m00s
[ 66/154] Installing libtasn1-0:4.19.0- 100% | 184.9 MiB/s | 189.3 KiB | 00m00s
[ 67/154] Installing libunistring-0:1.1 100% | 252.8 MiB/s | 1.8 MiB | 00m00s
[ 68/154] Installing libidn2-0:2.3.4-3. 100% | 80.3 MiB/s | 328.8 KiB | 00m00s
[ 69/154] Installing libpsl-0:0.21.5-1. 100% | 79.5 MiB/s | 81.4 KiB | 00m00s
[ 70/154] Installing util-linux-core-0: 100% | 138.5 MiB/s | 1.4 MiB | 00m00s
[ 71/154] Installing tar-2:1.35-2.fc40. 100% | 273.5 MiB/s | 3.0 MiB | 00m00s
[ 72/154] Installing libsemanage-0:3.6- 100% | 148.0 MiB/s | 303.1 KiB | 00m00s
[ 73/154] Installing shadow-utils-2:4.1 100% | 120.6 MiB/s | 4.1 MiB | 00m00s
>>> Running pre-install scriptlet: libutempter-0:1.2.1-10.fc39.s390x
>>> Stop pre-install scriptlet: libutempter-0:1.2.1-10.fc39.s390x
[ 74/154] Installing libutempter-0:1.2. 100% | 57.9 MiB/s | 59.3 KiB | 00m00s
[ 75/154] Installing zip-0:3.0-39.fc40. 100% | 185.1 MiB/s | 758.2 KiB | 00m00s
[ 76/154] Installing gdbm-1:1.23-4.fc39 100% | 159.1 MiB/s | 488.8 KiB | 00m00s
[ 77/154] Installing cyrus-sasl-lib-0:2 100% | 264.2 MiB/s | 2.4 MiB | 00m00s
[ 78/154] Installing zstd-0:1.5.5-4.fc3 100% | 298.4 MiB/s | 1.8 MiB | 00m00s
[ 79/154] Installing libfdisk-0:2.39.3- 100% | 191.4 MiB/s | 392.0 KiB | 00m00s
[ 80/154] Installing bzip2-0:1.0.8-16.f 100% | 50.6 MiB/s | 103.7 KiB | 00m00s
[ 81/154] Installing libxml2-0:2.12.4-1 100% | 267.8 MiB/s | 1.9 MiB | 00m00s
[ 82/154] Installing sqlite-libs-0:3.45 100% | 262.2 MiB/s | 1.6 MiB | 00m00s
[ 83/154] Installing ed-0:1.20-1.fc40.s 100% | 148.9 MiB/s | 152.5 KiB | 00m00s
[ 84/154] Installing patch-0:2.7.6-22.f 100% | 134.7 MiB/s | 275.8 KiB | 00m00s
[ 85/154] Installing elfutils-default-y 100% | 510.7 KiB/s | 2.0 KiB | 00m00s
>>> Running post-install scriptlet: elfutils-default-yama-scope-0:0.190-4.fc40.n
>>> Stop post-install scriptlet: elfutils-default-yama-scope-0:0.190-4.fc40.noar
[ 86/154] Installing cpio-0:2.15-1.fc40 100% | 186.5 MiB/s | 1.1 MiB | 00m00s
[ 87/154] Installing diffutils-0:3.10-3 100% | 227.0 MiB/s | 1.6 MiB | 00m00s
[ 88/154] Installing libpkgconf-0:1.9.5 100% | 84.9 MiB/s | 86.9 KiB | 00m00s
[ 89/154] Installing pkgconf-0:1.9.5-2. 100% | 84.1 MiB/s | 86.1 KiB | 00m00s
[ 90/154] Installing keyutils-libs-0:1. 100% | 54.3 MiB/s | 55.6 KiB | 00m00s
[ 91/154] Installing libverto-0:0.3.2-6 100% | 30.3 MiB/s | 31.1 KiB | 00m00s
[ 92/154] Installing libgomp-0:14.0.1-0 100% | 258.3 MiB/s | 529.0 KiB | 00m00s
[ 93/154] Installing libffi-0:3.4.4-5.f 100% | 65.0 MiB/s | 66.5 KiB | 00m00s
[ 94/154] Installing p11-kit-0:0.25.3-1 100% | 226.4 MiB/s | 2.5 MiB | 00m00s
[ 95/154] Installing p11-kit-trust-0:0. 100% | 65.4 MiB/s | 469.0 KiB | 00m00s
>>> Running post-install scriptlet: p11-kit-trust-0:0.25.3-1.fc40.s390x
>>> Stop post-install scriptlet: p11-kit-trust-0:0.25.3-1.fc40.s390x
[ 96/154] Installing openssl-libs-1:3.1 100% | 235.1 MiB/s | 5.6 MiB | 00m00s
[ 97/154] Installing coreutils-0:9.4-3. 100% | 214.3 MiB/s | 6.2 MiB | 00m00s
>>> Running pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.n
>>> Stop pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.noar
[ 98/154] Installing ca-certificates-0: 100% | 2.2 MiB/s | 2.3 MiB | 00m01s
>>> Running post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.
>>> Stop post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.noa
[ 99/154] Installing krb5-libs-0:1.21.2 100% | 163.5 MiB/s | 2.5 MiB | 00m00s
[100/154] Installing libtirpc-0:1.3.4-1 100% | 105.6 MiB/s | 216.3 KiB | 00m00s
[101/154] Installing gzip-0:1.12-6.fc39 100% | 95.0 MiB/s | 389.3 KiB | 00m00s
>>> Running pre-install scriptlet: authselect-libs-0:1.5.0-1.fc40.s390x
>>> Stop pre-install scriptlet: authselect-libs-0:1.5.0-1.fc40.s390x
[102/154] Installing authselect-libs-0: 100% | 140.1 MiB/s | 1.0 MiB | 00m00s
[103/154] Installing authselect-0:1.5.0 100% | 78.4 MiB/s | 160.6 KiB | 00m00s
[104/154] Installing cracklib-0:2.9.11- 100% | 51.1 MiB/s | 261.4 KiB | 00m00s
[105/154] Installing libpwquality-0:1.4 100% | 84.6 MiB/s | 433.2 KiB | 00m00s
[106/154] Installing libnsl2-0:2.0.0-6. 100% | 61.4 MiB/s | 62.8 KiB | 00m00s
[107/154] Installing pam-0:1.6.0-1.fc40 100% | 105.7 MiB/s | 1.8 MiB | 00m00s
[108/154] Installing libssh-0:0.10.6-2. 100% | 129.7 MiB/s | 531.1 KiB | 00m00s
[109/154] Installing libarchive-0:3.7.2 100% | 197.8 MiB/s | 1.0 MiB | 00m00s
[110/154] Installing rpm-sequoia-0:1.5. 100% | 200.7 MiB/s | 3.0 MiB | 00m00s
[111/154] Installing rpm-libs-0:4.19.1- 100% | 158.4 MiB/s | 811.1 KiB | 00m00s
[112/154] Installing libevent-0:2.1.12- 100% | 184.1 MiB/s | 942.5 KiB | 00m00s
[113/154] Installing openldap-0:2.6.6-1 100% | 131.4 MiB/s | 672.8 KiB | 00m00s
[114/154] Installing xxhash-libs-0:0.8. 100% | 0.0 B/s | 69.4 KiB | 00m00s
[115/154] Installing libbrotli-0:1.1.0- 100% | 224.5 MiB/s | 919.4 KiB | 00m00s
[116/154] Installing libnghttp2-0:1.59. 100% | 171.0 MiB/s | 175.1 KiB | 00m00s
[117/154] Installing libcurl-0:8.5.0-2. 100% | 267.5 MiB/s | 821.6 KiB | 00m00s
[118/154] Installing elfutils-debuginfo 100% | 64.9 MiB/s | 66.4 KiB | 00m00s
[119/154] Installing elfutils-libs-0:0. 100% | 239.6 MiB/s | 735.9 KiB | 00m00s
[120/154] Installing binutils-gold-0:2. 100% | 167.9 MiB/s | 2.9 MiB | 00m00s
>>> Running post-install scriptlet: binutils-gold-0:2.41-30.fc40.s390x
>>> Stop post-install scriptlet: binutils-gold-0:2.41-30.fc40.s390x
[121/154] Installing binutils-0:2.41-30 100% | 267.5 MiB/s | 25.9 MiB | 00m00s
>>> Running post-install scriptlet: binutils-0:2.41-30.fc40.s390x
>>> Stop post-install scriptlet: binutils-0:2.41-30.fc40.s390x
[122/154] Installing elfutils-0:0.190-4 100% | 266.5 MiB/s | 2.9 MiB | 00m00s
[123/154] Installing gdb-minimal-0:14.1 100% | 169.3 MiB/s | 12.5 MiB | 00m00s
[124/154] Installing debugedit-0:5.0-12 100% | 66.8 MiB/s | 205.2 KiB | 00m00s
[125/154] Installing rpm-build-libs-0:4 100% | 101.1 MiB/s | 207.0 KiB | 00m00s
[126/154] Installing curl-0:8.5.0-2.fc4 100% | 53.9 MiB/s | 828.5 KiB | 00m00s
>>> Running pre-install scriptlet: rpm-0:4.19.1-2.fc40.s390x
>>> Stop pre-install scriptlet: rpm-0:4.19.1-2.fc40.s390x
[127/154] Installing rpm-0:4.19.1-2.fc4 100% | 141.1 MiB/s | 2.4 MiB | 00m00s
[128/154] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.2 KiB | 00m00s
[129/154] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s
[130/154] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s
[131/154] Installing pkgconf-m4-0:1.9.5 100% | 0.0 B/s | 14.3 KiB | 00m00s
[132/154] Installing pkgconf-pkg-config 100% | 0.0 B/s | 1.8 KiB | 00m00s
[133/154] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.8 KiB | 00m00s
[134/154] Installing qt6-srpm-macros-0: 100% | 714.8 KiB/s | 732.0 B | 00m00s
[135/154] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 768.0 B | 00m00s
[136/154] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s
[137/154] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s
[138/154] Installing openblas-srpm-macr 100% | 0.0 B/s | 384.0 B | 00m00s
[139/154] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s
[140/154] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s
[141/154] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s
[142/154] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 648.0 B | 00m00s
[143/154] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s
[144/154] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s
[145/154] Installing fonts-srpm-macros- 100% | 55.1 MiB/s | 56.5 KiB | 00m00s
[146/154] Installing forge-srpm-macros- 100% | 0.0 B/s | 38.6 KiB | 00m00s
[147/154] Installing go-srpm-macros-0:3 100% | 60.2 MiB/s | 61.6 KiB | 00m00s
[148/154] Installing python-srpm-macros 100% | 50.1 MiB/s | 51.3 KiB | 00m00s
[149/154] Installing redhat-rpm-config- 100% | 92.6 MiB/s | 189.6 KiB | 00m00s
[150/154] Installing rpm-build-0:4.19.1 100% | 91.9 MiB/s | 188.3 KiB | 00m00s
[151/154] Installing pyproject-srpm-mac 100% | 2.0 MiB/s | 2.1 KiB | 00m00s
[152/154] Installing util-linux-0:2.39. 100% | 169.5 MiB/s | 3.6 MiB | 00m00s
[153/154] Installing which-0:2.21-40.fc 100% | 84.1 MiB/s | 86.1 KiB | 00m00s
[154/154] Installing info-0:7.1-1.fc40. 100% | 337.9 KiB/s | 405.5 KiB | 00m01s
>>> Running post-transaction scriptlet: filesystem-0:3.18-6.fc39.s390x
>>> Stop post-transaction scriptlet: filesystem-0:3.18-6.fc39.s390x
>>> Running post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.f
>>> Stop post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40
>>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-1.fc40.s390x
>>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-1.fc40.s390x
>>> Running post-transaction scriptlet: rpm-0:4.19.1-2.fc40.s390x
>>> Stop post-transaction scriptlet: rpm-0:4.19.1-2.fc40.s390x
>>> Running trigger-install scriptlet: glibc-common-0:2.38.9000-35.fc40.s390x
>>> Stop trigger-install scriptlet: glibc-common-0:2.38.9000-35.fc40.s390x
>>> Running trigger-install scriptlet: info-0:7.1-1.fc40.s390x
>>> Stop trigger-install scriptlet: info-0:7.1-1.fc40.s390x
Warning: skipped PGP checks for 152 package(s).
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.26-1.fc40.s390x
ansible-srpm-macros-1-12.fc40.noarch
audit-libs-4.0-5.fc40.s390x
authselect-1.5.0-1.fc40.s390x
authselect-libs-1.5.0-1.fc40.s390x
basesystem-11-18.fc39.noarch
bash-5.2.26-1.fc40.s390x
binutils-2.41-30.fc40.s390x
binutils-gold-2.41-30.fc40.s390x
bzip2-1.0.8-16.fc39.s390x
bzip2-libs-1.0.8-16.fc39.s390x
ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch
coreutils-9.4-3.fc40.s390x
coreutils-common-9.4-3.fc40.s390x
cpio-2.15-1.fc40.s390x
cracklib-2.9.11-2.fc39.s390x
crypto-policies-20231204-1.git1e3a2e4.fc40.noarch
curl-8.5.0-2.fc40.s390x
cyrus-sasl-lib-2.1.28-17.fc40.s390x
debugedit-5.0-12.fc40.s390x
diffutils-3.10-3.fc39.s390x
dwz-0.15-3.fc39.s390x
ed-1.20-1.fc40.s390x
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.190-4.fc40.s390x
elfutils-debuginfod-client-0.190-4.fc40.s390x
elfutils-default-yama-scope-0.190-4.fc40.noarch
elfutils-libelf-0.190-4.fc40.s390x
elfutils-libs-0.190-4.fc40.s390x
fedora-gpg-keys-40-0.2.noarch
fedora-release-40-0.29.noarch
fedora-release-common-40-0.29.noarch
fedora-release-identity-basic-40-0.29.noarch
fedora-repos-40-0.2.noarch
fedora-repos-rawhide-40-0.2.noarch
file-5.45-1.fc40.s390x
file-libs-5.45-1.fc40.s390x
filesystem-3.18-6.fc39.s390x
findutils-4.9.0-6.fc40.s390x
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.2.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.3.0-1.fc40.s390x
gdb-minimal-14.1-6.fc40.s390x
gdbm-1.23-4.fc39.s390x
gdbm-libs-1.23-4.fc39.s390x
ghc-srpm-macros-1.6.1-3.fc40.noarch
glibc-2.38.9000-35.fc40.s390x
glibc-common-2.38.9000-35.fc40.s390x
glibc-gconv-extra-2.38.9000-35.fc40.s390x
glibc-minimal-langpack-2.38.9000-35.fc40.s390x
gmp-6.2.1-5.fc39.s390x
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.3.1-1.fc40.noarch
grep-3.11-5.fc40.s390x
gzip-1.12-6.fc39.s390x
info-7.1-1.fc40.s390x
jansson-2.13.1-7.fc39.s390x
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.3-1.fc40.s390x
krb5-libs-1.21.2-3.fc40.s390x
libacl-2.3.2-1.fc40.s390x
libarchive-3.7.2-1.fc40.s390x
libattr-2.5.2-1.fc40.s390x
libblkid-2.39.3-2.fc40.s390x
libbrotli-1.1.0-1.fc40.s390x
libcap-2.69-1.fc40.s390x
libcap-ng-0.8.4-2.fc40.s390x
libcom_err-1.47.0-2.fc39.s390x
libcurl-8.5.0-2.fc40.s390x
libeconf-0.5.2-1.fc40.s390x
libevent-2.1.12-9.fc39.s390x
libfdisk-2.39.3-2.fc40.s390x
libffi-3.4.4-5.fc40.s390x
libgcc-14.0.1-0.2.fc40.s390x
libgomp-14.0.1-0.2.fc40.s390x
libidn2-2.3.4-3.fc39.s390x
libmount-2.39.3-2.fc40.s390x
libnghttp2-1.59.0-1.fc40.s390x
libnsl2-2.0.0-6.fc39.s390x
libpkgconf-1.9.5-2.fc39.s390x
libpsl-0.21.5-1.fc40.s390x
libpwquality-1.4.5-6.fc39.s390x
libselinux-3.6-2.fc40.s390x
libsemanage-3.6-1.fc40.s390x
libsepol-3.6-1.fc40.s390x
libsmartcols-2.39.3-2.fc40.s390x
libssh-0.10.6-2.fc40.s390x
libssh-config-0.10.6-2.fc40.noarch
libstdc++-14.0.1-0.2.fc40.s390x
libtasn1-4.19.0-3.fc39.s390x
libtirpc-1.3.4-1.rc1.fc40.s390x
libunistring-1.1-5.fc40.s390x
libutempter-1.2.1-10.fc39.s390x
libuuid-2.39.3-2.fc40.s390x
libverto-0.3.2-6.fc39.s390x
libxcrypt-4.4.36-4.fc40.s390x
libxml2-2.12.4-1.fc40.s390x
libzstd-1.5.5-4.fc39.s390x
lua-libs-5.4.6-3.fc39.s390x
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.s390x
mpfr-4.2.1-1.fc40.s390x
ncurses-base-6.4-9.20240113.fc40.noarch
ncurses-libs-6.4-9.20240113.fc40.s390x
ocaml-srpm-macros-9-1.fc40.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.s390x
openssl-libs-3.1.4-1.fc40.s390x
p11-kit-0.25.3-1.fc40.s390x
p11-kit-trust-0.25.3-1.fc40.s390x
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.6.0-1.fc40.s390x
pam-libs-1.6.0-1.fc40.s390x
patch-2.7.6-22.fc39.s390x
pcre2-10.42-2.fc40.s390x
pcre2-syntax-10.42-2.fc40.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.s390x
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.s390x
popt-1.19-3.fc39.s390x
publicsuffix-list-dafsa-20240107-1.fc40.noarch
pyproject-srpm-macros-1.11.0-1.fc40.noarch
python-srpm-macros-3.12-7.fc40.noarch
qt5-srpm-macros-5.15.12-1.fc40.noarch
qt6-srpm-macros-6.6.1-3.fc40.noarch
readline-8.2-7.fc40.s390x
redhat-rpm-config-280-1.fc40.noarch
rpm-4.19.1-2.fc40.s390x
rpm-build-4.19.1-2.fc40.s390x
rpm-build-libs-4.19.1-2.fc40.s390x
rpm-libs-4.19.1-2.fc40.s390x
rpm-sequoia-1.5.0-2.fc40.s390x
rust-srpm-macros-25.2-2.fc40.noarch
sed-4.8-14.fc39.s390x
setup-2.14.5-1.fc40.noarch
shadow-utils-4.14.0-2.fc40.s390x
sqlite-libs-3.45.0-1.fc40.s390x
systemd-libs-255.2-2.fc40.s390x
tar-1.35-2.fc40.s390x
unzip-6.0-62.fc39.s390x
util-linux-2.39.3-2.fc40.s390x
util-linux-core-2.39.3-2.fc40.s390x
which-2.21-40.fc39.s390x
xxhash-libs-0.8.2-1.fc39.s390x
xz-5.4.5-1.fc40.s390x
xz-libs-5.4.5-1.fc40.s390x
zig-srpm-macros-1-1.fc40.noarch
zip-3.0-39.fc40.s390x
zlib-ng-compat-2.1.6-1.fc40.s390x
zstd-1.5.5-4.fc39.s390x
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/percolator-3.06.04-3.fc40.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1706218334.596559/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-qqj151hc/percolator/percolator.spec) Config(child) 2 minutes 10 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/percolator-3.06.04-3.fc40.src.rpm) Config(fedora-rawhide-s390x)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1706218334.596559/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1706218334.596559/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-s390x-1706218334.596559/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
rpm-4.19.1-2.fc40.s390x
rpm-sequoia-1.5.0-2.fc40.s390x
python3-dnf-4.18.2-1.fc40.noarch
yum-4.18.2-1.fc40.noarch
dnf5-5.1.11-1.fc40.s390x
dnf5-plugins-5.1.11-1.fc40.s390x
Finish: chroot init
Start: build phase for percolator-3.06.04-3.fc40.src.rpm
Start: build setup for percolator-3.06.04-3.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/percolator-3.06.04-3.fc40.src.rpm
Updating and loading repositories:
fedora 100% | 44.0 KiB/s | 4.5 KiB | 00m00s
Additional repo http_kojipkgs_fedorapr 100% | 19.4 KiB/s | 4.1 KiB | 00m00s
Copr repository 100% | 2.5 KiB/s | 1.5 KiB | 00m01s
Repositories loaded.
Package Arch Version Repository Size
Installing:
boost-devel s390x 1.83.0-2.fc40 copr_base 143.0 MiB
boost-static s390x 1.83.0-2.fc40 copr_base 33.5 MiB
bzip2-devel s390x 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309.8 KiB
cmake s390x 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29.9 MiB
gcc s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 76.0 MiB
gcc-c++ s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28.6 MiB
gtest-devel s390x 1.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 MiB
libtirpc-devel s390x 1.3.4-1.rc1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251.5 KiB
make s390x 1:4.4.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 MiB
python3-devel s390x 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 MiB
sqlite-devel s390x 3.45.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 663.2 KiB
tokyocabinet-devel s390x 1.4.48-23.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 460.2 KiB
xerces-c-devel s390x 3.2.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.1 MiB
xsd s390x 4.1.0-0.12.a11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.7 MiB
zlib-ng-compat-devel s390x 2.1.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103.4 KiB
Installing dependencies:
annobin-docs noarch 12.38-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 95.6 KiB
annobin-plugin-gcc s390x 12.38-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 966.5 KiB
boost s390x 1.83.0-2.fc40 copr_base 1.3 KiB
boost-atomic s390x 1.83.0-2.fc40 copr_base 20.7 KiB
boost-chrono s390x 1.83.0-2.fc40 copr_base 41.2 KiB
boost-container s390x 1.83.0-2.fc40 copr_base 69.2 KiB
boost-context s390x 1.83.0-2.fc40 copr_base 16.3 KiB
boost-contract s390x 1.83.0-2.fc40 copr_base 106.4 KiB
boost-coroutine s390x 1.83.0-2.fc40 copr_base 20.9 KiB
boost-date-time s390x 1.83.0-2.fc40 copr_base 16.1 KiB
boost-fiber s390x 1.83.0-2.fc40 copr_base 86.1 KiB
boost-filesystem s390x 1.83.0-2.fc40 copr_base 150.7 KiB
boost-graph s390x 1.83.0-2.fc40 copr_base 369.2 KiB
boost-iostreams s390x 1.83.0-2.fc40 copr_base 94.0 KiB
boost-json s390x 1.83.0-2.fc40 copr_base 363.9 KiB
boost-locale s390x 1.83.0-2.fc40 copr_base 635.1 KiB
boost-log s390x 1.83.0-2.fc40 copr_base 1.5 MiB
boost-math s390x 1.83.0-2.fc40 copr_base 713.5 KiB
boost-nowide s390x 1.83.0-2.fc40 copr_base 24.7 KiB
boost-numpy3 s390x 1.83.0-2.fc40 copr_base 57.1 KiB
boost-program-options s390x 1.83.0-2.fc40 copr_base 291.2 KiB
boost-python3 s390x 1.83.0-2.fc40 copr_base 256.2 KiB
boost-random s390x 1.83.0-2.fc40 copr_base 33.4 KiB
boost-regex s390x 1.83.0-2.fc40 copr_base 302.1 KiB
boost-serialization s390x 1.83.0-2.fc40 copr_base 474.8 KiB
boost-stacktrace s390x 1.83.0-2.fc40 copr_base 63.2 KiB
boost-system s390x 1.83.0-2.fc40 copr_base 16.1 KiB
boost-test s390x 1.83.0-2.fc40 copr_base 675.8 KiB
boost-thread s390x 1.83.0-2.fc40 copr_base 140.1 KiB
boost-timer s390x 1.83.0-2.fc40 copr_base 24.8 KiB
boost-type_erasure s390x 1.83.0-2.fc40 copr_base 61.8 KiB
boost-wave s390x 1.83.0-2.fc40 copr_base 689.9 KiB
cmake-data noarch 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 MiB
cmake-filesystem s390x 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B
cmake-rpm-macros noarch 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.4 KiB
cpp s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25.4 MiB
emacs-filesystem noarch 1:29.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 0.0 B
expat s390x 2.5.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302.4 KiB
flexiblas s390x 3.4.1-3.fc40 copr_base 46.7 KiB
flexiblas-netlib s390x 3.4.1-3.fc40 copr_base 11.5 MiB
flexiblas-openblas-openmp s390x 3.4.1-3.fc40 copr_base 39.2 KiB
gc s390x 8.2.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 273.8 KiB
gcc-plugin-annobin s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 56.8 KiB
glibc-devel s390x 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 392.1 KiB
glibc-headers-s390 noarch 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 MiB
gmock s390x 1.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 133.6 KiB
gtest s390x 1.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 477.9 KiB
guile22 s390x 2.2.7-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43.8 MiB
jsoncpp s390x 1.9.5-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251.6 KiB
kernel-headers s390x 6.8.0-0.rc1.12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.2 MiB
libasan s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB
libatomic s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32.3 KiB
libb2 s390x 0.98.1-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41.9 KiB
libcutl s390x 1.10.0-27.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 MiB
libgfortran s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 MiB
libicu s390x 73.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36.5 MiB
libicu-devel s390x 73.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.5 MiB
libmpc s390x 1.3.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 164.5 KiB
libstdc++-devel s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14.3 MiB
libtool-ltdl s390x 2.4.7-10.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 74.0 KiB
libubsan s390x 14.0.1-0.2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 491.3 KiB
libuv s390x 1:1.47.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 547.0 KiB
libxcrypt-devel s390x 4.4.36-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 30.3 KiB
mpdecimal s390x 2.5.1-7.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 228.7 KiB
openblas s390x 0.3.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96.0 KiB
openblas-openmp s390x 0.3.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 15.2 MiB
pyproject-rpm-macros noarch 1.11.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 98.5 KiB
python-pip-wheel noarch 23.3.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 MiB
python-rpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22.1 KiB
python3 s390x 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31.6 KiB
python3-libs s390x 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41.8 MiB
python3-numpy s390x 1:1.26.2-4.fc40 copr_base 42.1 MiB
python3-packaging noarch 23.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 421.1 KiB
python3-rpm-generators noarch 14-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82.3 KiB
python3-rpm-macros noarch 3.12-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.4 KiB
rhash s390x 1.4.3-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 356.3 KiB
sqlite s390x 3.45.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 MiB
tokyocabinet s390x 1.4.48-23.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB
tzdata noarch 2023d-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 MiB
vim-filesystem noarch 2:9.1.031-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40.0 B
xerces-c s390x 3.2.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.7 MiB
Transaction Summary:
Installing: 96 packages
Total size of inbound packages is 137 MiB. Need to download 137 MiB.
After this operation 607 MiB will be used (install 607 MiB, remove 0 B).
[ 1/96] bzip2-devel-0:1.0.8-16.fc39.s39 100% | 5.6 MiB/s | 213.6 KiB | 00m00s
[ 2/96] cmake-0:3.27.7-1.fc40.s390x 100% | 185.3 MiB/s | 7.8 MiB | 00m00s
[ 3/96] gcc-0:14.0.1-0.2.fc40.s390x 100% | 256.5 MiB/s | 30.3 MiB | 00m00s
[ 4/96] gcc-c++-0:14.0.1-0.2.fc40.s390x 100% | 244.3 MiB/s | 11.7 MiB | 00m00s
[ 5/96] gtest-devel-0:1.14.0-2.fc40.s39 100% | 21.5 MiB/s | 242.1 KiB | 00m00s
[ 6/96] make-1:4.4.1-2.fc39.s390x 100% | 58.3 MiB/s | 597.5 KiB | 00m00s
[ 7/96] libtirpc-devel-0:1.3.4-1.rc1.fc 100% | 11.1 MiB/s | 113.2 KiB | 00m00s
[ 8/96] sqlite-devel-0:3.45.0-1.fc40.s3 100% | 29.0 MiB/s | 148.7 KiB | 00m00s
[ 9/96] tokyocabinet-devel-0:1.4.48-23. 100% | 3.2 MiB/s | 88.6 KiB | 00m00s
[10/96] xerces-c-devel-0:3.2.5-1.fc40.s 100% | 13.7 MiB/s | 434.8 KiB | 00m00s
[11/96] python3-devel-0:3.12.1-2.fc40.s 100% | 29.7 MiB/s | 273.9 KiB | 00m00s
[12/96] xsd-0:4.1.0-0.12.a11.fc39.s390x 100% | 24.0 MiB/s | 1.2 MiB | 00m00s
[13/96] zlib-ng-compat-devel-0:2.1.6-1. 100% | 5.0 MiB/s | 36.1 KiB | 00m00s
[14/96] boost-0:1.83.0-2.fc40.s390x 100% | 103.4 KiB/s | 14.5 KiB | 00m00s
[15/96] boost-static-0:1.83.0-2.fc40.s3 100% | 680.8 KiB/s | 3.3 MiB | 00m05s
[16/96] boost-numpy3-0:1.83.0-2.fc40.s3 100% | 6.7 KiB/s | 29.8 KiB | 00m04s
[17/96] boost-atomic-0:1.83.0-2.fc40.s3 100% | 342.4 KiB/s | 19.5 KiB | 00m00s
[18/96] boost-chrono-0:1.83.0-2.fc40.s3 100% | 457.5 KiB/s | 26.1 KiB | 00m00s
[19/96] boost-devel-0:1.83.0-2.fc40.s39 100% | 2.3 MiB/s | 11.8 MiB | 00m05s
[20/96] boost-context-0:1.83.0-2.fc40.s 100% | 302.9 KiB/s | 17.3 KiB | 00m00s
[21/96] boost-container-0:1.83.0-2.fc40 100% | 733.9 KiB/s | 41.8 KiB | 00m00s
[22/96] boost-contract-0:1.83.0-2.fc40. 100% | 817.9 KiB/s | 45.8 KiB | 00m00s
[23/96] boost-coroutine-0:1.83.0-2.fc40 100% | 363.4 KiB/s | 20.7 KiB | 00m00s
[24/96] boost-date-time-0:1.83.0-2.fc40 100% | 277.9 KiB/s | 16.1 KiB | 00m00s
[25/96] boost-fiber-0:1.83.0-2.fc40.s39 100% | 465.1 KiB/s | 43.3 KiB | 00m00s
[26/96] boost-filesystem-0:1.83.0-2.fc4 100% | 1.2 MiB/s | 69.1 KiB | 00m00s
[27/96] boost-graph-0:1.83.0-2.fc40.s39 100% | 2.7 MiB/s | 159.7 KiB | 00m00s
[28/96] boost-iostreams-0:1.83.0-2.fc40 100% | 722.2 KiB/s | 41.2 KiB | 00m00s
[29/96] boost-json-0:1.83.0-2.fc40.s390 100% | 2.7 MiB/s | 155.8 KiB | 00m00s
[30/96] boost-locale-0:1.83.0-2.fc40.s3 100% | 3.7 MiB/s | 219.1 KiB | 00m00s
[31/96] boost-log-0:1.83.0-2.fc40.s390x 100% | 8.3 MiB/s | 501.7 KiB | 00m00s
[32/96] boost-math-0:1.83.0-2.fc40.s390 100% | 3.9 MiB/s | 242.1 KiB | 00m00s
[33/96] boost-nowide-0:1.83.0-2.fc40.s3 100% | 370.7 KiB/s | 21.1 KiB | 00m00s
[34/96] boost-program-options-0:1.83.0- 100% | 1.9 MiB/s | 111.7 KiB | 00m00s
[35/96] boost-random-0:1.83.0-2.fc40.s3 100% | 438.3 KiB/s | 24.5 KiB | 00m00s
[36/96] boost-python3-0:1.83.0-2.fc40.s 100% | 1.6 MiB/s | 95.2 KiB | 00m00s
[37/96] boost-regex-0:1.83.0-2.fc40.s39 100% | 2.2 MiB/s | 124.7 KiB | 00m00s
[38/96] boost-stacktrace-0:1.83.0-2.fc4 100% | 536.9 KiB/s | 30.6 KiB | 00m00s
[39/96] boost-serialization-0:1.83.0-2. 100% | 2.3 MiB/s | 138.0 KiB | 00m00s
[40/96] boost-system-0:1.83.0-2.fc40.s3 100% | 287.7 KiB/s | 16.1 KiB | 00m00s
[41/96] boost-test-0:1.83.0-2.fc40.s390 100% | 4.2 MiB/s | 251.0 KiB | 00m00s
[42/96] boost-thread-0:1.83.0-2.fc40.s3 100% | 1.1 MiB/s | 62.9 KiB | 00m00s
[43/96] boost-timer-0:1.83.0-2.fc40.s39 100% | 391.0 KiB/s | 21.9 KiB | 00m00s
[44/96] glibc-devel-0:2.38.9000-35.fc40 100% | 14.1 MiB/s | 115.2 KiB | 00m00s
[45/96] glibc-headers-s390-0:2.38.9000- 100% | 72.0 MiB/s | 515.9 KiB | 00m00s
[46/96] boost-type_erasure-0:1.83.0-2.f 100% | 605.6 KiB/s | 33.9 KiB | 00m00s
[47/96] boost-wave-0:1.83.0-2.fc40.s390 100% | 3.8 MiB/s | 227.3 KiB | 00m00s
[48/96] python3-0:3.12.1-2.fc40.s390x 100% | 1.0 MiB/s | 26.4 KiB | 00m00s
[49/96] libicu-0:73.2-3.fc40.s390x 100% | 219.6 MiB/s | 10.5 MiB | 00m00s
[50/96] libicu-devel-0:73.2-3.fc40.s390 100% | 17.3 MiB/s | 850.1 KiB | 00m00s
[51/96] libcutl-0:1.10.0-27.fc39.s390x 100% | 9.1 MiB/s | 326.3 KiB | 00m00s
[52/96] xerces-c-0:3.2.5-1.fc40.s390x 100% | 33.7 MiB/s | 965.4 KiB | 00m00s
[53/96] tokyocabinet-0:1.4.48-23.fc39.s 100% | 12.8 MiB/s | 538.0 KiB | 00m00s
[54/96] sqlite-0:3.45.0-1.fc40.s390x 100% | 37.6 MiB/s | 924.5 KiB | 00m00s
[55/96] python3-libs-0:3.12.1-2.fc40.s3 100% | 226.5 MiB/s | 8.8 MiB | 00m00s
[56/96] expat-0:2.5.0-3.fc39.s390x 100% | 18.5 MiB/s | 113.9 KiB | 00m00s
[57/96] python3-numpy-1:1.26.2-4.fc40.s 100% | 39.3 MiB/s | 6.9 MiB | 00m00s
[58/96] gc-0:8.2.2-4.fc39.s390x 100% | 9.3 MiB/s | 114.4 KiB | 00m00s
[59/96] cmake-filesystem-0:3.27.7-1.fc4 100% | 3.7 MiB/s | 19.0 KiB | 00m00s
[60/96] libtool-ltdl-0:2.4.7-10.fc40.s3 100% | 1.6 MiB/s | 37.1 KiB | 00m00s
[61/96] guile22-0:2.2.7-9.fc39.s390x 100% | 86.8 MiB/s | 6.4 MiB | 00m00s
[62/96] gtest-0:1.14.0-2.fc40.s390x 100% | 16.9 MiB/s | 172.8 KiB | 00m00s
[63/96] libxcrypt-devel-0:4.4.36-4.fc40 100% | 4.7 MiB/s | 28.9 KiB | 00m00s
[64/96] gmock-0:1.14.0-2.fc40.s390x 100% | 2.0 MiB/s | 57.9 KiB | 00m00s
[65/96] kernel-headers-0:6.8.0-0.rc1.12 100% | 84.3 MiB/s | 1.4 MiB | 00m00s
[66/96] libmpc-0:1.3.1-3.fc39.s390x 100% | 14.3 MiB/s | 73.3 KiB | 00m00s
[67/96] libasan-0:14.0.1-0.2.fc40.s390x 100% | 39.0 MiB/s | 518.9 KiB | 00m00s
[68/96] libstdc++-devel-0:14.0.1-0.2.fc 100% | 107.6 MiB/s | 2.6 MiB | 00m00s
[69/96] libatomic-0:14.0.1-0.2.fc40.s39 100% | 3.1 MiB/s | 19.1 KiB | 00m00s
[70/96] libubsan-0:14.0.1-0.2.fc40.s390 100% | 23.0 MiB/s | 212.2 KiB | 00m00s
[71/96] cpp-0:14.0.1-0.2.fc40.s390x 100% | 212.9 MiB/s | 9.6 MiB | 00m00s
[72/96] jsoncpp-0:1.9.5-5.fc39.s390x 100% | 6.7 MiB/s | 95.7 KiB | 00m00s
[73/96] libuv-1:1.47.0-3.fc40.s390x 100% | 30.7 MiB/s | 251.8 KiB | 00m00s
[74/96] rhash-0:1.4.3-3.fc39.s390x 100% | 21.7 MiB/s | 199.7 KiB | 00m00s
[75/96] cmake-data-0:3.27.7-1.fc40.noar 100% | 36.2 MiB/s | 1.7 MiB | 00m00s
[76/96] flexiblas-0:3.4.1-3.fc40.s390x 100% | 453.4 KiB/s | 25.4 KiB | 00m00s
[77/96] openblas-openmp-0:0.3.26-1.fc40 100% | 145.0 MiB/s | 4.3 MiB | 00m00s
[78/96] libgfortran-0:14.0.1-0.2.fc40.s 100% | 84.1 MiB/s | 602.7 KiB | 00m00s
[79/96] libb2-0:0.98.1-9.fc39.s390x 100% | 6.5 MiB/s | 26.8 KiB | 00m00s
[80/96] mpdecimal-0:2.5.1-7.fc39.s390x 100% | 24.4 MiB/s | 100.0 KiB | 00m00s
[81/96] python-pip-wheel-0:23.3.1-3.fc4 100% | 147.0 MiB/s | 1.5 MiB | 00m00s
[82/96] tzdata-0:2023d-2.fc40.noarch 100% | 84.7 MiB/s | 433.6 KiB | 00m00s
[83/96] flexiblas-netlib-0:3.4.1-3.fc40 100% | 29.1 MiB/s | 3.7 MiB | 00m00s
[84/96] flexiblas-openblas-openmp-0:3.4 100% | 166.8 KiB/s | 18.2 KiB | 00m00s
[85/96] openblas-0:0.3.26-1.fc40.s390x 100% | 5.4 MiB/s | 38.4 KiB | 00m00s
[86/96] vim-filesystem-2:9.1.031-1.fc40 100% | 4.3 MiB/s | 17.5 KiB | 00m00s
[87/96] emacs-filesystem-1:29.2-2.fc40. 100% | 1.2 MiB/s | 7.6 KiB | 00m00s
[88/96] python-rpm-macros-0:3.12-7.fc40 100% | 5.9 MiB/s | 18.0 KiB | 00m00s
[89/96] python3-rpm-macros-0:3.12-7.fc4 100% | 3.1 MiB/s | 12.8 KiB | 00m00s
[90/96] pyproject-rpm-macros-0:1.11.0-1 100% | 13.8 MiB/s | 42.4 KiB | 00m00s
[91/96] python3-rpm-generators-0:14-8.f 100% | 5.9 MiB/s | 30.0 KiB | 00m00s
[92/96] gcc-plugin-annobin-0:14.0.1-0.2 100% | 7.9 MiB/s | 32.2 KiB | 00m00s
[93/96] cmake-rpm-macros-0:3.27.7-1.fc4 100% | 3.0 MiB/s | 18.5 KiB | 00m00s
[94/96] annobin-plugin-gcc-0:12.38-1.fc 100% | 84.9 MiB/s | 956.3 KiB | 00m00s
[95/96] annobin-docs-0:12.38-1.fc40.noa 100% | 17.5 MiB/s | 89.6 KiB | 00m00s
[96/96] python3-packaging-0:23.2-2.fc40 100% | 37.6 MiB/s | 115.5 KiB | 00m00s
--------------------------------------------------------------------------------
[96/96] Total 100% | 22.7 MiB/s | 137.0 MiB | 00m06s
Running transaction
[ 1/98] Verify package files 100% | 208.0 B/s | 96.0 B | 00m00s
[ 2/98] Prepare transaction 100% | 568.0 B/s | 96.0 B | 00m00s
[ 3/98] Installing boost-system-0:1.83. 100% | 16.7 MiB/s | 17.1 KiB | 00m00s
[ 4/98] Installing boost-chrono-0:1.83. 100% | 0.0 B/s | 42.2 KiB | 00m00s
[ 5/98] Installing boost-thread-0:1.83. 100% | 137.8 MiB/s | 141.1 KiB | 00m00s
[ 6/98] Installing libicu-0:73.2-3.fc40 100% | 264.2 MiB/s | 36.5 MiB | 00m00s
[ 7/98] Installing boost-regex-0:1.83.0 100% | 148.0 MiB/s | 303.1 KiB | 00m00s
[ 8/98] Installing python-rpm-macros-0: 100% | 0.0 B/s | 22.8 KiB | 00m00s
[ 9/98] Installing libmpc-0:1.3.1-3.fc3 100% | 162.1 MiB/s | 166.0 KiB | 00m00s
[10/98] Installing cmake-filesystem-0:3 100% | 7.1 MiB/s | 7.3 KiB | 00m00s
[11/98] Installing expat-0:2.5.0-3.fc39 100% | 148.7 MiB/s | 304.5 KiB | 00m00s
[12/98] Installing boost-context-0:1.83 100% | 0.0 B/s | 17.3 KiB | 00m00s
[13/98] Installing boost-atomic-0:1.83. 100% | 0.0 B/s | 21.7 KiB | 00m00s
[14/98] Installing boost-filesystem-0:1 100% | 148.1 MiB/s | 151.7 KiB | 00m00s
[15/98] Installing python3-rpm-macros-0 100% | 0.0 B/s | 6.7 KiB | 00m00s
[16/98] Installing libgfortran-0:14.0.1 100% | 241.3 MiB/s | 2.2 MiB | 00m00s
[17/98] Installing gtest-0:1.14.0-2.fc4 100% | 156.0 MiB/s | 479.3 KiB | 00m00s
[18/98] Installing xerces-c-0:3.2.5-1.f 100% | 280.9 MiB/s | 3.7 MiB | 00m00s
[19/98] Installing boost-date-time-0:1. 100% | 0.0 B/s | 17.1 KiB | 00m00s
[20/98] Installing boost-container-0:1. 100% | 68.5 MiB/s | 70.2 KiB | 00m00s
[21/98] Installing boost-json-0:1.83.0- 100% | 178.2 MiB/s | 364.9 KiB | 00m00s
[22/98] Installing boost-wave-0:1.83.0- 100% | 224.9 MiB/s | 690.8 KiB | 00m00s
[23/98] Installing gmock-0:1.14.0-2.fc4 100% | 131.9 MiB/s | 135.0 KiB | 00m00s
[24/98] Installing pyproject-rpm-macros 100% | 98.1 MiB/s | 100.5 KiB | 00m00s
[25/98] Installing boost-fiber-0:1.83.0 100% | 84.9 MiB/s | 86.9 KiB | 00m00s
[26/98] Installing boost-log-0:1.83.0-2 100% | 257.6 MiB/s | 1.5 MiB | 00m00s
[27/98] Installing boost-coroutine-0:1. 100% | 0.0 B/s | 21.9 KiB | 00m00s
[28/98] Installing libcutl-0:1.10.0-27. 100% | 263.9 MiB/s | 1.1 MiB | 00m00s
[29/98] Installing cpp-0:14.0.1-0.2.fc4 100% | 267.0 MiB/s | 25.4 MiB | 00m00s
[30/98] Installing boost-graph-0:1.83.0 100% | 180.8 MiB/s | 370.2 KiB | 00m00s
[31/98] Installing boost-locale-0:1.83. 100% | 155.3 MiB/s | 636.1 KiB | 00m00s
[32/98] Installing libicu-devel-0:73.2- 100% | 232.8 MiB/s | 5.6 MiB | 00m00s
[33/98] Installing boost-type_erasure-0 100% | 0.0 B/s | 62.7 KiB | 00m00s
[34/98] Installing boost-timer-0:1.83.0 100% | 25.2 MiB/s | 25.8 KiB | 00m00s
[35/98] Installing annobin-docs-0:12.38 100% | 94.3 MiB/s | 96.6 KiB | 00m00s
[36/98] Installing vim-filesystem-2:9.1 100% | 4.6 MiB/s | 4.7 KiB | 00m00s
[37/98] Installing emacs-filesystem-1:2 100% | 0.0 B/s | 544.0 B | 00m00s
[38/98] Installing openblas-0:0.3.26-1. 100% | 95.5 MiB/s | 97.8 KiB | 00m00s
[39/98] Installing openblas-openmp-0:0. 100% | 291.6 MiB/s | 15.2 MiB | 00m00s
[40/98] Installing flexiblas-0:3.4.1-3. 100% | 0.0 B/s | 47.9 KiB | 00m00s
[41/98] Installing flexiblas-openblas-o 100% | 0.0 B/s | 40.0 KiB | 00m00s
[42/98] Installing flexiblas-netlib-0:3 100% | 267.6 MiB/s | 11.5 MiB | 00m00s
[43/98] Installing tzdata-0:2023d-2.fc4 100% | 53.0 MiB/s | 1.9 MiB | 00m00s
[44/98] Installing python-pip-wheel-0:2 100% | 506.5 MiB/s | 1.5 MiB | 00m00s
[45/98] Installing mpdecimal-0:2.5.1-7. 100% | 224.4 MiB/s | 229.8 KiB | 00m00s
[46/98] Installing libb2-0:0.98.1-9.fc3 100% | 10.5 MiB/s | 43.0 KiB | 00m00s
[47/98] Installing python3-libs-0:3.12. 100% | 255.7 MiB/s | 42.2 MiB | 00m00s
[48/98] Installing python3-0:3.12.1-2.f 100% | 32.6 MiB/s | 33.4 KiB | 00m00s
[49/98] Installing boost-python3-0:1.83 100% | 251.2 MiB/s | 257.3 KiB | 00m00s
[50/98] Installing cmake-rpm-macros-0:3 100% | 2.6 MiB/s | 8.0 KiB | 00m00s
[51/98] Installing python3-numpy-1:1.26 100% | 302.6 MiB/s | 42.4 MiB | 00m00s
[52/98] Installing boost-numpy3-0:1.83. 100% | 0.0 B/s | 58.1 KiB | 00m00s
[53/98] Installing python3-packaging-0: 100% | 140.6 MiB/s | 431.9 KiB | 00m00s
[54/98] Installing python3-rpm-generato 100% | 81.5 MiB/s | 83.4 KiB | 00m00s
[55/98] Installing rhash-0:1.4.3-3.fc39 100% | 117.7 MiB/s | 361.5 KiB | 00m00s
[56/98] Installing libuv-1:1.47.0-3.fc4 100% | 179.0 MiB/s | 549.8 KiB | 00m00s
[57/98] Installing jsoncpp-0:1.9.5-5.fc 100% | 123.6 MiB/s | 253.1 KiB | 00m00s
[58/98] Installing libubsan-0:14.0.1-0. 100% | 160.2 MiB/s | 492.1 KiB | 00m00s
[59/98] Installing libatomic-0:14.0.1-0 100% | 0.0 B/s | 33.0 KiB | 00m00s
[60/98] Installing libasan-0:14.0.1-0.2 100% | 182.5 MiB/s | 1.6 MiB | 00m00s
[61/98] Installing libstdc++-devel-0:14 100% | 272.7 MiB/s | 14.5 MiB | 00m00s
[62/98] Installing kernel-headers-0:6.8 100% | 163.2 MiB/s | 6.4 MiB | 00m00s
[63/98] Installing libtool-ltdl-0:2.4.7 100% | 73.3 MiB/s | 75.1 KiB | 00m00s
[64/98] Installing gc-0:8.2.2-4.fc39.s3 100% | 89.9 MiB/s | 276.3 KiB | 00m00s
[65/98] Installing guile22-0:2.2.7-9.fc 100% | 357.4 MiB/s | 44.0 MiB | 00m00s
[66/98] Installing make-1:4.4.1-2.fc39. 100% | 154.9 MiB/s | 1.9 MiB | 00m00s
[67/98] Installing cmake-data-0:3.27.7- 100% | 102.0 MiB/s | 8.4 MiB | 00m00s
[68/98] Installing cmake-0:3.27.7-1.fc4 100% | 344.0 MiB/s | 29.9 MiB | 00m00s
[69/98] Installing sqlite-0:3.45.0-1.fc 100% | 192.0 MiB/s | 1.9 MiB | 00m00s
[70/98] Installing tokyocabinet-0:1.4.4 100% | 197.4 MiB/s | 1.6 MiB | 00m00s
[71/98] Installing glibc-headers-s390-0 100% | 137.8 MiB/s | 2.2 MiB | 00m00s
[72/98] Installing libxcrypt-devel-0:4. 100% | 31.8 MiB/s | 32.6 KiB | 00m00s
[73/98] Installing glibc-devel-0:2.38.9 100% | 193.2 MiB/s | 395.8 KiB | 00m00s
[74/98] Installing gcc-0:14.0.1-0.2.fc4 100% | 312.7 MiB/s | 76.0 MiB | 00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[75/98] Installing boost-test-0:1.83.0- 100% | 165.3 MiB/s | 677.2 KiB | 00m00s
[76/98] Installing boost-stacktrace-0:1 100% | 63.5 MiB/s | 65.0 KiB | 00m00s
[77/98] Installing boost-serialization- 100% | 232.6 MiB/s | 476.3 KiB | 00m00s
[78/98] Installing boost-random-0:1.83. 100% | 0.0 B/s | 34.4 KiB | 00m00s
[79/98] Installing boost-program-option 100% | 142.7 MiB/s | 292.3 KiB | 00m00s
[80/98] Installing boost-nowide-0:1.83. 100% | 0.0 B/s | 25.7 KiB | 00m00s
[81/98] Installing boost-math-0:1.83.0- 100% | 233.3 MiB/s | 716.7 KiB | 00m00s
[82/98] Installing boost-iostreams-0:1. 100% | 92.8 MiB/s | 95.0 KiB | 00m00s
[83/98] Installing boost-contract-0:1.8 100% | 104.9 MiB/s | 107.4 KiB | 00m00s
[84/98] Installing boost-0:1.83.0-2.fc4 100% | 66.1 KiB/s | 1.7 KiB | 00m00s
[85/98] Installing boost-devel-0:1.83.0 100% | 228.8 MiB/s | 145.8 MiB | 00m01s
[86/98] Installing boost-static-0:1.83. 100% | 446.3 MiB/s | 33.5 MiB | 00m00s
[87/98] Installing gcc-c++-0:14.0.1-0.2 100% | 283.4 MiB/s | 28.6 MiB | 00m00s
[88/98] Installing annobin-plugin-gcc-0 100% | 78.8 MiB/s | 968.1 KiB | 00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[89/98] Installing gcc-plugin-annobin-0 100% | 5.2 MiB/s | 58.3 KiB | 00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[90/98] Installing tokyocabinet-devel-0 100% | 226.2 MiB/s | 463.3 KiB | 00m00s
[91/98] Installing sqlite-devel-0:3.45. 100% | 324.1 MiB/s | 663.8 KiB | 00m00s
[92/98] Installing python3-devel-0:3.12 100% | 141.7 MiB/s | 1.3 MiB | 00m00s
[93/98] Installing xsd-0:4.1.0-0.12.a11 100% | 249.1 MiB/s | 5.7 MiB | 00m00s
[94/98] Installing gtest-devel-0:1.14.0 100% | 210.2 MiB/s | 1.1 MiB | 00m00s
[95/98] Installing xerces-c-devel-0:3.2 100% | 247.0 MiB/s | 4.2 MiB | 00m00s
[96/98] Installing zlib-ng-compat-devel 100% | 102.0 MiB/s | 104.5 KiB | 00m00s
[97/98] Installing libtirpc-devel-0:1.3 100% | 128.4 MiB/s | 262.9 KiB | 00m00s
[98/98] Installing bzip2-devel-0:1.0.8- 100% | 2.3 MiB/s | 310.7 KiB | 00m00s
>>> Running trigger-install scriptlet: glibc-common-0:2.38.9000-35.fc40.s390x
>>> Stop trigger-install scriptlet: glibc-common-0:2.38.9000-35.fc40.s390x
>>> Running trigger-install scriptlet: info-0:7.1-1.fc40.s390x
>>> Stop trigger-install scriptlet: info-0:7.1-1.fc40.s390x
Warning: skipped PGP checks for 96 package(s).
Finish: build setup for percolator-3.06.04-3.fc40.src.rpm
Start: rpmbuild percolator-3.06.04-3.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1706140800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.p565N0
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-06-04
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-06-04.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-06-04
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
+ find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.h' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.xx' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.txt' -exec chmod 0644 '{}' ';'
+ chmod a-x src/converters/MSToolkit/RAMP/README
+ mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README
+ mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt
+ cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt
+ sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.bsKInO
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ mkdir -p percolator
+ pushd percolator
~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ..
-- The C compiler identification is GNU 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
--
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST =
-- GOOGLE_TEST_PATH =
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE =
-- PROFILING =
-- -------------------------------------------------------------------------------
--
-- Architecture:
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
-- : /usr/include
-- Version: 3.2.5
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Locating CodeSynthesis library with XSDDIR set to
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from : /usr/lib64/libtirpc.so
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0") found components: filesystem system
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.14.0")
-- Using installed GoogleTest at:
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0")
-- Configuring done (1.1s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_Fortran_FLAGS_RELEASE
CMAKE_INSTALL_DO_STRIP
CMAKE_SKIP_INSTALL_RPATH
INCLUDE_INSTALL_DIR
LIB_INSTALL_DIR
LIB_SUFFIX
SHARE_INSTALL_PREFIX
SYSCONF_INSTALL_DIR
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/percolator
+ cd src
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd
+ cd ..
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 1%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 4%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 6%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Database.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp:985:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
985 | strncpy(protein_field_tail, protein_id, protein_field_free);
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp:976:35: note: length computed here
976 | size_t protein_id_len = strlen(protein_id);
| ~~~~~~^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 9%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PeptideConstraint.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 10%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PeptideSrc.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 2%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PickedProteinCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp
In function ‘PercolatorCrux::Protein::readRawSequence(_IO_FILE*, char*, unsigned int, char*, unsigned int*)’,
inlined from ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
505 | raw_sequence[i_seq] = '\0';
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)::buffer’ of size 40000
355 | static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
| ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/ProteinPeptideIterator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 16%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 16%] Built target picked_protein
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 17%] Building C object src/blas/CMakeFiles/blas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/daxpy.c.o -MF CMakeFiles/blas.dir/daxpy.c.o.d -o CMakeFiles/blas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/daxpy.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 18%] Building C object src/blas/CMakeFiles/blas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/ddot.c.o -MF CMakeFiles/blas.dir/ddot.c.o.d -o CMakeFiles/blas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/ddot.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 19%] Building C object src/blas/CMakeFiles/blas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dgemv.c.o -MF CMakeFiles/blas.dir/dgemv.c.o.d -o CMakeFiles/blas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dgemv.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 20%] Building C object src/blas/CMakeFiles/blas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dnrm2.c.o -MF CMakeFiles/blas.dir/dnrm2.c.o.d -o CMakeFiles/blas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dnrm2.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 22%] Building C object src/blas/CMakeFiles/blas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dscal.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 23%] Linking C static library libblas.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -E cmake_link_script CMakeFiles/blas.dir/link.txt --verbose=1
/usr/bin/ar rcv libblas.a CMakeFiles/blas.dir/daxpy.c.o CMakeFiles/blas.dir/ddot.c.o CMakeFiles/blas.dir/dgemv.c.o CMakeFiles/blas.dir/dnrm2.c.o CMakeFiles/blas.dir/dscal.c.o
a - CMakeFiles/blas.dir/daxpy.c.o
a - CMakeFiles/blas.dir/ddot.c.o
a - CMakeFiles/blas.dir/dgemv.c.o
a - CMakeFiles/blas.dir/dnrm2.c.o
a - CMakeFiles/blas.dir/dscal.c.o
/usr/bin/ranlib libblas.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 23%] Built target blas
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 24%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
185 | for (int k = 0; k < s.size(); k++) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
191 | for (int k = 0; k < s.size(); k++) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
200 | for (int k = 0; k < associatedProteinsBySection.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
211 | for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
217 | for (int k = 0; k < associatedProteinsBySection.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
218 | for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
265 | for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
274 | for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
384 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: 381 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
9 | for (int k = 0; k < rhs.size(); k++) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 44 | if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 18 | if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 10 | if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 381 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int k=0; k<size(); k++) {
| ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 12%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:106:33: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
106 | std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning: ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
102 | DOMImplementation& dom_impl_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning: when initialized here [-Wreorder]
144 | parser_impl::parser_impl() : clean_(true),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
178 | size_t n(s.size());
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
170 | int i(1);
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 29%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
126 | std::string peptide;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning: ‘int PSMDescription::specFileNr’ [-Wreorder]
122 | int specFileNr;
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:23:1: warning: when initialized here [-Wreorder]
23 | PSMDescription::PSMDescription() :
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription(const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
126 | std::string peptide;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning: ‘int PSMDescription::specFileNr’ [-Wreorder]
122 | int specFileNr;
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:28:1: warning: when initialized here [-Wreorder]
28 | PSMDescription::PSMDescription(const std::string& pep) :
| ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ResultHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 25%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
47 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
79 | for (int k=0; k<s.size(); k++) {
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
90 | for (int k=0; k<s.size(); k++) {
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
100 | for (int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
168 | for (int k=0; k<n.size(); k++)
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
179 | for (int k = 0; k < originalN.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
289 | for (int k=0; k<result.size(); k++) {
| make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
322 | for ( int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: 71 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
9 | for (int k = 0; k < rhs.size(); k++) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 44 | if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 18 | if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 10 | if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 71 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int k=0; k<size(); k++) {
| ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:30,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
119 | bool reportPepXML_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:111:8: warning: ‘bool XMLInterface::printDecoys_’ [-Wreorder]
111 | bool printDecoys_, printExpMass_;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:58:1: warning: when initialized here [-Wreorder]
58 | XMLInterface::XMLInterface(const std::string& outputFN,
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:258:26: warning: unused variable ‘numFeatures’ [-Wunused-variable]
258 | const unsigned int numFeatures = FeatureNames::getNumFeatures();
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘void XMLInterface::writePepXML_PSMs(Scores&, double, std::string)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:641:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
641 | if (sh->q < selectionFdr_)
| ^~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:643:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
643 | index++;
| ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 34%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
10 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
22 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | for (; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
77 | for (int k = 0; k < groupProtNames_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
94 | for (int k=0; k<sorted.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (int k=0; k<subgraphs_.size(); k++) {
| ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for (int k = 0; k < preResult.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
188 | for (int k = 0; k < subBasic.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
202 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
210 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
222 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 37%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Numerical.cpp.o -MF CMakeFiles/fido.dir/Numerical.cpp.o.d -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 38%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
65 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 39%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Set.cpp.o -MF CMakeFiles/fido.dir/Set.cpp.o.d -o CMakeFiles/fido.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
142 | for (int k=0; k<size()-1; k++) {
| ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
91 | bool hasScannr = false, hasRt = false, hasDm = false;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
91 | bool hasScannr = false, hasRt = false, hasDm = false;
| ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 40%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Vector.cpp.o -MF CMakeFiles/fido.dir/Vector.cpp.o.d -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
382 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
392 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
530 | for (int k=0; k<result.size(); k++)
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
542 | for (int k=0; k<u.size(); k++)
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
545 | if ( k != u.size() - 1 )
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
559 | for (int i=0; i<s.size(); i++)
| ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 44%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 44%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp: In function ‘svm_train’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
42 | #define Malloc(type,n) (type *)malloc((static_cast<std::size_t>(n))*sizeof(type))
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/std_abs.h:38,
from /usr/include/c++/14/cmath:49,
from /usr/include/c++/14/math.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:1:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:28,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:100:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
100 | bool trainBestPositive_;
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:89:16: warning: ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
89 | unsigned int numThreads_;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:32:1: warning: when initialized here [-Wreorder]
32 | CrossValidation::CrossValidation(bool quickValidation,
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
110 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(Normalizer*, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:296:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<candidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
296 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::mergeCpCnPairs(double, options&, std::vector<std::vector<Scores> >&, const std::vector<double>&, const std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:370:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
370 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:410:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
410 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
441 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::unnormalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:40:10: warning: unused variable ‘sum’ [-Wunused-variable]
40 | double sum = 0;
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::normalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:49:10: warning: unused variable ‘sum’ [-Wunused-variable]
49 | double sum = 0;
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:111:27: warning: ‘Caller::analytics_’ will be initialized after [-Wreorder]
111 | skipNormalizeScores_, analytics_;
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:97:8: warning: ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
97 | bool xmlPrintDecoys_, xmlPrintExpMass_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning: when initialized here [-Wreorder]
36 | Caller::Caller() :
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:110:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
110 | bool reportEachIteration_, quickValidation_, trainBestPositive_,
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:108:59: warning: ‘unsigned int Caller::numThreads_’ [-Wreorder]
108 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning: when initialized here [-Wreorder]
36 | Caller::Caller() :
| ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
87 | bool concatenatedSearch_;
| ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:72:10: warning: ‘double SanityCheck::test_fdr_’ [-Wreorder]
72 | double test_fdr_, initial_train_fdr_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder]
31 | SanityCheck::SanityCheck() :
| ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
238 | double pi0_, absenceRatio_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:10: warning: ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
238 | double pi0_, absenceRatio_;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder]
25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
242 | unsigned int numberTargetProteins_;
| ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:237:8: warning: ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
237 | bool usePi0_;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder]
25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
243 | std::string decoyPattern_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:240:10: warning: ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
240 | double fdr_;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder]
25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
| ^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ssl.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.h:11,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Matrix.cpp.o -MF CMakeFiles/perclibrary.dir/Matrix.cpp.o.d -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In member function ‘const Matrix& Matrix::operator=(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:10:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
10 | for (int k=0; k<rhs.size(); k++)
| ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In function ‘Array<Array<double> > operator-(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
519 | for (int k=0; k<result.size(); k++)
| ~^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -MF CMakeFiles/perclibrary.dir/FidoInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:20,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h: In constructor ‘FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:110:10: warning: ‘FidoInterface::mseThreshold_’ will be initialized after [-Wreorder]
110 | double mseThreshold_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:106:8: warning: ‘bool FidoInterface::doGridSearch_’ [-Wreorder]
106 | bool doGridSearch_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:76:1: warning: when initialized here [-Wreorder]
76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp: In member function ‘double FidoInterface::estimatePriors(Scores&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:132:10: warning: variable ‘prior’ set but not used [-Wunused-but-set-variable]
132 | double prior, prior2, prior3, prior4;
| ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
108 | bool isDecoy_;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:106:7: warning: ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
106 | int groupId_;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder]
20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
| ^~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:35:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:163:16: warning: unused variable ‘native_id’ [-Wunused-variable]
163 | unsigned int native_id = scan - 1;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:167:10: warning: unused variable ‘RT’ [-Wunused-variable]
167 | double RT = pPSM->getRetentionTime();
| ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:27,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
86 | double maxPeptidePval_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:8: warning: ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
85 | bool reportFragmentProteins_, reportDuplicateProteins_;
| ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder]
22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
85 | bool reportFragmentProteins_, reportDuplicateProteins_;
| ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:83:26: warning: ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
83 | ProteinInferenceMethod protInferenceMethod_;
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder]
22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
165 | if (total_non_enzymatic_flanks > peptideScores.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Timer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.h:6,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -MF CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o.d -o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/GoogleAnalytics.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
/usr/bin/ranlib libperclibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] Built target perclibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 87%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/./BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/./LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 86%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 88%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality -L/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src ../libperclibrary.a ../fido/libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 90%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 91%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 95%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
65 | if (n > 0)
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:140:9: warning: unused variable ‘numInit’ [-Wunused-variable]
140 | int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
| ^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -ltirpc -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a
In function ‘readRawSequence’,
inlined from ‘parseProteinFastaFile’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
505 | raw_sequence[i_seq] = '\0';
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘parseProteinFastaFile’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object ‘buffer’ of size 40000
355 | static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit ../../../src/libperclibrary.a ../../../src/blas/libblas.a ../../../src/fido/libfido.a -lpthread /usr/lib64/libgtest_main.so.1.14.0 /usr/lib64/libgtest.so.1.14.0
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-06-04/fido ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ../src/fido
-- The C compiler identification is GNU 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.5s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_C_FLAGS_RELEASE
CMAKE_EXE_LINKER_FLAGS_RELEASE
CMAKE_Fortran_FLAGS_RELEASE
CMAKE_INSTALL_DO_STRIP
CMAKE_SKIP_INSTALL_RPATH
CMAKE_SKIP_RPATH
INCLUDE_INSTALL_DIR
LIB_INSTALL_DIR
LIB_SUFFIX
SHARE_INSTALL_PREFIX
SYSCONF_INSTALL_DIR
TARGET_ARCH
TokyoCabinet_INCLUDE_DIR
TokyoCabinet_LIBRARY
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/fido
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -B/builddir/build/BUILD/percolator-rel-3-06-04/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/fido//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
cd /builddir/build/BUILD/percolator-rel-3-06-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 25%] Building CXX object CMakeFiles/fido.dir/BasicGroupBigraph.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicGroupBigraph.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
107 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
117 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
129 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
138 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
144 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
150 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
47 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
58 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
79 | for (int k=0; k<s.size(); k++) {
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
90 | for (int k=0; k<s.size(); k++) {
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
100 | for (int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
168 | for (int k=0; k<n.size(); k++)
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
179 | for (int k = 0; k < originalN.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
252 | for (int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
289 | for (int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
322 | for ( int k=0; k<result.size(); k++) {
| ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: 71 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
9 | for (int k = 0; k < rhs.size(); k++) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 44 | if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 18 | if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 10 | if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 71 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int k=0; k<size(); k++) {
| ~^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:4:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
107 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
117 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
129 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
138 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
144 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
150 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
185 | for (int k = 0; k < s.size(); k++) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
191 | for (int k = 0; k < s.size(); k++) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
200 | for (int k = 0; k < associatedProteinsBySection.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
211 | for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
217 | for (int k = 0; k < associatedProteinsBySection.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
218 | for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
265 | for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
274 | for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
384 | for (int k = 0; k < groups.size(); k++) {
| ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: 381 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
9 | for (int k = 0; k < rhs.size(); k++) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 44 | if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 18 | if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 10 | if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: 381 | Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int k=0; k<size(); k++) {
| ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 62%] Building CXX object CMakeFiles/fido.dir/Random.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
65 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 75%] Building CXX object CMakeFiles/fido.dir/Set.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Set.o -MF CMakeFiles/fido.dir/Set.o.d -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
142 | for (int k=0; k<size()-1; k++) {
| ~^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Vector.o -MF CMakeFiles/fido.dir/Vector.o.d -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
382 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
392 | for (int k=0; k<lhs.size(); k++)
| ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
530 | for (int k=0; k<result.size(); k++)
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
542 | for (int k=0; k<u.size(); k++)
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
545 | if ( k != u.size() - 1 )
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
559 | for (int i=0; i<s.size(); i++)
| ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 37%] Building CXX object CMakeFiles/fido.dir/GroupPowerBigraph.o
/usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/GroupPowerBigraph.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
52 | T & Array<T>::operator [] (std::size_t k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
45 | const T & Array<T>::operator [] (std::size_t k) const
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
38 | T & Array<T>::operator [] (int k)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’
31 | const int & operator [](int k) const {
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:56:3: warning: when initialized here [-Wreorder]
56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
54 | int label;
| ^~~~~
../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
53 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:57:3: warning: when initialized here [-Wreorder]
57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
107 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
117 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
129 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
138 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
144 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
150 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
10 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘lonmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
g unsigned int’} [-Wsign-compare]
22 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | for (; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
77 | for (int k = 0; k < groupProtNames_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
94 | for (int k=0; k<sorted.size(); k++) {
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (int k=0; k<subgraphs_.size(); k++) {
| ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for (int k = 0; k < preResult.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
188 | for (int k = 0; k < subBasic.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
202 | for (int k = 0; k < subgraphs_.size(); k++) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
210 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
222 | for (int k = 0; k < sorted.size(); k++) {
| ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[100%] Linking CXX static library libfido.a
/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-06-04/converters ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=s390x ../src/converters
-- The C compiler identification is GNU 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
--
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- Indicate the type of XML serialization scheme :
-DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet"
or -DSERIALIZE="LevelDB".
By setting up the variable SERIALIZE to either Boost
or TokyoCabinet or LevelDB you will choose the serialization
scheme that will be used to build Converters.
Boost serialization option will be used as default if no option is given.
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- XML_SUPPORT = ON
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../..
-- CMAKE_PREFIX_PATH = ../
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE =
-- SERIALIZE = TokyoCabinet
-- PROFILING =
-- Using Tokyo Cabinet Serialization scheme
-- -------------------------------------------------------------------------------
--
-- Architecture:
-- Checking packages..
-- Found Xerces-C: /usr/lib64/libxerces-c.so
-- : /usr/include
-- Version: 3.2.5
-- Package CodeSynthesis XSD found: /usr/include
-- Executable: /usr/bin/xsdcxx
-- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so
-- Package Tokyo Cabinet found : /usr/include
-- Found BZip2: /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found
-- Bzip2 found
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0") found components: filesystem system
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from : /usr/lib64/libtirpc.so
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.3.0")
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done (1.3s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_Fortran_FLAGS_RELEASE
CMAKE_INSTALL_DO_STRIP
CMAKE_SKIP_INSTALL_RPATH
INCLUDE_INSTALL_DIR
LIB_INSTALL_DIR
LIB_SUFFIX
SHARE_INSTALL_PREFIX
SYSCONF_INSTALL_DIR
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
/usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 5%] Built target generate_perc_xsdfiles
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o -MF CMakeFiles/RAMP.dir/ramp_base64.cpp.o.d -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 8%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o -MF CMakeFiles/RAMP.dir/ramp.cpp.o.d -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
1698 | int err;
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.h:134,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
In function ‘*strchr’,
inlined from ‘readPeaks(RAMPFILE*, long)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function ‘readPeaks(RAMPFILE*, long)’:
cc1plus: note: source object is likely at address zero
In function ‘*strchr’,
inlined from ‘readPeaks(RAMPFILE*, long)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function ‘readPeaks(RAMPFILE*, long)’:
cc1plus: note: source object is likely at address zero
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘rampSelfTest(char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
2050 | strncpy(buf, filename, sizeof(buf));
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
2054 | strncpy(buf, filename, sizeof(buf));
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 10%] Linking CXX static library libRAMP.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -P CMakeFiles/RAMP.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1
/usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o
/usr/bin/ranlib libRAMP.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 10%] Built target RAMP
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 1%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 14%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 12%] Building CXX object CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -MF CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o.d -o CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/mzIdentML1.1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 16%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 19%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 21%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 23%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 25%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 26%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:106:33: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
106 | std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning: ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
102 | DOMImplementation& dom_impl_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning: when initialized here [-Wreorder]
144 | parser_impl::parser_impl() : clean_(true),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
178 | size_t n(s.size());
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
170 | int i(1);
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 28%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 30%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 32%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 33%] Linking CXX static library libperclibrary_part.a
/usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary_part.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary_part.a CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o"
/usr/bin/ranlib libperclibrary_part.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 37%] Built target perclibrary_part
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 17%] Building CXX object CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 39%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.H:28,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In function ‘LazyMatrix* flip_lazy_matrix(LazyMatrix&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
21 | for ( uint j = 0 ; j < lm.rows() ; j++ ) {
| ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
22 | for ( uint i = 0 ; i < lm.cols() ; i++ ) {
| ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In constructor ‘LazyMatrix::LazyMatrix(int, int, sparse_level, FILE*, off_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:39:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
39 | for ( std::size_t i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:44:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
44 | for ( std::size_t i = 0 ; i < nrows; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor ‘LazyMatrix::LazyMatrix(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
56 | *data_copies++;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::copy_m_flip(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
67 | for ( uint i = 0 ; i < x.nrows ; i++ ) {
| ~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::set_col(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:150:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
150 | for ( std::size_t i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::_get_row_retain(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
179 | std::vector<float>::iterator b = this->m[static_cast<std::size_t>(i)]->begin();
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_cols(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:290:72: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
290 | for ( std::size_t i = static_cast<std::size_t>(start_idx); i < stop_idx ; i++ ) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_start_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:298:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
298 | for ( std::size_t i = 0 ; i < rows() ; i++ ) {
| ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_stop_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:305:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
305 | for ( std::size_t i =0 ; i < rows() ; i++ ) {
| ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::column_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
369 | for ( uint i = 0 ;i < rows() ; i++ ) {
| ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
370 | for ( uint j = 0 ; j < cols() ; j++ ) {
| ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
373 | if ( dest_idx >= cols() ) break;
| ~~~~~~~~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::linear_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
389 | for ( uint i = 0; i < shift ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:393:62: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
393 | for ( std::size_t i = static_cast<std::size_t>(shift); i < nrows; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:409:31: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
igned int’} and ‘int’ [-Wsign-compare]
409 | for ( uint i = offset ; i < nrows - static_cast<int>(offset); i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:412:76: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
412 | for ( uint i = static_cast<uint>(nrows - static_cast<int>(offset)) ; i < nrows; i++ ) {
| ~~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 42%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSConvertFile.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 44%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSObject.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 46%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeFile(const char*, bool, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:509:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
509 | for(unsigned int j=0;j<m.size();j++){
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeSqlite(const char*, MSObject&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:634:34: warning: the address of ‘MSHeader::header’ will never be NULL [-Waddress]
634 | if(m.getHeader().header[i] != 0)
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:4,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.h:4,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: ‘MSHeader::header’ declared here
54 | char header[16][128];
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
750 | int err;
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:756:17: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
756 | unsigned long sizeM;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:757:17: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
757 | unsigned long sizeI;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(char*, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1016:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1016 | for(i=0;i<m.size();i++) writeTextSpec(fileOut,m.at(i));
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1025:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1025 | for(i=0;i<m.size();i++){
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1034:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1034 | for(i=0;i<m.size();i++){
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1043:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1043 | for(i=0;i<m.size();i++){
| ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘bool MSReader::executeSqlStmt(Spectrum&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable ‘charge’ [-Wunused-variable]
1187 | int charge=-1;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeCompressSpec(FILE*, Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1610:13: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
1610 | int err;
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1616:23: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
1616 | unsigned long sizeM;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1617:23: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
1617 | unsigned long sizeI;
| ^~~~~
In file included from /usr/include/stdio.h:980,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/parallel/compiletime_settings.h:33,
from /usr/include/c++/14/parallel/parallel.h:37,
from /usr/include/c++/14/parallel/base.h:40,
from /usr/include/c++/14/parallel/algobase.h:40,
from /usr/include/c++/14/bits/stl_algobase.h:2330,
from /usr/include/c++/14/vector:62,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:5:
In function ‘sprintf’,
inlined from ‘MSReader::appendFile(Spectrum&)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:869:11:
/usr/include/bits/stdio2.h:30:34: warning: ‘lastScanID’ may be used uninitialized [-Wmaybe-uninitialized]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:853:7: note: ‘lastScanID’ was declared here
853 | int lastScanID;
| ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -MF CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable ‘ff’ set but not used [-Wunused-but-set-variable]
26 | MSFileFormat ff;
| ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 51%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 53%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -MF CMakeFiles/MSToolkit.dir/MSWarper.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
594 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
697 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
806 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
807 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
809 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
812 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
813 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
| ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 41%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/tandem2011.12.01.1.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 55%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp: In member function ‘bool Spectrum::getRawFilter(char*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
282 | if(sz<strlen(rawFilter)) {
| ~~^~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 57%] Building CXX object CMakeFiles/converters.dir/Reader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Reader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 60%] Building CXX object CMakeFiles/converters.dir/SqtReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SqtReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 58%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:21:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rankties(std::vector<float>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable ‘start_idx’ [-Wunused-variable]
261 | int start_idx = -1;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable ‘stop_idx’ [-Wunused-variable]
262 | int stop_idx = -1;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<float, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
354 | if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[static_cast<std::size_t>(i)].first == last_val) ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable ‘last_rank’ [-Wunused-variable]
346 | int last_rank = -1;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_3(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:455:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
455 | for ( std::size_t i = 0 ; i < (int)s1.size(); i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_4(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:488:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
488 | for ( std::size_t i = 0 ; i < (int)s1.size(); i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:976:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
976 | for (idx = 1; idx < (int)y.size(); idx++)
| ~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1090:10: warning: unused variable ‘last_tryp’ [-Wunused-variable]
1090 | bool last_tryp = false;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawstats::pi0_from_StoreySplineFit(const std::vector<std::pair<float, float> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1402:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1402 | for (std::size_t i = 1; i <= n - 1; i++)
| ~~^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp: In member function ‘virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
86 | } catch (ifstream::failure e) {
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=]
94 | } catch (MyException e) {
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
97 | } catch (std::exception e) {
| ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 66%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/SequestReader.cpp.o -MF CMakeFiles/converters.dir/SequestReader.cpp.o.d -o CMakeFiles/converters.dir/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp: In member function ‘virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:169:12: warning: unused variable ‘PI’ [-Wunused-variable]
169 | double PI = boost::lexical_cast<double>(item.calculatedPI().get());
| ^~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:174:14: warning: unused variable ‘peptide_length’ [-Wunused-variable]
174 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
| ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 64%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:17:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
594 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
697 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In constructor ‘transition_manager::transition_manager(std::vector<transition_info>)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:47:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<transition_info>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
47 | for ( int i = 0 ; i < transitions.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::init_transitions_from_labels()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:76:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
76 | for ( int i = 0 ; i < labels.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_input(std::ifstream&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:107:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
107 | for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::zero_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:185:70: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
185 | for ( std::size_t i = static_cast<std::size_t>(start_scan_idx) ; i <= stop_scan_idx ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_dist_set(int, std::vector<int>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:216:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
216 | for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:225:9: warning: unused variable ‘set_idx’ [-Wunused-variable]
225 | int set_idx = 0;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:251:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
251 | for ( std::size_t i = 0 ; i < start_scan_idx ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘int msmat::check_size_from_position() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:271:30: warning: comparison of integer expressions of different signedness: ‘off64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
271 | if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::calc_bp_chrom()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:668:36: warning: variable ‘scan_length’ set but not used [-Wunused-but-set-variable]
668 | std::size_t scan_idx, num_scans, scan_length;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::pad_start_stop(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:775:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
775 | for ( int i = stop_mapped_coord+1 ; i < get_num_rts() ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::time_interpolate(double, msmat&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1056:14: warning: variable ‘dim’ set but not used [-Wunused-but-set-variable]
1056 | matrix_dim dim = get_data_dim();
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_median() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1266:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1266 | for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1267:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1267 | for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_avg(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/srmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
c/converters/MSToolkit/msmat.cpp:1282:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1282 | if ( i < 0 || i >= get_num_rts() ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_twomat_num(const msmat&, double, double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1313:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1313 | for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
| ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1315:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1315 | if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_mat_denom(double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1338:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1338 | if ( i < 0 || i >= get_num_rts() ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::correlation_w_shift(const msmat&, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1356:17: warning: unused variable ‘self’ [-Wunused-variable]
1356 | const msmat & self = *this;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1411:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1411 | for ( std::size_t i = 0; i < r_stop - r_start ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1410:9: warning: unused variable ‘foo’ [-Wunused-variable]
1410 | int foo = 5;
| ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘virtual void msmat_scans::get_chrom(int, std::vector<float>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1486:11: warning: unused variable ‘volatile_this’ [-Wunused-variable]
1486 | msmat * volatile_this;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In function ‘msmat* test_msmat(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:19: warning: variable ‘ti_file’ set but not used [-Wunused-but-set-variable]
1593 | FILE * o_file, *ti_file, *sg_file;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:29: warning: variable ‘sg_file’ set but not used [-Wunused-but-set-variable]
1593 | FILE * o_file, *ti_file, *sg_file;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1816:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1816 | new_cnt < mzs.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1818:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1818 | for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1846:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1846 | new_cnt < rts.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1848:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1848 | for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1868:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1868 | new_cnt < mzs.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1886:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1886 | new_cnt < rts.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘bool msmat::equals_data(const msmat&, double) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1909:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1909 | for ( int i = 0 ; i < get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::sum_abs_diffs(const msmat&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1932:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1932 | for ( int i = 0 ; i < get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1929:10: warning: unused variable ‘nrows’ [-Wunused-variable]
1929 | size_t nrows = get_num_rows();
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1978:13: warning: unused variable ‘num_mzs’ [-Wunused-variable]
1978 | const int num_mzs = static_cast<int>(get_num_mzs());
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2097:7: warning: unused variable ‘start_rt_idx’ [-Wunused-variable]
2097 | int start_rt_idx = this->rt_to_rtidx(start_rt);
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2098:7: warning: unused variable ‘stop_rt_idx’ [-Wunused-variable]
2098 | int stop_rt_idx = this->rt_to_rtidx(stop_rt);
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
806 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
807 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1728:9: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ defined but not used [-Wunused-function]
1728 | msmat * msmat_from_thevoid
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1701:6: warning: ‘void output_bp_chrom(msmat&, char*)’ defined but not used [-Wunused-function]
1701 | void output_bp_chrom( msmat & m, char * fname ) {
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1570:9: warning: ‘msmat* test_msmat(int, char**)’ defined but not used [-Wunused-function]
1570 | msmat * test_msmat ( int argc , char ** argv ) {
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 71%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.H:20,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:19:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
594 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
697 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable ‘should_be_semi’ [-Wunused-variable]
92 | char should_be_semi = (char)fgetc(header_fh);
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘void msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char>, float>&, const char*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:361:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
361 | for ( std::size_t i = c1_loc+1 ; i < key_last+1 ; i++ ) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:14: warning: unused variable ‘key_fields_len’ [-Wunused-variable]
343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:30: warning: unused variable ‘key_last_loc’ [-Wunused-variable]
343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:44: warning: unused variable ‘key_data_len’ [-Wunused-variable]
343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable ‘key_len_data’ [-Wunused-variable]
344 | char key_len_data[128], val_len_data[128];
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable ‘val_len_data’ [-Wunused-variable]
344 | char key_len_data[128], val_len_data[128];
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:359:7: warning: unused variable ‘key_data_idx’ [-Wunused-variable]
359 | int key_data_idx;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
806 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
807 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
809 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
812 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
813 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘msmat_header_parser::load_map_from_str(std::map<float, float, std::less<float>, std::allocator<std::pair<float const, float> > >&, char const*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
314 | delete k;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from ‘operator new[](unsigned long)’
306 | flt_map_type * k = new flt_map_type[num_items];
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
315 | delete v;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from ‘operator new[](unsigned long)’
307 | flt_map_type * v = new flt_map_type[num_items];
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/convertmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
ers/MSToolkit/msmat_header_parser.cpp: In member function ‘msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, float, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, float> > >&, char const*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:386:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
386 | delete values;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:381:37: note: returned from ‘operator new[](unsigned long)’
381 | float * values = new float[val_len];
| ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 67%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp: In member function ‘virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
332 | else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
332 | else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:271:14: warning: unused variable ‘peptide_length’ [-Wunused-variable]
271 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:290:12: warning: variable ‘SpecEValue’ set but not used [-Wunused-but-set-variable]
290 | double SpecEValue = 0.0;
| ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 73%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:4:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
594 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
697 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable ‘m’ [-Wunused-variable]
13 | msmat * m;
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
806 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
807 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
809 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
812 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
813 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 76%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1
/usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
/usr/bin/ranlib libMSToolkit.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 76%] Built target MSToolkit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 78%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp: In member function ‘std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
81 | if (it->first <= peptideSeq.length()) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 75%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘virtual void TandemReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:248:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=]
248 | } catch (MyException e) {
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:251:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
251 | } catch (std::exception e) {
| ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr<FragSpectrumScanDatabase>, const peptideProteinMapType&, const std::string&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:468:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
468 | f_seq.push_back( charge == c ? 1.0 : 0.0);
| ~~~~~~~^~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 82%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function ‘virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable ‘valueSize’ [-Wunused-variable]
165 | size_t valueSize(buf.size ());
| ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 80%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h: In constructor ‘Interface::Interface()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:50:14: warning: ‘Interface::xmlOutput’ will be initialized after [-Wreorder]
50 | bool xmlOutput;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:47:21: warning: ‘std::string Interface::outputFN’ [-Wreorder]
47 | std::string outputFN;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:21:1: warning: when initialized here [-Wreorder]
21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
| ^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 83%] Linking CXX static library libconverters.a
/usr/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/converters.dir/link.txt --verbose=1
/usr/bin/ar qc libconverters.a CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/ranlib libconverters.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 89%] Built target converters
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 92%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Sqt2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 91%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Msgfplus2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 94%] Linking CXX executable sqt2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 96%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 98%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -MF CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o.d -o CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 96%] Linking CXX executable msgf2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Linking CXX executable tandem2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/tandem2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
241 | return __builtin_strchr (__s, __c);
| ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.96q77M
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x
++ dirname /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] Built target perclibrary
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 68%] Built target picked_protein
/usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] Built target blas
/usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] Built target fido
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 87%] Built target percolator
/usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Built target qvality
/usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/qvality
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/./bin/gtest_unit
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 25%] Built target perclibrary_part
/usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 28%] Built target generate_perc_xsdfiles
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 57%] Built target converters
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] Built target RAMP
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 89%] Built target MSToolkit
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 92%] Built target msgf2pin
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 96%] Built target sqt2pin
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/lib64/percolator
+ rm -f /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.06.04-3.fc40 --unique-debug-suffix -3.06.04-3.fc40.s390x --unique-debug-src-base percolator-3.06.04-3.fc40.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-06-04
find-debuginfo: starting
Extracting debug info from 5 files
DWARF-compressing 5 files
sepdebugcrcfix: Updated 5 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.06.04-3.fc40.s390x
5448 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.sSOAsz
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ mkdir -p test
+ pushd test
~/build/BUILD/percolator-rel-3-06-04/test ~/build/BUILD/percolator-rel-3-06-04
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
Pin-converter version 3.06.4, Build Date Jan 25 2024 00:00:00
Copyright (c) 2013 Lukas Käll. All rights reserved.
Written by Lukas Käll (lukas.kall@scilifelab.se) in the
School of Biotechnology at KTH - Royal Institute of Technology, Stockholm.
Issued command:
../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
on 7558c4e4e5de48f58840931bbaa3b193
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Protein decoy-prefix used is random_
All files have been read
Percolator version 3.06.4, Build Date Jan 25 2024 00:00:00
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
../percolator/src/percolator -X pout.xml pin.tab
Started Thu Jan 25 21:40:50 2024
on 7558c4e4e5de48f58840931bbaa3b193
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile pin.tab
Features:
lnrSp deltLCn deltCn Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM
Found 139410 PSMs
Separate target and decoy search inputs detected, using mix-max method.
Train/test set contains 69705 positives and 69705 negatives, size ratio=1 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Found 7004 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.5765 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1: Estimated 10193 PSMs with q<0.01
Iteration 2: Estimated 11236 PSMs with q<0.01
Iteration 3: Estimated 11461 PSMs with q<0.01
Iteration 4: Estimated 11509 PSMs with q<0.01
Iteration 5: Estimated 11560 PSMs with q<0.01
Iteration 6: Estimated 11576 PSMs with q<0.01
Iteration 7: Estimated 11602 PSMs with q<0.01
Iteration 8: Estimated 11617 PSMs with q<0.01
Iteration 9: Estimated 11617 PSMs with q<0.01
Iteration 10: Estimated 11616 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
Split1 Split2 Split3 FeatureName
-0.4835 -0.3200 -0.4134 lnrSp
0.1414 0.1989 0.1695 deltLCn
0.6622 0.6394 0.7524 deltCn
0.6588 0.6486 0.6804 Xcorr
-0.0413 0.0625 -0.0978 Sp
0.0244 0.1588 0.2191 IonFrac
0.8867 0.6292 0.4141 Mass
-0.7489 -0.3031 -0.0249 PepLen
0.1083 0.1800 0.1009 Charge1
0.0250 0.0242 0.0043 Charge2
-0.0471 -0.0610 -0.0250 Charge3
1.3220 1.2346 1.2522 enzN
1.3377 1.1510 1.1172 enzC
-1.9073 -1.7718 -1.6438 enzInt
-0.0159 -0.0088 0.1201 lnNumSP
0.0188 0.0011 0.0218 dM
0.0044 0.0139 0.0016 absdM
-6.5792 -6.3779 -5.8394 m0
Found 11446 test set PSMs with q<0.01.
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
Selecting pi_0=0.86749
Calculating q values.
New pi_0 estimate on final list yields 7371 target peptides with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 22.6580 cpu seconds or 14 seconds wall clock time.
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ pushd percolator
~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04
+ /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j2
Test project /builddir/build/BUILD/percolator-rel-3-06-04/percolator
Start 1: UnitTest_Percolator_RunAllTests
1/1 Test #1: UnitTest_Percolator_RunAllTests ... Passed 0.04 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 0.04 sec
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.06.04-3.fc40.s390x
Provides: percolator = 3.06.04-3.fc40 percolator(s390-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libc.so.6(GLIBC_2.9)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtirpc.so.3()(64bit) libtirpc.so.3(TIRPC_0.3.0)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.06.04-3.fc40.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.d1hxtd
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.jwQs9j
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.06.04-3.fc40.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.AdTCPJ
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.cIXIBG
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.06.04-3.fc40 percolator-static(s390-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.06.04-3.fc40.s390x
Provides: percolator-debugsource = 3.06.04-3.fc40 percolator-debugsource(s390-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.06.04-3.fc40.s390x
Provides: debuginfo(build-id) = 91215e31c03ef0ca6d030f2ddac079145e1a39c0 debuginfo(build-id) = a7a15d99cac338148d65b2c0a6d0f05258b5c12a debuginfo(build-id) = c3d64b1a47e1ab15047438bb9c0485f6ba001b47 debuginfo(build-id) = f24af542be5ad6a387ac7405ebd51a4c3de0e37b debuginfo(build-id) = f28233222c1e6b70a54b9fb828ec09ca50c723ff percolator-debuginfo = 3.06.04-3.fc40 percolator-debuginfo(s390-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(s390-64) = 3.06.04-3.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x
Wrote: /builddir/build/RPMS/percolator-static-3.06.04-3.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-3.06.04-3.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.06.04-3.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.06.04-3.fc40.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-3.fc40.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ResZAo
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.UiXJk5
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ rm -rf percolator-rel-3-06-04 percolator-rel-3-06-04.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.06.04-3.fc40.src.rpm
Finish: build phase for percolator-3.06.04-3.fc40.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1706218334.596559/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.06.04-3.fc40.src.rpm) Config(child) 7 minutes 3 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
"packages": [
{
"name": "percolator",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "s390x"
},
{
"name": "percolator-static",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "s390x"
},
{
"name": "percolator-data",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "noarch"
},
{
"name": "percolator",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "src"
},
{
"name": "percolator-debuginfo",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "s390x"
},
{
"name": "percolator-debugsource",
"epoch": null,
"version": "3.06.04",
"release": "3.fc40",
"arch": "s390x"
}
]
}
RPMResults finished