Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c2a6' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5174200 --chroot fedora-rawhide-ppc64le --detached
Version: 0.62
PID: 5802
Logging PID: 5803
Task:
{'appstream': False,
'background': True,
'build_id': 5174200,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-ppc64le',
'enable_net': False,
'fedora_review': False,
'git_hash': '8a2eaf4d26f44c0df2ba49251d3666a8b439c286',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'percolator',
'package_version': '3.05-10',
'project_dirname': 'gcc-13-test',
'project_name': 'gcc-13-test',
'project_owner': 'jakub',
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-ppc64le/',
'id': 'copr_base',
'name': 'Copr repository'},
{'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
'sandbox': 'jakub/gcc-13-test--jakub',
'source_json': {},
'source_type': None,
'submitter': 'jakub',
'tags': [],
'task_id': '5174200-fedora-rawhide-ppc64le',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator /var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator'...
Running: git checkout 8a2eaf4d26f44c0df2ba49251d3666a8b439c286
cmd: ['git', 'checkout', '8a2eaf4d26f44c0df2ba49251d3666a8b439c286']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator
rc: 0
stdout:
stderr: Note: switching to '8a2eaf4d26f44c0df2ba49251d3666a8b439c286'.
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 8a2eaf4 automatic import of percolator
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator
rc: 0
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
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-3-05.tar.gz
INFO: Calling: curl -H Pragma: -o percolator-rel-3-05.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/percolator/percolator-rel-3-05.tar.gz/md5/46a10770d808f8db4bd5bd2d30c9be4d/percolator-rel-3-05.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.5M 100 11.5M 0 0 23.0M 0 --:--:-- --:--:-- --:--:-- 23.0M
INFO: Reading stdout from command: md5sum percolator-rel-3-05.tar.gz
INFO: Downloading yeast-01.sqt.tar.gz
INFO: Calling: curl -H Pragma: -o yeast-01.sqt.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/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 27.9M 0 0:00:01 0:00:01 --:--:-- 27.9M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz
Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672042909.556246 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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-yqovix85/percolator/percolator.spec) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672042909.556246/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity
This system is not registered with an entitlement server. You can use subscription-manager to register.
Copr repository 46 MB/s | 30 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 257 kB/s | 84 kB 00:00
fedora 7.2 MB/s | 60 MB 00:08
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing:
dnf noarch 4.14.0-1.fc38 fedora 480 k
dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 copr_base 41 k
audit-libs ppc64le 3.0.9-2.fc38 fedora 130 k
basesystem noarch 11-14.fc37 fedora 7.0 k
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2-libs ppc64le 1.0.8-12.fc38 copr_base 48 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils ppc64le 9.1-8.fc38 copr_base 1.3 M
coreutils-common ppc64le 9.1-8.fc38 copr_base 2.0 M
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 copr_base 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 copr_base 882 k
dbus-libs ppc64le 1:1.14.4-1.fc38 copr_base 177 k
dnf-data noarch 4.14.0-1.fc38 fedora 43 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf ppc64le 0.188-3.fc38 copr_base 205 k
elfutils-libs ppc64le 0.188-3.fc38 copr_base 291 k
expat ppc64le 2.5.0-1.fc38 copr_base 117 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-common noarch 38-0.6 fedora 21 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file-libs ppc64le 5.42-4.fc38 copr_base 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
findutils ppc64le 1:4.9.0-2.fc38 copr_base 530 k
gawk ppc64le 5.1.1-4.fc38 copr_base 1.0 M
gdbm-libs ppc64le 1:1.23-2.fc38 copr_base 62 k
glib2 ppc64le 2.74.1-2.fc38 copr_base 2.8 M
glibc ppc64le 2.36.9000-19.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-19.fc38 fedora 322 k
glibc-minimal-langpack ppc64le 2.36.9000-19.fc38 fedora 30 k
gmp ppc64le 1:6.2.1-3.fc38 copr_base 304 k
gnupg2 ppc64le 2.3.8-1.fc38 copr_base 2.7 M
gnutls ppc64le 3.7.8-9.fc38 copr_base 1.1 M
gpgme ppc64le 1.17.1-3.fc38 copr_base 229 k
grep ppc64le 3.8-1.fc38 copr_base 293 k
ima-evm-utils ppc64le 1.4-6.fc38 copr_base 67 k
json-c ppc64le 0.16-3.fc38 copr_base 46 k
keyutils-libs ppc64le 1.6.1-5.fc38 copr_base 33 k
krb5-libs ppc64le 1.20.1-3.fc38 copr_base 805 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 copr_base 464 k
libassuan ppc64le 2.5.5-5.fc38 copr_base 71 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libb2 ppc64le 0.98.1-7.fc38 copr_base 26 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc38 copr_base 345 k
libcap ppc64le 2.48-5.fc38 copr_base 73 k
libcap-ng ppc64le 0.8.3-4.fc38 copr_base 34 k
libcom_err ppc64le 1.46.5-3.fc38 copr_base 26 k
libcomps ppc64le 0.1.18-4.fc38 copr_base 84 k
libcurl ppc64le 7.87.0-1.fc38 copr_base 334 k
libdnf ppc64le 0.68.0-1.fc38 copr_base 668 k
libevent ppc64le 2.1.12-7.fc38 copr_base 276 k
libffi ppc64le 3.4.4-1.fc38 copr_base 39 k
libfsverity ppc64le 1.4-8.fc38 copr_base 20 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgcrypt ppc64le 1.10.1-6.fc38 copr_base 596 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libgpg-error ppc64le 1.46-1.fc38 copr_base 233 k
libidn2 ppc64le 2.3.4-1.fc38 copr_base 157 k
libksba ppc64le 1.6.3-1.fc38 copr_base 175 k
libmodulemd ppc64le 2.14.0-4.fc38 copr_base 233 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 copr_base 85 k
libnsl2 ppc64le 2.0.0-4.fc38 copr_base 33 k
libpsl ppc64le 0.21.1-6.fc38 copr_base 67 k
librepo ppc64le 1.15.1-1.fc38 copr_base 104 k
libreport-filesystem noarch 2.17.6-1.fc38 copr_base 14 k
libselinux ppc64le 3.4-6.fc38 copr_base 100 k
libsemanage ppc64le 3.4-6.fc38 copr_base 131 k
libsepol ppc64le 3.4-4.fc38 copr_base 355 k
libsigsegv ppc64le 2.14-3.fc38 copr_base 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libsolv ppc64le 0.7.22-3.fc38 copr_base 467 k
libssh ppc64le 0.10.4-2.fc38 copr_base 236 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 copr_base 81 k
libtirpc ppc64le 1.3.3-0.fc38 copr_base 108 k
libunistring ppc64le 1.0-2.fc38 copr_base 575 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc38 copr_base 23 k
libxcrypt ppc64le 4.4.33-5.fc38 copr_base 133 k
libxml2 ppc64le 2.10.3-2.fc38 copr_base 780 k
libyaml ppc64le 0.2.5-8.fc38 copr_base 70 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 copr_base 149 k
lz4-libs ppc64le 1.9.3-5.fc38 copr_base 90 k
mpdecimal ppc64le 2.5.1-4.fc38 copr_base 118 k
mpfr ppc64le 4.1.1-2.fc38 copr_base 609 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 copr_base 374 k
nettle ppc64le 3.8-2.fc38 copr_base 443 k
npth ppc64le 1.6-10.fc38 copr_base 25 k
openldap ppc64le 2.6.3-1.fc38 copr_base 288 k
openssl-libs ppc64le 1:3.0.5-6.fc38 copr_base 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 copr_base 359 k
p11-kit-trust ppc64le 0.24.1-5.fc38 copr_base 150 k
pcre2 ppc64le 10.40-1.fc38.1 copr_base 242 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
popt ppc64le 1.19-1.fc38 fedora 71 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k
python3-dbus ppc64le 1.3.2-1.fc38 copr_base 152 k
python3-distro noarch 1.8.0-1.fc38 fedora 49 k
python3-dnf noarch 4.14.0-1.fc38 fedora 607 k
python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k
python3-gpg ppc64le 1.17.1-3.fc38 copr_base 285 k
python3-hawkey ppc64le 0.68.0-1.fc38 copr_base 109 k
python3-libcomps ppc64le 0.1.18-4.fc38 copr_base 53 k
python3-libdnf ppc64le 0.68.0-1.fc38 copr_base 815 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
python3-rpm ppc64le 4.18.0-8.fc38 fedora 101 k
python3-six noarch 1.16.0-8.fc37 fedora 42 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpm-sign-libs ppc64le 4.18.0-8.fc38 fedora 27 k
sed ppc64le 4.8-11.fc37 fedora 313 k
setup noarch 2.14.3-1.fc38 fedora 152 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tpm2-tss ppc64le 4.0.0-0.1.rc2.fc38 fedora 631 k
tzdata noarch 2022g-1.fc38 fedora 716 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zchunk-libs ppc64le 1.2.3-1.fc38 fedora 55 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
Transaction Summary
==========================================================================================================================
Install 137 Packages
Total download size: 60 M
Installed size: 284 M
Downloading Packages:
(1/137): alternatives-1.21-1.fc38.ppc64le.rpm 218 kB/s | 41 kB 00:00
(2/137): bzip2-libs-1.0.8-12.fc38.ppc64le.rpm 244 kB/s | 48 kB 00:00
(3/137): bash-5.2.9-3.fc38.ppc64le.rpm 7.5 MB/s | 1.9 MB 00:00
(4/137): coreutils-9.1-8.fc38.ppc64le.rpm 19 MB/s | 1.3 MB 00:00
(5/137): coreutils-common-9.1-8.fc38.ppc64le.rp 27 MB/s | 2.0 MB 00:00
(6/137): curl-7.87.0-1.fc38.ppc64le.rpm 13 MB/s | 348 kB 00:00
(7/137): cyrus-sasl-lib-2.1.28-8.fc38.ppc64le.r 42 MB/s | 882 kB 00:00
(8/137): dbus-libs-1.14.4-1.fc38.ppc64le.rpm 16 MB/s | 177 kB 00:00
(9/137): elfutils-default-yama-scope-0.188-3.fc 1.4 MB/s | 16 kB 00:00
(10/137): elfutils-libelf-0.188-3.fc38.ppc64le. 18 MB/s | 205 kB 00:00
(11/137): elfutils-libs-0.188-3.fc38.ppc64le.rp 23 MB/s | 291 kB 00:00
(12/137): expat-2.5.0-1.fc38.ppc64le.rpm 8.7 MB/s | 117 kB 00:00
(13/137): file-libs-5.42-4.fc38.ppc64le.rpm 39 MB/s | 688 kB 00:00
(14/137): findutils-4.9.0-2.fc38.ppc64le.rpm 33 MB/s | 530 kB 00:00
(15/137): gawk-5.1.1-4.fc38.ppc64le.rpm 40 MB/s | 1.0 MB 00:00
(16/137): gdbm-libs-1.23-2.fc38.ppc64le.rpm 3.3 MB/s | 62 kB 00:00
(17/137): glib2-2.74.1-2.fc38.ppc64le.rpm 48 MB/s | 2.8 MB 00:00
(18/137): gmp-6.2.1-3.fc38.ppc64le.rpm 5.6 MB/s | 304 kB 00:00
(19/137): gnupg2-2.3.8-1.fc38.ppc64le.rpm 41 MB/s | 2.7 MB 00:00
(20/137): gnutls-3.7.8-9.fc38.ppc64le.rpm 48 MB/s | 1.1 MB 00:00
(21/137): gpgme-1.17.1-3.fc38.ppc64le.rpm 11 MB/s | 229 kB 00:00
(22/137): grep-3.8-1.fc38.ppc64le.rpm 24 MB/s | 293 kB 00:00
(23/137): ima-evm-utils-1.4-6.fc38.ppc64le.rpm 4.8 MB/s | 67 kB 00:00
(24/137): json-c-0.16-3.fc38.ppc64le.rpm 3.4 MB/s | 46 kB 00:00
(25/137): keyutils-libs-1.6.1-5.fc38.ppc64le.rp 2.7 MB/s | 33 kB 00:00
(26/137): krb5-libs-1.20.1-3.fc38.ppc64le.rpm 37 MB/s | 805 kB 00:00
(27/137): libacl-2.3.1-4.fc38.ppc64le.rpm 1.2 MB/s | 26 kB 00:00
(28/137): libarchive-3.6.1-3.fc38.ppc64le.rpm 23 MB/s | 464 kB 00:00
(29/137): libassuan-2.5.5-5.fc38.ppc64le.rpm 7.0 MB/s | 71 kB 00:00
(30/137): libattr-2.5.1-5.fc38.ppc64le.rpm 1.9 MB/s | 19 kB 00:00
(31/137): libb2-0.98.1-7.fc38.ppc64le.rpm 2.9 MB/s | 26 kB 00:00
(32/137): libbrotli-1.0.9-9.fc38.ppc64le.rpm 24 MB/s | 345 kB 00:00
(33/137): libcap-2.48-5.fc38.ppc64le.rpm 4.9 MB/s | 73 kB 00:00
(34/137): libcap-ng-0.8.3-4.fc38.ppc64le.rpm 2.3 MB/s | 34 kB 00:00
(35/137): libcom_err-1.46.5-3.fc38.ppc64le.rpm 2.7 MB/s | 26 kB 00:00
(36/137): libcomps-0.1.18-4.fc38.ppc64le.rpm 7.9 MB/s | 84 kB 00:00
(37/137): libcurl-7.87.0-1.fc38.ppc64le.rpm 24 MB/s | 334 kB 00:00
(38/137): libdnf-0.68.0-1.fc38.ppc64le.rpm 36 MB/s | 668 kB 00:00
(39/137): libevent-2.1.12-7.fc38.ppc64le.rpm 14 MB/s | 276 kB 00:00
(40/137): libffi-3.4.4-1.fc38.ppc64le.rpm 2.2 MB/s | 39 kB 00:00
(41/137): libfsverity-1.4-8.fc38.ppc64le.rpm 2.3 MB/s | 20 kB 00:00
(42/137): libgcrypt-1.10.1-6.fc38.ppc64le.rpm 34 MB/s | 596 kB 00:00
(43/137): libgpg-error-1.46-1.fc38.ppc64le.rpm 12 MB/s | 233 kB 00:00
(44/137): libidn2-2.3.4-1.fc38.ppc64le.rpm 12 MB/s | 157 kB 00:00
(45/137): libksba-1.6.3-1.fc38.ppc64le.rpm 16 MB/s | 175 kB 00:00
(46/137): libmodulemd-2.14.0-4.fc38.ppc64le.rpm 19 MB/s | 233 kB 00:00
(47/137): libnghttp2-1.51.0-1.fc38.ppc64le.rpm 6.6 MB/s | 85 kB 00:00
(48/137): libnsl2-2.0.0-4.fc38.ppc64le.rpm 3.7 MB/s | 33 kB 00:00
(49/137): libpsl-0.21.1-6.fc38.ppc64le.rpm 7.2 MB/s | 67 kB 00:00
(50/137): librepo-1.15.1-1.fc38.ppc64le.rpm 11 MB/s | 104 kB 00:00
(51/137): libreport-filesystem-2.17.6-1.fc38.no 1.6 MB/s | 14 kB 00:00
(52/137): libselinux-3.4-6.fc38.ppc64le.rpm 9.2 MB/s | 100 kB 00:00
(53/137): libsemanage-3.4-6.fc38.ppc64le.rpm 12 MB/s | 131 kB 00:00
(54/137): libsepol-3.4-4.fc38.ppc64le.rpm 27 MB/s | 355 kB 00:00
(55/137): libsigsegv-2.14-3.fc38.ppc64le.rpm 3.2 MB/s | 28 kB 00:00
(56/137): libsolv-0.7.22-3.fc38.ppc64le.rpm 32 MB/s | 467 kB 00:00
(57/137): libssh-0.10.4-2.fc38.ppc64le.rpm 19 MB/s | 236 kB 00:00
(58/137): libssh-config-0.10.4-2.fc38.noarch.rp 917 kB/s | 9.2 kB 00:00
(59/137): libtasn1-4.19.0-1.fc38.ppc64le.rpm 8.2 MB/s | 81 kB 00:00
(60/137): libtirpc-1.3.3-0.fc38.ppc64le.rpm 10 MB/s | 108 kB 00:00
(61/137): libunistring-1.0-2.fc38.ppc64le.rpm 34 MB/s | 575 kB 00:00
(62/137): libverto-0.3.2-4.fc38.ppc64le.rpm 2.0 MB/s | 23 kB 00:00
(63/137): libxcrypt-4.4.33-5.fc38.ppc64le.rpm 13 MB/s | 133 kB 00:00
(64/137): libxml2-2.10.3-2.fc38.ppc64le.rpm 41 MB/s | 780 kB 00:00
(65/137): libyaml-0.2.5-8.fc38.ppc64le.rpm 3.5 MB/s | 70 kB 00:00
(66/137): lua-libs-5.4.4-6.fc38.ppc64le.rpm 8.9 MB/s | 149 kB 00:00
(67/137): lz4-libs-1.9.3-5.fc38.ppc64le.rpm 9.3 MB/s | 90 kB 00:00
(68/137): mpdecimal-2.5.1-4.fc38.ppc64le.rpm 11 MB/s | 118 kB 00:00
(69/137): mpfr-4.1.1-2.fc38.ppc64le.rpm 34 MB/s | 609 kB 00:00
(70/137): ncurses-base-6.3-5.20221126.fc38.noar 6.0 MB/s | 62 kB 00:00
(71/137): ncurses-libs-6.3-5.20221126.fc38.ppc6 28 MB/s | 374 kB 00:00
(72/137): nettle-3.8-2.fc38.ppc64le.rpm 30 MB/s | 443 kB 00:00
(73/137): npth-1.6-10.fc38.ppc64le.rpm 1.7 MB/s | 25 kB 00:00
(74/137): openldap-2.6.3-1.fc38.ppc64le.rpm 24 MB/s | 288 kB 00:00
(75/137): openssl-libs-3.0.5-6.fc38.ppc64le.rpm 48 MB/s | 2.2 MB 00:00
(76/137): p11-kit-0.24.1-5.fc38.ppc64le.rpm 7.1 MB/s | 359 kB 00:00
(77/137): p11-kit-trust-0.24.1-5.fc38.ppc64le.r 3.1 MB/s | 150 kB 00:00
(78/137): pcre2-10.40-1.fc38.1.ppc64le.rpm 18 MB/s | 242 kB 00:00
(79/137): python3-dbus-1.3.2-1.fc38.ppc64le.rpm 13 MB/s | 152 kB 00:00
(80/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp 11 MB/s | 143 kB 00:00
(81/137): python3-gpg-1.17.1-3.fc38.ppc64le.rpm 22 MB/s | 285 kB 00:00
(82/137): python3-hawkey-0.68.0-1.fc38.ppc64le. 8.3 MB/s | 109 kB 00:00
(83/137): python3-libcomps-0.1.18-4.fc38.ppc64l 4.2 MB/s | 53 kB 00:00
(84/137): python3-libdnf-0.68.0-1.fc38.ppc64le. 42 MB/s | 815 kB 00:00
(85/137): libgcc-13.0.0-0.4.fc38.ppc64le.rpm 367 kB/s | 88 kB 00:00
(86/137): libgomp-13.0.0-0.4.fc38.ppc64le.rpm 1.0 MB/s | 314 kB 00:00
(87/137): audit-libs-3.0.9-2.fc38.ppc64le.rpm 1.1 MB/s | 130 kB 00:00
(88/137): basesystem-11-14.fc37.noarch.rpm 94 kB/s | 7.0 kB 00:00
(89/137): ca-certificates-2022.2.54-5.fc37.noar 37 MB/s | 829 kB 00:00
(90/137): crypto-policies-20221215-1.gita4c31a3 16 MB/s | 90 kB 00:00
(91/137): dnf-data-4.14.0-1.fc38.noarch.rpm 21 MB/s | 43 kB 00:00
(92/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 19 MB/s | 34 kB 00:00
(93/137): dnf-4.14.0-1.fc38.noarch.rpm 43 MB/s | 480 kB 00:00
(94/137): fedora-gpg-keys-38-0.3.noarch.rpm 21 MB/s | 125 kB 00:00
(95/137): fedora-release-38-0.6.noarch.rpm 7.3 MB/s | 11 kB 00:00
(96/137): libstdc++-13.0.0-0.4.fc38.ppc64le.rpm 2.4 MB/s | 932 kB 00:00
(97/137): fedora-release-common-38-0.6.noarch.r 4.2 MB/s | 21 kB 00:00
(98/137): fedora-release-identity-basic-38-0.6. 2.2 MB/s | 11 kB 00:00
(99/137): fedora-repos-38-0.3.noarch.rpm 201 kB/s | 10 kB 00:00
(100/137): filesystem-3.18-2.fc37.ppc64le.rpm 45 MB/s | 1.1 MB 00:00
(101/137): glibc-common-2.36.9000-19.fc38.ppc64 41 MB/s | 322 kB 00:00
(102/137): glibc-minimal-langpack-2.36.9000-19. 21 MB/s | 30 kB 00:00
(103/137): libblkid-2.38.1-3.fc38.ppc64le.rpm 33 MB/s | 122 kB 00:00
(104/137): libmount-2.38.1-3.fc38.ppc64le.rpm 35 MB/s | 154 kB 00:00
(105/137): glibc-2.36.9000-19.fc38.ppc64le.rpm 43 MB/s | 2.2 MB 00:00
(106/137): libsmartcols-2.38.1-3.fc38.ppc64le.r 6.2 MB/s | 70 kB 00:00
(107/137): libuuid-2.38.1-3.fc38.ppc64le.rpm 18 MB/s | 29 kB 00:00
(108/137): popt-1.19-1.fc38.ppc64le.rpm 29 MB/s | 71 kB 00:00
(109/137): publicsuffix-list-dafsa-20221208-1.f 26 MB/s | 59 kB 00:00
(110/137): libzstd-1.5.2-3.fc37.ppc64le.rpm 42 MB/s | 316 kB 00:00
(111/137): python-setuptools-wheel-65.5.1-1.fc3 38 MB/s | 715 kB 00:00
(112/137): python3-3.11.1-1.fc38.ppc64le.rpm 16 MB/s | 27 kB 00:00
(113/137): python-pip-wheel-22.3.1-1.fc38.noarc 47 MB/s | 1.4 MB 00:00
(114/137): python3-distro-1.8.0-1.fc38.noarch.r 26 MB/s | 49 kB 00:00
(115/137): python3-dateutil-2.8.2-4.fc37.noarch 26 MB/s | 361 kB 00:00
(116/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 47 MB/s | 607 kB 00:00
(117/137): python3-dnf-plugins-core-4.3.1-1.fc3 26 MB/s | 277 kB 00:00
(118/137): python3-rpm-4.18.0-8.fc38.ppc64le.rp 35 MB/s | 101 kB 00:00
(119/137): python3-six-1.16.0-8.fc37.noarch.rpm 25 MB/s | 42 kB 00:00
(120/137): readline-8.2-2.fc38.ppc64le.rpm 44 MB/s | 228 kB 00:00
(121/137): rpm-4.18.0-8.fc38.ppc64le.rpm 52 MB/s | 568 kB 00:00
(122/137): rpm-build-libs-4.18.0-8.fc38.ppc64le 41 MB/s | 103 kB 00:00
(123/137): rpm-libs-4.18.0-8.fc38.ppc64le.rpm 42 MB/s | 355 kB 00:00
(124/137): rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm 46 MB/s | 1.4 MB 00:00
(125/137): rpm-sign-libs-4.18.0-8.fc38.ppc64le. 14 MB/s | 27 kB 00:00
(126/137): sed-4.8-11.fc37.ppc64le.rpm 38 MB/s | 313 kB 00:00
(127/137): setup-2.14.3-1.fc38.noarch.rpm 25 MB/s | 152 kB 00:00
(128/137): fedora-repos-rawhide-38-0.3.noarch.r 38 kB/s | 9.7 kB 00:00
(129/137): shadow-utils-4.13-3.fc38.ppc64le.rpm 43 MB/s | 1.3 MB 00:00
(130/137): systemd-libs-252.4-598.fc38.ppc64le. 34 MB/s | 666 kB 00:00
(131/137): sqlite-libs-3.40.0-1.fc38.ppc64le.rp 21 MB/s | 776 kB 00:00
(132/137): tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le. 30 MB/s | 631 kB 00:00
(133/137): xz-libs-5.2.9-1.fc38.ppc64le.rpm 26 MB/s | 104 kB 00:00
(134/137): zchunk-libs-1.2.3-1.fc38.ppc64le.rpm 18 MB/s | 55 kB 00:00
(135/137): tzdata-2022g-1.fc38.noarch.rpm 24 MB/s | 716 kB 00:00
(136/137): zlib-1.2.13-1.fc38.ppc64le.rpm 12 MB/s | 100 kB 00:00
(137/137): python3-libs-3.11.1-1.fc38.ppc64le.r 44 MB/s | 9.7 MB 00:00
--------------------------------------------------------------------------------
Total 38 MB/s | 60 MB 00:01
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
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warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew
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useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
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Verifying : glib2-2.74.1-2.fc38.ppc64le 17/137
Verifying : gmp-1:6.2.1-3.fc38.ppc64le 18/137
Verifying : gnupg2-2.3.8-1.fc38.ppc64le 19/137
Verifying : gnutls-3.7.8-9.fc38.ppc64le 20/137
Verifying : gpgme-1.17.1-3.fc38.ppc64le 21/137
Verifying : grep-3.8-1.fc38.ppc64le 22/137
Verifying : ima-evm-utils-1.4-6.fc38.ppc64le 23/137
Verifying : json-c-0.16-3.fc38.ppc64le 24/137
Verifying : keyutils-libs-1.6.1-5.fc38.ppc64le 25/137
Verifying : krb5-libs-1.20.1-3.fc38.ppc64le 26/137
Verifying : libacl-2.3.1-4.fc38.ppc64le 27/137
Verifying : libarchive-3.6.1-3.fc38.ppc64le 28/137
Verifying : libassuan-2.5.5-5.fc38.ppc64le 29/137
Verifying : libattr-2.5.1-5.fc38.ppc64le 30/137
Verifying : libb2-0.98.1-7.fc38.ppc64le 31/137
Verifying : libbrotli-1.0.9-9.fc38.ppc64le 32/137
Verifying : libcap-2.48-5.fc38.ppc64le 33/137
Verifying : libcap-ng-0.8.3-4.fc38.ppc64le 34/137
Verifying : libcom_err-1.46.5-3.fc38.ppc64le 35/137
Verifying : libcomps-0.1.18-4.fc38.ppc64le 36/137
Verifying : libcurl-7.87.0-1.fc38.ppc64le 37/137
Verifying : libdnf-0.68.0-1.fc38.ppc64le 38/137
Verifying : libevent-2.1.12-7.fc38.ppc64le 39/137
Verifying : libffi-3.4.4-1.fc38.ppc64le 40/137
Verifying : libfsverity-1.4-8.fc38.ppc64le 41/137
Verifying : libgcrypt-1.10.1-6.fc38.ppc64le 42/137
Verifying : libgpg-error-1.46-1.fc38.ppc64le 43/137
Verifying : libidn2-2.3.4-1.fc38.ppc64le 44/137
Verifying : libksba-1.6.3-1.fc38.ppc64le 45/137
Verifying : libmodulemd-2.14.0-4.fc38.ppc64le 46/137
Verifying : libnghttp2-1.51.0-1.fc38.ppc64le 47/137
Verifying : libnsl2-2.0.0-4.fc38.ppc64le 48/137
Verifying : libpsl-0.21.1-6.fc38.ppc64le 49/137
Verifying : librepo-1.15.1-1.fc38.ppc64le 50/137
Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 51/137
Verifying : libselinux-3.4-6.fc38.ppc64le 52/137
Verifying : libsemanage-3.4-6.fc38.ppc64le 53/137
Verifying : libsepol-3.4-4.fc38.ppc64le 54/137
Verifying : libsigsegv-2.14-3.fc38.ppc64le 55/137
Verifying : libsolv-0.7.22-3.fc38.ppc64le 56/137
Verifying : libssh-0.10.4-2.fc38.ppc64le 57/137
Verifying : libssh-config-0.10.4-2.fc38.noarch 58/137
Verifying : libtasn1-4.19.0-1.fc38.ppc64le 59/137
Verifying : libtirpc-1.3.3-0.fc38.ppc64le 60/137
Verifying : libunistring-1.0-2.fc38.ppc64le 61/137
Verifying : libverto-0.3.2-4.fc38.ppc64le 62/137
Verifying : libxcrypt-4.4.33-5.fc38.ppc64le 63/137
Verifying : libxml2-2.10.3-2.fc38.ppc64le 64/137
Verifying : libyaml-0.2.5-8.fc38.ppc64le 65/137
Verifying : lua-libs-5.4.4-6.fc38.ppc64le 66/137
Verifying : lz4-libs-1.9.3-5.fc38.ppc64le 67/137
Verifying : mpdecimal-2.5.1-4.fc38.ppc64le 68/137
Verifying : mpfr-4.1.1-2.fc38.ppc64le 69/137
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 70/137
Verifying : ncurses-libs-6.3-5.20221126.fc38.ppc64le 71/137
Verifying : nettle-3.8-2.fc38.ppc64le 72/137
Verifying : npth-1.6-10.fc38.ppc64le 73/137
Verifying : openldap-2.6.3-1.fc38.ppc64le 74/137
Verifying : openssl-libs-1:3.0.5-6.fc38.ppc64le 75/137
Verifying : p11-kit-0.24.1-5.fc38.ppc64le 76/137
Verifying : p11-kit-trust-0.24.1-5.fc38.ppc64le 77/137
Verifying : pcre2-10.40-1.fc38.1.ppc64le 78/137
Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 79/137
Verifying : python3-dbus-1.3.2-1.fc38.ppc64le 80/137
Verifying : python3-gpg-1.17.1-3.fc38.ppc64le 81/137
Verifying : python3-hawkey-0.68.0-1.fc38.ppc64le 82/137
Verifying : python3-libcomps-0.1.18-4.fc38.ppc64le 83/137
Verifying : python3-libdnf-0.68.0-1.fc38.ppc64le 84/137
Verifying : libgcc-13.0.0-0.4.fc38.ppc64le 85/137
Verifying : libgomp-13.0.0-0.4.fc38.ppc64le 86/137
Verifying : libstdc++-13.0.0-0.4.fc38.ppc64le 87/137
Verifying : audit-libs-3.0.9-2.fc38.ppc64le 88/137
Verifying : basesystem-11-14.fc37.noarch 89/137
Verifying : ca-certificates-2022.2.54-5.fc37.noarch 90/137
Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 91/137
Verifying : dnf-4.14.0-1.fc38.noarch 92/137
Verifying : dnf-data-4.14.0-1.fc38.noarch 93/137
Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 94/137
Verifying : fedora-gpg-keys-38-0.3.noarch 95/137
Verifying : fedora-release-38-0.6.noarch 96/137
Verifying : fedora-release-common-38-0.6.noarch 97/137
Verifying : fedora-release-identity-basic-38-0.6.noarch 98/137
Verifying : fedora-repos-38-0.3.noarch 99/137
Verifying : fedora-repos-rawhide-38-0.3.noarch 100/137
Verifying : filesystem-3.18-2.fc37.ppc64le 101/137
Verifying : glibc-2.36.9000-19.fc38.ppc64le 102/137
Verifying : glibc-common-2.36.9000-19.fc38.ppc64le 103/137
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le 104/137
Verifying : libblkid-2.38.1-3.fc38.ppc64le 105/137
Verifying : libmount-2.38.1-3.fc38.ppc64le 106/137
Verifying : libsmartcols-2.38.1-3.fc38.ppc64le 107/137
Verifying : libuuid-2.38.1-3.fc38.ppc64le 108/137
Verifying : libzstd-1.5.2-3.fc37.ppc64le 109/137
Verifying : popt-1.19-1.fc38.ppc64le 110/137
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 111/137
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 112/137
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 113/137
Verifying : python3-3.11.1-1.fc38.ppc64le 114/137
Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 115/137
Verifying : python3-distro-1.8.0-1.fc38.noarch 116/137
Verifying : python3-dnf-4.14.0-1.fc38.noarch 117/137
Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 118/137
Verifying : python3-libs-3.11.1-1.fc38.ppc64le 119/137
Verifying : python3-rpm-4.18.0-8.fc38.ppc64le 120/137
Verifying : python3-six-1.16.0-8.fc37.noarch 121/137
Verifying : readline-8.2-2.fc38.ppc64le 122/137
Verifying : rpm-4.18.0-8.fc38.ppc64le 123/137
Verifying : rpm-build-libs-4.18.0-8.fc38.ppc64le 124/137
Verifying : rpm-libs-4.18.0-8.fc38.ppc64le 125/137
Verifying : rpm-sequoia-1.2.0-1.fc38.ppc64le 126/137
Verifying : rpm-sign-libs-4.18.0-8.fc38.ppc64le 127/137
Verifying : sed-4.8-11.fc37.ppc64le 128/137
Verifying : setup-2.14.3-1.fc38.noarch 129/137
Verifying : shadow-utils-2:4.13-3.fc38.ppc64le 130/137
Verifying : sqlite-libs-3.40.0-1.fc38.ppc64le 131/137
Verifying : systemd-libs-252.4-598.fc38.ppc64le 132/137
Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le 133/137
Verifying : tzdata-2022g-1.fc38.noarch 134/137
Verifying : xz-libs-5.2.9-1.fc38.ppc64le 135/137
Verifying : zchunk-libs-1.2.3-1.fc38.ppc64le 136/137
Verifying : zlib-1.2.13-1.fc38.ppc64le 137/137
Installed products updated.
Installed:
alternatives-1.21-1.fc38.ppc64le
audit-libs-3.0.9-2.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
dbus-libs-1:1.14.4-1.fc38.ppc64le
dnf-4.14.0-1.fc38.noarch
dnf-data-4.14.0-1.fc38.noarch
dnf-plugins-core-4.3.1-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
expat-2.5.0-1.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc38.ppc64le
gawk-5.1.1-4.fc38.ppc64le
gdbm-libs-1:1.23-2.fc38.ppc64le
glib2-2.74.1-2.fc38.ppc64le
glibc-2.36.9000-19.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
gmp-1:6.2.1-3.fc38.ppc64le
gnupg2-2.3.8-1.fc38.ppc64le
gnutls-3.7.8-9.fc38.ppc64le
gpgme-1.17.1-3.fc38.ppc64le
grep-3.8-1.fc38.ppc64le
ima-evm-utils-1.4-6.fc38.ppc64le
json-c-0.16-3.fc38.ppc64le
keyutils-libs-1.6.1-5.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libassuan-2.5.5-5.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libb2-0.98.1-7.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
libcap-2.48-5.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
libcomps-0.1.18-4.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdnf-0.68.0-1.fc38.ppc64le
libevent-2.1.12-7.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libfsverity-1.4-8.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgcrypt-1.10.1-6.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libgpg-error-1.46-1.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libksba-1.6.3-1.fc38.ppc64le
libmodulemd-2.14.0-4.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc38.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
librepo-1.15.1-1.fc38.ppc64le
libreport-filesystem-2.17.6-1.fc38.noarch
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libsolv-0.7.22-3.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc38.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libyaml-0.2.5-8.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lz4-libs-1.9.3-5.fc38.ppc64le
mpdecimal-2.5.1-4.fc38.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc38.ppc64le
npth-1.6-10.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-dateutil-1:2.8.2-4.fc37.noarch
python3-dbus-1.3.2-1.fc38.ppc64le
python3-distro-1.8.0-1.fc38.noarch
python3-dnf-4.14.0-1.fc38.noarch
python3-dnf-plugins-core-4.3.1-1.fc38.noarch
python3-gpg-1.17.1-3.fc38.ppc64le
python3-hawkey-0.68.0-1.fc38.ppc64le
python3-libcomps-0.1.18-4.fc38.ppc64le
python3-libdnf-0.68.0-1.fc38.ppc64le
python3-libs-3.11.1-1.fc38.ppc64le
python3-rpm-4.18.0-8.fc38.ppc64le
python3-six-1.16.0-8.fc37.noarch
readline-8.2-2.fc38.ppc64le
rpm-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpm-sign-libs-4.18.0-8.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
xz-libs-5.2.9-1.fc38.ppc64le
zchunk-libs-1.2.3-1.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
Complete!
Finish(bootstrap): dnf install
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-ppc64le-1672042909.556246/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
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 30 MB/s | 30 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 124 kB/s | 84 kB 00:00
fedora 16 MB/s | 60 MB 00:03
Last metadata expiration check: 0:00:01 ago on Mon Dec 26 08:23:21 2022.
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing group/module packages:
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2 ppc64le 1.0.8-12.fc38 copr_base 54 k
coreutils ppc64le 9.1-8.fc38 copr_base 1.3 M
cpio ppc64le 2.13-13.fc38 copr_base 277 k
diffutils ppc64le 3.8-3.fc38 copr_base 381 k
fedora-release-common noarch 38-0.6 fedora 21 k
findutils ppc64le 1:4.9.0-2.fc38 copr_base 530 k
gawk ppc64le 5.1.1-4.fc38 copr_base 1.0 M
glibc-minimal-langpack ppc64le 2.36.9000-19.fc38 fedora 30 k
grep ppc64le 3.8-1.fc38 copr_base 293 k
gzip ppc64le 1.12-2.fc38 copr_base 163 k
info ppc64le 7.0.1-1.fc38 fedora 199 k
patch ppc64le 2.7.6-17.fc38 copr_base 136 k
redhat-rpm-config noarch 235-1.fc38 fedora 80 k
rpm-build ppc64le 4.18.0-8.fc38 fedora 78 k
sed ppc64le 4.8-11.fc37 fedora 313 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
tar ppc64le 2:1.34-5.fc38 fedora 914 k
unzip ppc64le 6.0-58.fc38 fedora 188 k
util-linux ppc64le 2.38.1-3.fc38 fedora 2.4 M
which ppc64le 2.21-36.fc38 fedora 42 k
xz ppc64le 5.2.9-1.fc38 fedora 310 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 copr_base 41 k
ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k
audit-libs ppc64le 3.0.9-2.fc38 fedora 130 k
authselect ppc64le 1.4.2-1.fc38 copr_base 141 k
authselect-libs ppc64le 1.4.2-1.fc38 copr_base 241 k
basesystem noarch 11-14.fc37 fedora 7.0 k
binutils ppc64le 2.39-6.fc38 copr_base 6.2 M
binutils-gold ppc64le 2.39-6.fc38 copr_base 1.1 M
bzip2-libs ppc64le 1.0.8-12.fc38 copr_base 48 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils-common ppc64le 9.1-8.fc38 copr_base 2.0 M
cracklib ppc64le 2.9.7-30.fc38 copr_base 84 k
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 copr_base 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 copr_base 882 k
debugedit ppc64le 5.0-5.fc37 fedora 80 k
dwz ppc64le 0.15-1.fc38 copr_base 143 k
ed ppc64le 1.18-2.fc38 copr_base 82 k
efi-srpm-macros noarch 5-6.fc37 fedora 22 k
elfutils ppc64le 0.188-3.fc38 copr_base 555 k
elfutils-debuginfod-client ppc64le 0.188-3.fc38 copr_base 42 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf ppc64le 0.188-3.fc38 copr_base 205 k
elfutils-libs ppc64le 0.188-3.fc38 copr_base 291 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file ppc64le 5.42-4.fc38 copr_base 50 k
file-libs ppc64le 5.42-4.fc38 copr_base 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k
fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k
gdb-minimal ppc64le 12.1-10.fc38 fedora 3.7 M
gdbm-libs ppc64le 1:1.23-2.fc38 copr_base 62 k
ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k
glibc ppc64le 2.36.9000-19.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-19.fc38 fedora 322 k
glibc-gconv-extra ppc64le 2.36.9000-19.fc38 fedora 1.9 M
gmp ppc64le 1:6.2.1-3.fc38 copr_base 304 k
gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k
go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k
jansson ppc64le 2.13.1-5.fc38 copr_base 50 k
kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k
keyutils-libs ppc64le 1.6.1-5.fc38 copr_base 33 k
krb5-libs ppc64le 1.20.1-3.fc38 copr_base 805 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 copr_base 464 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc38 copr_base 345 k
libcap ppc64le 2.48-5.fc38 copr_base 73 k
libcap-ng ppc64le 0.8.3-4.fc38 copr_base 34 k
libcom_err ppc64le 1.46.5-3.fc38 copr_base 26 k
libcurl ppc64le 7.87.0-1.fc38 copr_base 334 k
libdb ppc64le 5.3.28-54.fc38 copr_base 842 k
libeconf ppc64le 0.4.0-4.fc38 copr_base 31 k
libevent ppc64le 2.1.12-7.fc38 copr_base 276 k
libfdisk ppc64le 2.38.1-3.fc38 fedora 176 k
libffi ppc64le 3.4.4-1.fc38 copr_base 39 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libidn2 ppc64le 2.3.4-1.fc38 copr_base 157 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 copr_base 85 k
libnsl2 ppc64le 2.0.0-4.fc38 copr_base 33 k
libpkgconf ppc64le 1.8.0-3.fc37 fedora 40 k
libpsl ppc64le 0.21.1-6.fc38 copr_base 67 k
libpwquality ppc64le 1.4.5-1.fc38 fedora 122 k
librtas ppc64le 2.0.3-1.fc38 copr_base 68 k
libselinux ppc64le 3.4-6.fc38 copr_base 100 k
libsemanage ppc64le 3.4-6.fc38 copr_base 131 k
libsepol ppc64le 3.4-4.fc38 copr_base 355 k
libsigsegv ppc64le 2.14-3.fc38 copr_base 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libssh ppc64le 0.10.4-2.fc38 copr_base 236 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 copr_base 81 k
libtirpc ppc64le 1.3.3-0.fc38 copr_base 108 k
libunistring ppc64le 1.0-2.fc38 copr_base 575 k
libutempter ppc64le 1.2.1-7.fc38 copr_base 27 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc38 copr_base 23 k
libxcrypt ppc64le 4.4.33-5.fc38 copr_base 133 k
libxml2 ppc64le 2.10.3-2.fc38 copr_base 780 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 copr_base 149 k
lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k
lz4-libs ppc64le 1.9.3-5.fc38 copr_base 90 k
mpfr ppc64le 4.1.1-2.fc38 copr_base 609 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 copr_base 374 k
nettle ppc64le 3.8-2.fc38 copr_base 443 k
nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k
ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k
openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k
openldap ppc64le 2.6.3-1.fc38 copr_base 288 k
openssl-libs ppc64le 1:3.0.5-6.fc38 copr_base 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 copr_base 359 k
p11-kit-trust ppc64le 0.24.1-5.fc38 copr_base 150 k
package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k
pam ppc64le 1.5.2-15.fc38 copr_base 569 k
pam-libs ppc64le 1.5.2-15.fc38 copr_base 64 k
pcre2 ppc64le 10.40-1.fc38.1 copr_base 242 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k
pkgconf ppc64le 1.8.0-3.fc37 fedora 43 k
pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k
pkgconf-pkg-config ppc64le 1.8.0-3.fc37 fedora 10 k
popt ppc64le 1.19-1.fc38 fedora 71 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-srpm-macros noarch 3.11-6.fc38 fedora 25 k
qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k
rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k
setup noarch 2.14.3-1.fc38 fedora 152 k
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tzdata noarch 2022g-1.fc38 fedora 716 k
util-linux-core ppc64le 2.38.1-3.fc38 fedora 515 k
xxhash-libs ppc64le 0.8.1-3.fc37 fedora 38 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zip ppc64le 3.0-35.fc38 fedora 267 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
zstd ppc64le 1.5.2-3.fc37 fedora 466 k
Installing Groups:
Buildsystem building group
Transaction Summary
==========================================================================================================================
Install 154 Packages
Total download size: 57 M
Installed size: 328 M
Downloading Packages:
(1/154): alternatives-1.21-1.fc38.ppc64le.rpm 148 kB/s | 41 kB 00:00
(2/154): authselect-1.4.2-1.fc38.ppc64le.rpm 491 kB/s | 141 kB 00:00
(3/154): authselect-libs-1.4.2-1.fc38.ppc64le.r 817 kB/s | 241 kB 00:00
(4/154): bash-5.2.9-3.fc38.ppc64le.rpm 23 MB/s | 1.9 MB 00:00
(5/154): binutils-gold-2.39-6.fc38.ppc64le.rpm 15 MB/s | 1.1 MB 00:00
(6/154): binutils-2.39-6.fc38.ppc64le.rpm 39 MB/s | 6.2 MB 00:00
(7/154): bzip2-1.0.8-12.fc38.ppc64le.rpm 582 kB/s | 54 kB 00:00
(8/154): bzip2-libs-1.0.8-12.fc38.ppc64le.rpm 629 kB/s | 48 kB 00:00
(9/154): cpio-2.13-13.fc38.ppc64le.rpm 18 MB/s | 277 kB 00:00
(10/154): coreutils-9.1-8.fc38.ppc64le.rpm 34 MB/s | 1.3 MB 00:00
(11/154): coreutils-common-9.1-8.fc38.ppc64le.r 39 MB/s | 2.0 MB 00:00
(12/154): cracklib-2.9.7-30.fc38.ppc64le.rpm 2.3 MB/s | 84 kB 00:00
(13/154): curl-7.87.0-1.fc38.ppc64le.rpm 23 MB/s | 348 kB 00:00
(14/154): diffutils-3.8-3.fc38.ppc64le.rpm 24 MB/s | 381 kB 00:00
(15/154): dwz-0.15-1.fc38.ppc64le.rpm 8.5 MB/s | 143 kB 00:00
(16/154): cyrus-sasl-lib-2.1.28-8.fc38.ppc64le. 32 MB/s | 882 kB 00:00
(17/154): ed-1.18-2.fc38.ppc64le.rpm 7.3 MB/s | 82 kB 00:00
(18/154): elfutils-0.188-3.fc38.ppc64le.rpm 32 MB/s | 555 kB 00:00
(19/154): elfutils-debuginfod-client-0.188-3.fc 4.1 MB/s | 42 kB 00:00
(20/154): elfutils-default-yama-scope-0.188-3.f 1.6 MB/s | 16 kB 00:00
(21/154): elfutils-libelf-0.188-3.fc38.ppc64le. 16 MB/s | 205 kB 00:00
(22/154): elfutils-libs-0.188-3.fc38.ppc64le.rp 20 MB/s | 291 kB 00:00
(23/154): file-5.42-4.fc38.ppc64le.rpm 3.6 MB/s | 50 kB 00:00
(24/154): file-libs-5.42-4.fc38.ppc64le.rpm 36 MB/s | 688 kB 00:00
(25/154): findutils-4.9.0-2.fc38.ppc64le.rpm 22 MB/s | 530 kB 00:00
(26/154): gawk-5.1.1-4.fc38.ppc64le.rpm 32 MB/s | 1.0 MB 00:00
(27/154): gdbm-libs-1.23-2.fc38.ppc64le.rpm 4.1 MB/s | 62 kB 00:00
(28/154): gmp-6.2.1-3.fc38.ppc64le.rpm 22 MB/s | 304 kB 00:00
(29/154): gzip-1.12-2.fc38.ppc64le.rpm 14 MB/s | 163 kB 00:00
(30/154): grep-3.8-1.fc38.ppc64le.rpm 19 MB/s | 293 kB 00:00
(31/154): jansson-2.13.1-5.fc38.ppc64le.rpm 4.8 MB/s | 50 kB 00:00
(32/154): keyutils-libs-1.6.1-5.fc38.ppc64le.rp 3.4 MB/s | 33 kB 00:00
(33/154): libacl-2.3.1-4.fc38.ppc64le.rpm 2.6 MB/s | 26 kB 00:00
(34/154): libarchive-3.6.1-3.fc38.ppc64le.rpm 27 MB/s | 464 kB 00:00
(35/154): krb5-libs-1.20.1-3.fc38.ppc64le.rpm 29 MB/s | 805 kB 00:00
(36/154): libattr-2.5.1-5.fc38.ppc64le.rpm 1.1 MB/s | 19 kB 00:00
(37/154): libbrotli-1.0.9-9.fc38.ppc64le.rpm 22 MB/s | 345 kB 00:00
(38/154): libcap-2.48-5.fc38.ppc64le.rpm 5.7 MB/s | 73 kB 00:00
(39/154): libcap-ng-0.8.3-4.fc38.ppc64le.rpm 2.6 MB/s | 34 kB 00:00
(40/154): libcom_err-1.46.5-3.fc38.ppc64le.rpm 2.8 MB/s | 26 kB 00:00
(41/154): libcurl-7.87.0-1.fc38.ppc64le.rpm 20 MB/s | 334 kB 00:00
(42/154): libdb-5.3.28-54.fc38.ppc64le.rpm 36 MB/s | 842 kB 00:00
(43/154): libeconf-0.4.0-4.fc38.ppc64le.rpm 2.0 MB/s | 31 kB 00:00
(44/154): libevent-2.1.12-7.fc38.ppc64le.rpm 21 MB/s | 276 kB 00:00
(45/154): libffi-3.4.4-1.fc38.ppc64le.rpm 3.7 MB/s | 39 kB 00:00
(46/154): libidn2-2.3.4-1.fc38.ppc64le.rpm 12 MB/s | 157 kB 00:00
(47/154): libnghttp2-1.51.0-1.fc38.ppc64le.rpm 8.3 MB/s | 85 kB 00:00
(48/154): libnsl2-2.0.0-4.fc38.ppc64le.rpm 3.4 MB/s | 33 kB 00:00
(49/154): libpsl-0.21.1-6.fc38.ppc64le.rpm 6.9 MB/s | 67 kB 00:00
(50/154): librtas-2.0.3-1.fc38.ppc64le.rpm 6.6 MB/s | 68 kB 00:00
(51/154): libselinux-3.4-6.fc38.ppc64le.rpm 9.3 MB/s | 100 kB 00:00
(52/154): libsemanage-3.4-6.fc38.ppc64le.rpm 12 MB/s | 131 kB 00:00
(53/154): libsepol-3.4-4.fc38.ppc64le.rpm 25 MB/s | 355 kB 00:00
(54/154): libsigsegv-2.14-3.fc38.ppc64le.rpm 2.6 MB/s | 28 kB 00:00
(55/154): libssh-0.10.4-2.fc38.ppc64le.rpm 15 MB/s | 236 kB 00:00
(56/154): libssh-config-0.10.4-2.fc38.noarch.rp 995 kB/s | 9.2 kB 00:00
(57/154): libtasn1-4.19.0-1.fc38.ppc64le.rpm 7.6 MB/s | 81 kB 00:00
(58/154): libtirpc-1.3.3-0.fc38.ppc64le.rpm 9.6 MB/s | 108 kB 00:00
(59/154): libutempter-1.2.1-7.fc38.ppc64le.rpm 2.5 MB/s | 27 kB 00:00
(60/154): libunistring-1.0-2.fc38.ppc64le.rpm 34 MB/s | 575 kB 00:00
(61/154): libverto-0.3.2-4.fc38.ppc64le.rpm 2.4 MB/s | 23 kB 00:00
(62/154): libxcrypt-4.4.33-5.fc38.ppc64le.rpm 12 MB/s | 133 kB 00:00
(63/154): libxml2-2.10.3-2.fc38.ppc64le.rpm 37 MB/s | 780 kB 00:00
(64/154): lua-libs-5.4.4-6.fc38.ppc64le.rpm 7.7 MB/s | 149 kB 00:00
(65/154): lz4-libs-1.9.3-5.fc38.ppc64le.rpm 5.4 MB/s | 90 kB 00:00
(66/154): mpfr-4.1.1-2.fc38.ppc64le.rpm 33 MB/s | 609 kB 00:00
(67/154): ncurses-base-6.3-5.20221126.fc38.noar 3.6 MB/s | 62 kB 00:00
(68/154): ncurses-libs-6.3-5.20221126.fc38.ppc6 19 MB/s | 374 kB 00:00
(69/154): openldap-2.6.3-1.fc38.ppc64le.rpm 17 MB/s | 288 kB 00:00
(70/154): nettle-3.8-2.fc38.ppc64le.rpm 23 MB/s | 443 kB 00:00
(71/154): openssl-libs-3.0.5-6.fc38.ppc64le.rpm 50 MB/s | 2.2 MB 00:00
(72/154): p11-kit-0.24.1-5.fc38.ppc64le.rpm 11 MB/s | 359 kB 00:00
(73/154): p11-kit-trust-0.24.1-5.fc38.ppc64le.r 4.8 MB/s | 150 kB 00:00
(74/154): pam-libs-1.5.2-15.fc38.ppc64le.rpm 6.3 MB/s | 64 kB 00:00
(75/154): patch-2.7.6-17.fc38.ppc64le.rpm 12 MB/s | 136 kB 00:00
(76/154): pam-1.5.2-15.fc38.ppc64le.rpm 31 MB/s | 569 kB 00:00
(77/154): pcre2-10.40-1.fc38.1.ppc64le.rpm 19 MB/s | 242 kB 00:00
(78/154): pcre2-syntax-10.40-1.fc38.1.noarch.rp 12 MB/s | 143 kB 00:00
(79/154): libgcc-13.0.0-0.4.fc38.ppc64le.rpm 289 kB/s | 88 kB 00:00
(80/154): libgomp-13.0.0-0.4.fc38.ppc64le.rpm 935 kB/s | 314 kB 00:00
(81/154): ansible-srpm-macros-1-8.1.fc38.noarch 140 kB/s | 8.6 kB 00:00
(82/154): libstdc++-13.0.0-0.4.fc38.ppc64le.rpm 2.4 MB/s | 932 kB 00:00
(83/154): basesystem-11-14.fc37.noarch.rpm 365 kB/s | 7.0 kB 00:00
(84/154): crypto-policies-20221215-1.gita4c31a3 1.4 MB/s | 90 kB 00:00
(85/154): audit-libs-3.0.9-2.fc38.ppc64le.rpm 1.0 MB/s | 130 kB 00:00
(86/154): ca-certificates-2022.2.54-5.fc37.noar 6.9 MB/s | 829 kB 00:00
(87/154): debugedit-5.0-5.fc37.ppc64le.rpm 1.4 MB/s | 80 kB 00:00
(88/154): fedora-release-38-0.6.noarch.rpm 698 kB/s | 11 kB 00:00
(89/154): fedora-gpg-keys-38-0.3.noarch.rpm 5.8 MB/s | 125 kB 00:00
(90/154): efi-srpm-macros-5-6.fc37.noarch.rpm 384 kB/s | 22 kB 00:00
(91/154): fedora-release-common-38-0.6.noarch.r 1.3 MB/s | 21 kB 00:00
(92/154): fedora-release-identity-basic-38-0.6. 611 kB/s | 11 kB 00:00
(93/154): fedora-repos-38-0.3.noarch.rpm 542 kB/s | 10 kB 00:00
(94/154): fedora-repos-rawhide-38-0.3.noarch.rp 628 kB/s | 9.7 kB 00:00
(95/154): fonts-srpm-macros-2.0.5-10.fc38.noarc 774 kB/s | 26 kB 00:00
(96/154): fpc-srpm-macros-1.3-6.fc37.noarch.rpm 212 kB/s | 7.7 kB 00:00
(97/154): filesystem-3.18-2.fc37.ppc64le.rpm 20 MB/s | 1.1 MB 00:00
(98/154): glibc-2.36.9000-19.fc38.ppc64le.rpm 32 MB/s | 2.2 MB 00:00
(99/154): ghc-srpm-macros-1.5.0-7.fc37.noarch.r 93 kB/s | 7.8 kB 00:00
(100/154): glibc-common-2.36.9000-19.fc38.ppc64 8.2 MB/s | 322 kB 00:00
(101/154): glibc-minimal-langpack-2.36.9000-19. 1.3 MB/s | 30 kB 00:00
(102/154): gdb-minimal-12.1-10.fc38.ppc64le.rpm 21 MB/s | 3.7 MB 00:00
(103/154): gnat-srpm-macros-4-16.fc37.noarch.rp 263 kB/s | 8.3 kB 00:00
(104/154): go-srpm-macros-3.2.0-1.fc38.noarch.r 651 kB/s | 27 kB 00:00
(105/154): glibc-gconv-extra-2.36.9000-19.fc38. 14 MB/s | 1.9 MB 00:00
(106/154): info-7.0.1-1.fc38.ppc64le.rpm 3.7 MB/s | 199 kB 00:00
(107/154): libblkid-2.38.1-3.fc38.ppc64le.rpm 4.0 MB/s | 122 kB 00:00
(108/154): libfdisk-2.38.1-3.fc38.ppc64le.rpm 3.2 MB/s | 176 kB 00:00
(109/154): kernel-srpm-macros-1.0-15.fc37.noarc 117 kB/s | 9.4 kB 00:00
(110/154): libmount-2.38.1-3.fc38.ppc64le.rpm 3.8 MB/s | 154 kB 00:00
(111/154): libsmartcols-2.38.1-3.fc38.ppc64le.r 2.6 MB/s | 70 kB 00:00
(112/154): libpkgconf-1.8.0-3.fc37.ppc64le.rpm 850 kB/s | 40 kB 00:00
(113/154): libuuid-2.38.1-3.fc38.ppc64le.rpm 1.7 MB/s | 29 kB 00:00
(114/154): libpwquality-1.4.5-1.fc38.ppc64le.rp 2.1 MB/s | 122 kB 00:00
(115/154): libzstd-1.5.2-3.fc37.ppc64le.rpm 6.1 MB/s | 316 kB 00:00
(116/154): lua-srpm-macros-1-7.fc37.noarch.rpm 207 kB/s | 8.8 kB 00:00
(117/154): nim-srpm-macros-3-7.fc37.noarch.rpm 122 kB/s | 8.4 kB 00:00
(118/154): ocaml-srpm-macros-7-2.fc37.noarch.rp 220 kB/s | 13 kB 00:00
(119/154): openblas-srpm-macros-2-12.fc37.noarc 115 kB/s | 7.5 kB 00:00
(120/154): package-notes-srpm-macros-0.5-6.fc38 173 kB/s | 11 kB 00:00
(121/154): perl-srpm-macros-1-47.fc38.noarch.rp 151 kB/s | 8.2 kB 00:00
(122/154): pkgconf-1.8.0-3.fc37.ppc64le.rpm 666 kB/s | 43 kB 00:00
(123/154): pkgconf-m4-1.8.0-3.fc37.noarch.rpm 427 kB/s | 14 kB 00:00
(124/154): pkgconf-pkg-config-1.8.0-3.fc37.ppc6 509 kB/s | 10 kB 00:00
(125/154): publicsuffix-list-dafsa-20221208-1.f 2.9 MB/s | 59 kB 00:00
(126/154): popt-1.19-1.fc38.ppc64le.rpm 2.2 MB/s | 71 kB 00:00
(127/154): python-srpm-macros-3.11-6.fc38.noarc 662 kB/s | 25 kB 00:00
(128/154): readline-8.2-2.fc38.ppc64le.rpm 7.4 MB/s | 228 kB 00:00
(129/154): qt5-srpm-macros-5.15.7-1.fc38.noarch 194 kB/s | 7.9 kB 00:00
(130/154): redhat-rpm-config-235-1.fc38.noarch. 1.7 MB/s | 80 kB 00:00
(131/154): rpm-4.18.0-8.fc38.ppc64le.rpm 11 MB/s | 568 kB 00:00
(132/154): rpm-build-4.18.0-8.fc38.ppc64le.rpm 1.5 MB/s | 78 kB 00:00
(133/154): rpm-build-libs-4.18.0-8.fc38.ppc64le 3.1 MB/s | 103 kB 00:00
(134/154): rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm 16 MB/s | 1.4 MB 00:00
(135/154): rpm-libs-4.18.0-8.fc38.ppc64le.rpm 3.7 MB/s | 355 kB 00:00
(136/154): rpmautospec-rpm-macros-0.3.1-1.fc38. 102 kB/s | 8.8 kB 00:00
(137/154): setup-2.14.3-1.fc38.noarch.rpm 8.5 MB/s | 152 kB 00:00
(138/154): rust-srpm-macros-23-1.fc38.noarch.rp 299 kB/s | 9.4 kB 00:00
(139/154): sed-4.8-11.fc37.ppc64le.rpm 8.6 MB/s | 313 kB 00:00
(140/154): sqlite-libs-3.40.0-1.fc38.ppc64le.rp 14 MB/s | 776 kB 00:00
(141/154): shadow-utils-4.13-3.fc38.ppc64le.rpm 16 MB/s | 1.3 MB 00:00
(142/154): systemd-libs-252.4-598.fc38.ppc64le. 9.7 MB/s | 666 kB 00:00
(143/154): tzdata-2022g-1.fc38.noarch.rpm 24 MB/s | 716 kB 00:00
(144/154): unzip-6.0-58.fc38.ppc64le.rpm 2.8 MB/s | 188 kB 00:00
(145/154): tar-1.34-5.fc38.ppc64le.rpm 9.3 MB/s | 914 kB 00:00
(146/154): util-linux-2.38.1-3.fc38.ppc64le.rpm 24 MB/s | 2.4 MB 00:00
(147/154): util-linux-core-2.38.1-3.fc38.ppc64l 7.4 MB/s | 515 kB 00:00
(148/154): which-2.21-36.fc38.ppc64le.rpm 564 kB/s | 42 kB 00:00
(149/154): xz-libs-5.2.9-1.fc38.ppc64le.rpm 3.7 MB/s | 104 kB 00:00
(150/154): xxhash-libs-0.8.1-3.fc37.ppc64le.rpm 687 kB/s | 38 kB 00:00
(151/154): xz-5.2.9-1.fc38.ppc64le.rpm 4.3 MB/s | 310 kB 00:00
(152/154): zip-3.0-35.fc38.ppc64le.rpm 6.7 MB/s | 267 kB 00:00
(153/154): zlib-1.2.13-1.fc38.ppc64le.rpm 2.9 MB/s | 100 kB 00:00
(154/154): zstd-1.5.2-3.fc37.ppc64le.rpm 7.2 MB/s | 466 kB 00:00
--------------------------------------------------------------------------------
Total 20 MB/s | 57 MB 00:02
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
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Verifying : libfdisk-2.38.1-3.fc38.ppc64le 109/154
Verifying : libmount-2.38.1-3.fc38.ppc64le 110/154
Verifying : libpkgconf-1.8.0-3.fc37.ppc64le 111/154
Verifying : libpwquality-1.4.5-1.fc38.ppc64le 112/154
Verifying : libsmartcols-2.38.1-3.fc38.ppc64le 113/154
Verifying : libuuid-2.38.1-3.fc38.ppc64le 114/154
Verifying : libzstd-1.5.2-3.fc37.ppc64le 115/154
Verifying : lua-srpm-macros-1-7.fc37.noarch 116/154
Verifying : nim-srpm-macros-3-7.fc37.noarch 117/154
Verifying : ocaml-srpm-macros-7-2.fc37.noarch 118/154
Verifying : openblas-srpm-macros-2-12.fc37.noarch 119/154
Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 120/154
Verifying : perl-srpm-macros-1-47.fc38.noarch 121/154
Verifying : pkgconf-1.8.0-3.fc37.ppc64le 122/154
Verifying : pkgconf-m4-1.8.0-3.fc37.noarch 123/154
Verifying : pkgconf-pkg-config-1.8.0-3.fc37.ppc64le 124/154
Verifying : popt-1.19-1.fc38.ppc64le 125/154
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 126/154
Verifying : python-srpm-macros-3.11-6.fc38.noarch 127/154
Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 128/154
Verifying : readline-8.2-2.fc38.ppc64le 129/154
Verifying : redhat-rpm-config-235-1.fc38.noarch 130/154
Verifying : rpm-4.18.0-8.fc38.ppc64le 131/154
Verifying : rpm-build-4.18.0-8.fc38.ppc64le 132/154
Verifying : rpm-build-libs-4.18.0-8.fc38.ppc64le 133/154
Verifying : rpm-libs-4.18.0-8.fc38.ppc64le 134/154
Verifying : rpm-sequoia-1.2.0-1.fc38.ppc64le 135/154
Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 136/154
Verifying : rust-srpm-macros-23-1.fc38.noarch 137/154
Verifying : sed-4.8-11.fc37.ppc64le 138/154
Verifying : setup-2.14.3-1.fc38.noarch 139/154
Verifying : shadow-utils-2:4.13-3.fc38.ppc64le 140/154
Verifying : sqlite-libs-3.40.0-1.fc38.ppc64le 141/154
Verifying : systemd-libs-252.4-598.fc38.ppc64le 142/154
Verifying : tar-2:1.34-5.fc38.ppc64le 143/154
Verifying : tzdata-2022g-1.fc38.noarch 144/154
Verifying : unzip-6.0-58.fc38.ppc64le 145/154
Verifying : util-linux-2.38.1-3.fc38.ppc64le 146/154
Verifying : util-linux-core-2.38.1-3.fc38.ppc64le 147/154
Verifying : which-2.21-36.fc38.ppc64le 148/154
Verifying : xxhash-libs-0.8.1-3.fc37.ppc64le 149/154
Verifying : xz-5.2.9-1.fc38.ppc64le 150/154
Verifying : xz-libs-5.2.9-1.fc38.ppc64le 151/154
Verifying : zip-3.0-35.fc38.ppc64le 152/154
Verifying : zlib-1.2.13-1.fc38.ppc64le 153/154
Verifying : zstd-1.5.2-3.fc37.ppc64le 154/154
Installed:
alternatives-1.21-1.fc38.ppc64le
ansible-srpm-macros-1-8.1.fc38.noarch
audit-libs-3.0.9-2.fc38.ppc64le
authselect-1.4.2-1.fc38.ppc64le
authselect-libs-1.4.2-1.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
binutils-2.39-6.fc38.ppc64le
binutils-gold-2.39-6.fc38.ppc64le
bzip2-1.0.8-12.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
cpio-2.13-13.fc38.ppc64le
cracklib-2.9.7-30.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
debugedit-5.0-5.fc37.ppc64le
diffutils-3.8-3.fc38.ppc64le
dwz-0.15-1.fc38.ppc64le
ed-1.18-2.fc38.ppc64le
efi-srpm-macros-5-6.fc37.noarch
elfutils-0.188-3.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-5.42-4.fc38.ppc64le
file-libs-5.42-4.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc38.ppc64le
fonts-srpm-macros-1:2.0.5-10.fc38.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
gawk-5.1.1-4.fc38.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
gdbm-libs-1:1.23-2.fc38.ppc64le
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-2.36.9000-19.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
glibc-gconv-extra-2.36.9000-19.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
gmp-1:6.2.1-3.fc38.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
grep-3.8-1.fc38.ppc64le
gzip-1.12-2.fc38.ppc64le
info-7.0.1-1.fc38.ppc64le
jansson-2.13.1-5.fc38.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
keyutils-libs-1.6.1-5.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
libcap-2.48-5.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdb-5.3.28-54.fc38.ppc64le
libeconf-0.4.0-4.fc38.ppc64le
libevent-2.1.12-7.fc38.ppc64le
libfdisk-2.38.1-3.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc38.ppc64le
libpkgconf-1.8.0-3.fc37.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
libpwquality-1.4.5-1.fc38.ppc64le
librtas-2.0.3-1.fc38.ppc64le
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
libutempter-1.2.1-7.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc38.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
lz4-libs-1.9.3-5.fc38.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc38.ppc64le
nim-srpm-macros-3-7.fc37.noarch
ocaml-srpm-macros-7-2.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
pam-1.5.2-15.fc38.ppc64le
pam-libs-1.5.2-15.fc38.ppc64le
patch-2.7.6-17.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
perl-srpm-macros-1-47.fc38.noarch
pkgconf-1.8.0-3.fc37.ppc64le
pkgconf-m4-1.8.0-3.fc37.noarch
pkgconf-pkg-config-1.8.0-3.fc37.ppc64le
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
qt5-srpm-macros-5.15.7-1.fc38.noarch
readline-8.2-2.fc38.ppc64le
redhat-rpm-config-235-1.fc38.noarch
rpm-4.18.0-8.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tar-2:1.34-5.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
unzip-6.0-58.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
util-linux-core-2.38.1-3.fc38.ppc64le
which-2.21-36.fc38.ppc64le
xxhash-libs-0.8.1-3.fc37.ppc64le
xz-5.2.9-1.fc38.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
zip-3.0-35.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: libeconf-0.4.0-4.fc38.ppc64le
glibc-2.36.9000-19.fc38.ppc64le
file-libs-5.42-4.fc38.ppc64le
diffutils-3.8-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
keyutils-libs-1.6.1-5.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
tar-1.34-5.fc38.ppc64le
debugedit-5.0-5.fc37.ppc64le
glibc-gconv-extra-2.36.9000-19.fc38.ppc64le
libpsl-0.21.1-6.fc38.ppc64le
bzip2-libs-1.0.8-12.fc38.ppc64le
rpm-4.18.0-8.fc38.ppc64le
pcre2-syntax-10.40-1.fc38.1.noarch
gpg-pubkey-5323552a-6112bcdc
fedora-release-38-0.6.noarch
libevent-2.1.12-7.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
rust-srpm-macros-23-1.fc38.noarch
libxcrypt-4.4.33-5.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
libdb-5.3.28-54.fc38.ppc64le
efi-srpm-macros-5-6.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
libgomp-13.0.0-0.4.fc38.ppc64le
info-7.0.1-1.fc38.ppc64le
findutils-4.9.0-2.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
libtasn1-4.19.0-1.fc38.ppc64le
openblas-srpm-macros-2-12.fc37.noarch
gmp-6.2.1-3.fc38.ppc64le
pkgconf-pkg-config-1.8.0-3.fc37.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
libxml2-2.10.3-2.fc38.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
audit-libs-3.0.9-2.fc38.ppc64le
libselinux-3.4-6.fc38.ppc64le
shadow-utils-4.13-3.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
pam-1.5.2-15.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
ansible-srpm-macros-1-8.1.fc38.noarch
libverto-0.3.2-4.fc38.ppc64le
popt-1.19-1.fc38.ppc64le
authselect-libs-1.4.2-1.fc38.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
libfdisk-2.38.1-3.fc38.ppc64le
nettle-3.8-2.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
gzip-1.12-2.fc38.ppc64le
file-5.42-4.fc38.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-19.fc38.ppc64le
patch-2.7.6-17.fc38.ppc64le
pkgconf-m4-1.8.0-3.fc37.noarch
lz4-libs-1.9.3-5.fc38.ppc64le
pcre2-10.40-1.fc38.1.ppc64le
openssl-libs-3.0.5-6.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
glibc-common-2.36.9000-19.fc38.ppc64le
ghc-srpm-macros-1.5.0-7.fc37.noarch
util-linux-core-2.38.1-3.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
dwz-0.15-1.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
zip-3.0-35.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
gdbm-libs-1.23-2.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
coreutils-9.1-8.fc38.ppc64le
which-2.21-36.fc38.ppc64le
jansson-2.13.1-5.fc38.ppc64le
ncurses-libs-6.3-5.20221126.fc38.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libpkgconf-1.8.0-3.fc37.ppc64le
nim-srpm-macros-3-7.fc37.noarch
libmount-2.38.1-3.fc38.ppc64le
binutils-gold-2.39-6.fc38.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
libnsl2-2.0.0-4.fc38.ppc64le
redhat-rpm-config-235-1.fc38.noarch
librtas-2.0.3-1.fc38.ppc64le
cpio-2.13-13.fc38.ppc64le
elfutils-libelf-0.188-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libtirpc-1.3.3-0.fc38.ppc64le
unzip-6.0-58.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
fonts-srpm-macros-2.0.5-10.fc38.noarch
perl-srpm-macros-1-47.fc38.noarch
pam-libs-1.5.2-15.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libutempter-1.2.1-7.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libstdc++-13.0.0-0.4.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
libidn2-2.3.4-1.fc38.ppc64le
grep-3.8-1.fc38.ppc64le
libunistring-1.0-2.fc38.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
ncurses-base-6.3-5.20221126.fc38.noarch
pkgconf-1.8.0-3.fc37.ppc64le
libbrotli-1.0.9-9.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
fedora-repos-38-0.3.noarch
publicsuffix-list-dafsa-20221208-1.fc38.noarch
ed-1.18-2.fc38.ppc64le
fedora-release-identity-basic-38-0.6.noarch
ca-certificates-2022.2.54-5.fc37.noarch
fedora-repos-rawhide-38-0.3.noarch
cracklib-2.9.7-30.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
elfutils-0.188-3.fc38.ppc64le
libcom_err-1.46.5-3.fc38.ppc64le
fedora-release-common-38-0.6.noarch
alternatives-1.21-1.fc38.ppc64le
libsigsegv-2.14-3.fc38.ppc64le
bash-5.2.9-3.fc38.ppc64le
authselect-1.4.2-1.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
xz-5.2.9-1.fc38.ppc64le
bzip2-1.0.8-12.fc38.ppc64le
ocaml-srpm-macros-7-2.fc37.noarch
filesystem-3.18-2.fc37.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
gawk-5.1.1-4.fc38.ppc64le
readline-8.2-2.fc38.ppc64le
xxhash-libs-0.8.1-3.fc37.ppc64le
libpwquality-1.4.5-1.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
fpc-srpm-macros-1.3-6.fc37.noarch
mpfr-4.1.1-2.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
basesystem-11-14.fc37.noarch
curl-7.87.0-1.fc38.ppc64le
gpg-pubkey-eb10b464-6202d9c6
libcap-2.48-5.fc38.ppc64le
binutils-2.39-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
qt5-srpm-macros-5.15.7-1.fc38.noarch
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-yqovix85/percolator/percolator.spec) Config(child) 2 minutes 15 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 (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672042909.556246 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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/results/percolator-3.05-10.fc38.src.rpm) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672042909.556246/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1672042909.556246/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/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
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 9.5 kB/s | 3.0 kB 00:00
Copr repository 24 MB/s | 30 MB 00:01
Additional repo https_jakub_fedorapeople_org_fe 8.8 kB/s | 3.0 kB 00:00
fedora 61 kB/s | 5.6 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for percolator-3.05-10.fc38.src.rpm
Start: build setup for percolator-3.05-10.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 11 kB/s | 3.0 kB 00:00
Copr repository 29 MB/s | 30 MB 00:01
Additional repo https_jakub_fedorapeople_org_fe 9.0 kB/s | 3.0 kB 00:00
fedora 64 kB/s | 5.6 kB 00:00
Dependencies resolved.
===============================================================================================================
Package Arch Version Repository Size
===============================================================================================================
Installing:
boost-devel ppc64le 1.78.0-9.fc38 copr_base 11 M
boost-static ppc64le 1.78.0-9.fc38 copr_base 3.9 M
bzip2-devel ppc64le 1.0.8-12.fc38 copr_base 214 k
cmake ppc64le 3.25.1-1.fc38 copr_base 6.8 M
gcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 30 M
gcc-c++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 12 M
libtirpc-devel ppc64le 1.3.3-0.fc38 copr_base 113 k
make ppc64le 1:4.3-11.fc38 copr_base 549 k
sqlite-devel ppc64le 3.40.0-1.fc38 fedora 143 k
tokyocabinet-devel ppc64le 1.4.48-20.fc37 fedora 93 k
xerces-c-devel ppc64le 3.2.3-7.fc37 fedora 509 k
xsd ppc64le 4.1.0-0.10.a11.fc37 fedora 1.2 M
zlib-devel ppc64le 1.2.13-1.fc38 fedora 45 k
Installing dependencies:
annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k
annobin-plugin-gcc ppc64le 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 890 k
boost ppc64le 1.78.0-9.fc38 copr_base 15 k
boost-atomic ppc64le 1.78.0-9.fc38 copr_base 20 k
boost-chrono ppc64le 1.78.0-9.fc38 copr_base 28 k
boost-container ppc64le 1.78.0-9.fc38 copr_base 43 k
boost-context ppc64le 1.78.0-9.fc38 copr_base 18 k
boost-contract ppc64le 1.78.0-9.fc38 copr_base 48 k
boost-coroutine ppc64le 1.78.0-9.fc38 copr_base 24 k
boost-date-time ppc64le 1.78.0-9.fc38 copr_base 17 k
boost-fiber ppc64le 1.78.0-9.fc38 copr_base 45 k
boost-filesystem ppc64le 1.78.0-9.fc38 copr_base 68 k
boost-graph ppc64le 1.78.0-9.fc38 copr_base 160 k
boost-iostreams ppc64le 1.78.0-9.fc38 copr_base 42 k
boost-json ppc64le 1.78.0-9.fc38 copr_base 117 k
boost-locale ppc64le 1.78.0-9.fc38 copr_base 245 k
boost-log ppc64le 1.78.0-9.fc38 copr_base 524 k
boost-math ppc64le 1.78.0-9.fc38 copr_base 295 k
boost-nowide ppc64le 1.78.0-9.fc38 copr_base 22 k
boost-numpy3 ppc64le 1.78.0-9.fc38 copr_base 30 k
boost-program-options ppc64le 1.78.0-9.fc38 copr_base 117 k
boost-python3 ppc64le 1.78.0-9.fc38 copr_base 119 k
boost-random ppc64le 1.78.0-9.fc38 copr_base 27 k
boost-regex ppc64le 1.78.0-9.fc38 copr_base 122 k
boost-serialization ppc64le 1.78.0-9.fc38 copr_base 139 k
boost-stacktrace ppc64le 1.78.0-9.fc38 copr_base 32 k
boost-system ppc64le 1.78.0-9.fc38 copr_base 17 k
boost-test ppc64le 1.78.0-9.fc38 copr_base 251 k
boost-thread ppc64le 1.78.0-9.fc38 copr_base 63 k
boost-timer ppc64le 1.78.0-9.fc38 copr_base 46 k
boost-type_erasure ppc64le 1.78.0-9.fc38 copr_base 35 k
boost-wave ppc64le 1.78.0-9.fc38 copr_base 239 k
cmake-data noarch 3.25.1-1.fc38 copr_base 1.7 M
cmake-filesystem ppc64le 3.25.1-1.fc38 copr_base 17 k
cmake-rpm-macros noarch 3.25.1-1.fc38 copr_base 16 k
cpp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 9.8 M
emacs-filesystem noarch 1:28.1-3.fc37 fedora 9.5 k
expat ppc64le 2.5.0-1.fc38 copr_base 117 k
flexiblas ppc64le 3.2.1-3.fc38 fedora 32 k
flexiblas-netlib ppc64le 3.2.1-3.fc38 fedora 2.7 M
flexiblas-openblas-openmp ppc64le 3.2.1-3.fc38 fedora 16 k
gc ppc64le 8.2.2-1.fc38 copr_base 122 k
gcc-plugin-annobin ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 32 k
glibc-devel ppc64le 2.36.9000-19.fc38 fedora 546 k
guile22 ppc64le 2.2.7-6.fc38 copr_base 6.5 M
jsoncpp ppc64le 1.9.5-3.fc38 copr_base 101 k
kernel-headers ppc64le 6.1.0-1.fc38 fedora 1.5 M
libasan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 477 k
libatomic ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 19 k
libb2 ppc64le 0.98.1-7.fc38 copr_base 26 k
libcutl ppc64le 1.10.0-25.fc38 copr_base 330 k
libgfortran ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 597 k
libicu ppc64le 71.1-2.fc38 copr_base 10 M
libicu-devel ppc64le 71.1-2.fc38 copr_base 844 k
libmpc ppc64le 1.2.1-5.fc38 copr_base 85 k
libquadmath ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 195 k
libstdc++-devel ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 2.4 M
libtool-ltdl ppc64le 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 41 k
libubsan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 234 k
libuv ppc64le 1:1.44.2-2.fc38 copr_base 162 k
libxcrypt-devel ppc64le 4.4.33-5.fc38 copr_base 31 k
mpdecimal ppc64le 2.5.1-4.fc38 copr_base 118 k
openblas ppc64le 0.3.21-4.fc38 fedora 35 k
openblas-openmp ppc64le 0.3.21-4.fc38 fedora 4.4 M
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
python3-numpy ppc64le 1:1.23.5-1.fc38 copr_base 7.3 M
rhash ppc64le 1.4.3-1.fc38 fedora 205 k
sqlite ppc64le 3.40.0-1.fc38 fedora 940 k
tokyocabinet ppc64le 1.4.48-20.fc37 fedora 574 k
vim-filesystem noarch 2:9.0.1054-1.fc38 fedora 19 k
xerces-c ppc64le 3.2.3-7.fc37 fedora 957 k
Transaction Summary
===============================================================================================================
Install 87 Packages
Total download size: 136 M
Installed size: 676 M
Downloading Packages:
(1/87): boost-1.78.0-9.fc38.ppc64le.rpm 112 kB/s | 15 kB 00:00
(2/87): boost-atomic-1.78.0-9.fc38.ppc64le.rpm 151 kB/s | 20 kB 00:00
(3/87): boost-chrono-1.78.0-9.fc38.ppc64le.rpm 196 kB/s | 28 kB 00:00
(4/87): boost-container-1.78.0-9.fc38.ppc64le.r 3.2 MB/s | 43 kB 00:00
(5/87): boost-context-1.78.0-9.fc38.ppc64le.rpm 1.0 MB/s | 18 kB 00:00
(6/87): boost-contract-1.78.0-9.fc38.ppc64le.rp 4.0 MB/s | 48 kB 00:00
(7/87): boost-coroutine-1.78.0-9.fc38.ppc64le.r 1.7 MB/s | 24 kB 00:00
(8/87): boost-date-time-1.78.0-9.fc38.ppc64le.r 1.6 MB/s | 17 kB 00:00
(9/87): boost-fiber-1.78.0-9.fc38.ppc64le.rpm 1.3 MB/s | 45 kB 00:00
(10/87): boost-filesystem-1.78.0-9.fc38.ppc64le 2.1 MB/s | 68 kB 00:00
(11/87): boost-graph-1.78.0-9.fc38.ppc64le.rpm 2.6 MB/s | 160 kB 00:00
(12/87): boost-iostreams-1.78.0-9.fc38.ppc64le. 665 kB/s | 42 kB 00:00
(13/87): boost-devel-1.78.0-9.fc38.ppc64le.rpm 63 MB/s | 11 MB 00:00
(14/87): boost-json-1.78.0-9.fc38.ppc64le.rpm 1.4 MB/s | 117 kB 00:00
(15/87): boost-locale-1.78.0-9.fc38.ppc64le.rpm 3.0 MB/s | 245 kB 00:00
(16/87): boost-log-1.78.0-9.fc38.ppc64le.rpm 32 MB/s | 524 kB 00:00
(17/87): boost-math-1.78.0-9.fc38.ppc64le.rpm 18 MB/s | 295 kB 00:00
(18/87): boost-nowide-1.78.0-9.fc38.ppc64le.rpm 1.3 MB/s | 22 kB 00:00
(19/87): boost-numpy3-1.78.0-9.fc38.ppc64le.rpm 3.2 MB/s | 30 kB 00:00
(20/87): boost-program-options-1.78.0-9.fc38.pp 11 MB/s | 117 kB 00:00
(21/87): boost-python3-1.78.0-9.fc38.ppc64le.rp 10 MB/s | 119 kB 00:00
(22/87): boost-random-1.78.0-9.fc38.ppc64le.rpm 3.0 MB/s | 27 kB 00:00
(23/87): boost-regex-1.78.0-9.fc38.ppc64le.rpm 12 MB/s | 122 kB 00:00
(24/87): boost-serialization-1.78.0-9.fc38.ppc6 12 MB/s | 139 kB 00:00
(25/87): boost-stacktrace-1.78.0-9.fc38.ppc64le 3.4 MB/s | 32 kB 00:00
(26/87): boost-system-1.78.0-9.fc38.ppc64le.rpm 1.8 MB/s | 17 kB 00:00
(27/87): boost-test-1.78.0-9.fc38.ppc64le.rpm 17 MB/s | 251 kB 00:00
(28/87): boost-thread-1.78.0-9.fc38.ppc64le.rpm 4.6 MB/s | 63 kB 00:00
(29/87): boost-timer-1.78.0-9.fc38.ppc64le.rpm 2.2 MB/s | 46 kB 00:00
(30/87): boost-type_erasure-1.78.0-9.fc38.ppc64 1.5 MB/s | 35 kB 00:00
(31/87): boost-static-1.78.0-9.fc38.ppc64le.rpm 54 MB/s | 3.9 MB 00:00
(32/87): boost-wave-1.78.0-9.fc38.ppc64le.rpm 6.6 MB/s | 239 kB 00:00
(33/87): bzip2-devel-1.0.8-12.fc38.ppc64le.rpm 7.6 MB/s | 214 kB 00:00
(34/87): cmake-filesystem-3.25.1-1.fc38.ppc64le 826 kB/s | 17 kB 00:00
(35/87): cmake-data-3.25.1-1.fc38.noarch.rpm 34 MB/s | 1.7 MB 00:00
(36/87): cmake-3.25.1-1.fc38.ppc64le.rpm 58 MB/s | 6.8 MB 00:00
(37/87): cmake-rpm-macros-3.25.1-1.fc38.noarch. 174 kB/s | 16 kB 00:00
(38/87): expat-2.5.0-1.fc38.ppc64le.rpm 1.7 MB/s | 117 kB 00:00
(39/87): gc-8.2.2-1.fc38.ppc64le.rpm 11 MB/s | 122 kB 00:00
(40/87): jsoncpp-1.9.5-3.fc38.ppc64le.rpm 6.5 MB/s | 101 kB 00:00
(41/87): libb2-0.98.1-7.fc38.ppc64le.rpm 667 kB/s | 26 kB 00:00
(42/87): guile22-2.2.7-6.fc38.ppc64le.rpm 67 MB/s | 6.5 MB 00:00
(43/87): libicu-71.1-2.fc38.ppc64le.rpm 57 MB/s | 10 MB 00:00
(44/87): libcutl-1.10.0-25.fc38.ppc64le.rpm 1.5 MB/s | 330 kB 00:00
(45/87): libicu-devel-71.1-2.fc38.ppc64le.rpm 5.7 MB/s | 844 kB 00:00
(46/87): libmpc-1.2.1-5.fc38.ppc64le.rpm 7.2 MB/s | 85 kB 00:00
(47/87): libuv-1.44.2-2.fc38.ppc64le.rpm 14 MB/s | 162 kB 00:00
(48/87): libtirpc-devel-1.3.3-0.fc38.ppc64le.rp 8.8 MB/s | 113 kB 00:00
(49/87): libxcrypt-devel-4.4.33-5.fc38.ppc64le. 3.3 MB/s | 31 kB 00:00
(50/87): make-4.3-11.fc38.ppc64le.rpm 31 MB/s | 549 kB 00:00
(51/87): mpdecimal-2.5.1-4.fc38.ppc64le.rpm 6.1 MB/s | 118 kB 00:00
(52/87): python3-numpy-1.23.5-1.fc38.ppc64le.rp 60 MB/s | 7.3 MB 00:00
(53/87): annobin-docs-10.99-1.0.1.fc38.noarch.r 496 kB/s | 93 kB 00:00
(54/87): annobin-plugin-gcc-10.99-1.0.1.fc38.pp 3.0 MB/s | 890 kB 00:00
(55/87): gcc-c++-13.0.0-0.4.fc38.ppc64le.rpm 36 MB/s | 12 MB 00:00
(56/87): gcc-plugin-annobin-13.0.0-0.4.fc38.ppc 723 kB/s | 32 kB 00:00
(57/87): cpp-13.0.0-0.4.fc38.ppc64le.rpm 15 MB/s | 9.8 MB 00:00
(58/87): libasan-13.0.0-0.4.fc38.ppc64le.rpm 5.5 MB/s | 477 kB 00:00
(59/87): libgfortran-13.0.0-0.4.fc38.ppc64le.rp 20 MB/s | 597 kB 00:00
(60/87): libatomic-13.0.0-0.4.fc38.ppc64le.rpm 575 kB/s | 19 kB 00:00
(61/87): libquadmath-13.0.0-0.4.fc38.ppc64le.rp 5.9 MB/s | 195 kB 00:00
(62/87): libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le. 1.4 MB/s | 41 kB 00:00
(63/87): libstdc++-devel-13.0.0-0.4.fc38.ppc64l 30 MB/s | 2.4 MB 00:00
(64/87): libubsan-13.0.0-0.4.fc38.ppc64le.rpm 4.6 MB/s | 234 kB 00:00
(65/87): gcc-13.0.0-0.4.fc38.ppc64le.rpm 36 MB/s | 30 MB 00:00
(66/87): emacs-filesystem-28.1-3.fc37.noarch.rp 33 kB/s | 9.5 kB 00:00
(67/87): flexiblas-3.2.1-3.fc38.ppc64le.rpm 121 kB/s | 32 kB 00:00
(68/87): flexiblas-openblas-openmp-3.2.1-3.fc38 351 kB/s | 16 kB 00:00
(69/87): glibc-devel-2.36.9000-19.fc38.ppc64le. 2.0 MB/s | 546 kB 00:00
(70/87): flexiblas-netlib-3.2.1-3.fc38.ppc64le. 5.9 MB/s | 2.7 MB 00:00
(71/87): kernel-headers-6.1.0-1.fc38.ppc64le.rp 5.3 MB/s | 1.5 MB 00:00
(72/87): openblas-0.3.21-4.fc38.ppc64le.rpm 574 kB/s | 35 kB 00:00
(73/87): openblas-openmp-0.3.21-4.fc38.ppc64le. 34 MB/s | 4.4 MB 00:00
(74/87): python-pip-wheel-22.3.1-1.fc38.noarch. 9.7 MB/s | 1.4 MB 00:00
(75/87): python-setuptools-wheel-65.5.1-1.fc38. 4.1 MB/s | 715 kB 00:00
(76/87): python3-3.11.1-1.fc38.ppc64le.rpm 525 kB/s | 27 kB 00:00
(77/87): rhash-1.4.3-1.fc38.ppc64le.rpm 1.3 MB/s | 205 kB 00:00
(78/87): python3-libs-3.11.1-1.fc38.ppc64le.rpm 41 MB/s | 9.7 MB 00:00
(79/87): sqlite-3.40.0-1.fc38.ppc64le.rpm 4.4 MB/s | 940 kB 00:00
(80/87): sqlite-devel-3.40.0-1.fc38.ppc64le.rpm 2.1 MB/s | 143 kB 00:00
(81/87): tokyocabinet-1.4.48-20.fc37.ppc64le.rp 6.1 MB/s | 574 kB 00:00
(82/87): tokyocabinet-devel-1.4.48-20.fc37.ppc6 1.0 MB/s | 93 kB 00:00
(83/87): vim-filesystem-9.0.1054-1.fc38.noarch. 188 kB/s | 19 kB 00:00
(84/87): xerces-c-3.2.3-7.fc37.ppc64le.rpm 16 MB/s | 957 kB 00:00
(85/87): xerces-c-devel-3.2.3-7.fc37.ppc64le.rp 6.1 MB/s | 509 kB 00:00
(86/87): xsd-4.1.0-0.10.a11.fc37.ppc64le.rpm 8.9 MB/s | 1.2 MB 00:00
(87/87): zlib-devel-1.2.13-1.fc38.ppc64le.rpm 502 kB/s | 45 kB 00:00
--------------------------------------------------------------------------------
Total 42 MB/s | 136 MB 00:03
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Installing : boost-system-1.78.0-9.fc38.ppc64le 1/87
Installing : boost-chrono-1.78.0-9.fc38.ppc64le 2/87
Installing : boost-thread-1.78.0-9.fc38.ppc64le 3/87
Installing : libicu-71.1-2.fc38.ppc64le 4/87
Installing : boost-regex-1.78.0-9.fc38.ppc64le 5/87
Installing : libmpc-1.2.1-5.fc38.ppc64le 6/87
Installing : expat-2.5.0-1.fc38.ppc64le 7/87
Installing : boost-context-1.78.0-9.fc38.ppc64le 8/87
Installing : boost-atomic-1.78.0-9.fc38.ppc64le 9/87
Installing : boost-filesystem-1.78.0-9.fc38.ppc64le 10/87
Installing : xerces-c-3.2.3-7.fc37.ppc64le 11/87
Installing : flexiblas-3.2.1-3.fc38.ppc64le 12/87
Installing : libquadmath-13.0.0-0.4.fc38.ppc64le 13/87
Installing : libgfortran-13.0.0-0.4.fc38.ppc64le 14/87
Installing : cmake-filesystem-3.25.1-1.fc38.ppc64le 15/87
Installing : boost-date-time-1.78.0-9.fc38.ppc64le 16/87
Installing : boost-container-1.78.0-9.fc38.ppc64le 17/87
Installing : boost-json-1.78.0-9.fc38.ppc64le 18/87
Installing : boost-wave-1.78.0-9.fc38.ppc64le 19/87
Installing : boost-fiber-1.78.0-9.fc38.ppc64le 20/87
Installing : boost-log-1.78.0-9.fc38.ppc64le 21/87
Installing : boost-coroutine-1.78.0-9.fc38.ppc64le 22/87
Installing : libcutl-1.10.0-25.fc38.ppc64le 23/87
Installing : cpp-13.0.0-0.4.fc38.ppc64le 24/87
Installing : boost-graph-1.78.0-9.fc38.ppc64le 25/87
Installing : boost-locale-1.78.0-9.fc38.ppc64le 26/87
Installing : libicu-devel-71.1-2.fc38.ppc64le 27/87
Installing : boost-type_erasure-1.78.0-9.fc38.ppc64le 28/87
Installing : boost-timer-1.78.0-9.fc38.ppc64le 29/87
Installing : vim-filesystem-2:9.0.1054-1.fc38.noarch 30/87
Installing : tokyocabinet-1.4.48-20.fc37.ppc64le 31/87
Installing : sqlite-3.40.0-1.fc38.ppc64le 32/87
Installing : rhash-1.4.3-1.fc38.ppc64le 33/87
Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 34/87
Installing : python-pip-wheel-22.3.1-1.fc38.noarch 35/87
Installing : openblas-0.3.21-4.fc38.ppc64le 36/87
Installing : openblas-openmp-0.3.21-4.fc38.ppc64le 37/87
Installing : flexiblas-netlib-3.2.1-3.fc38.ppc64le 38/87
Installing : flexiblas-openblas-openmp-3.2.1-3.fc38.ppc64le 39/87
Installing : kernel-headers-6.1.0-1.fc38.ppc64le 40/87
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Installing : libxcrypt-devel-4.4.33-5.fc38.ppc64le 42/87
Installing : emacs-filesystem-1:28.1-3.fc37.noarch 43/87
Installing : libubsan-13.0.0-0.4.fc38.ppc64le 44/87
Installing : libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le 45/87
Installing : libstdc++-devel-13.0.0-0.4.fc38.ppc64le 46/87
Installing : libatomic-13.0.0-0.4.fc38.ppc64le 47/87
Installing : libasan-13.0.0-0.4.fc38.ppc64le 48/87
Installing : annobin-docs-10.99-1.0.1.fc38.noarch 49/87
Installing : mpdecimal-2.5.1-4.fc38.ppc64le 50/87
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Installing : libb2-0.98.1-7.fc38.ppc64le 52/87
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Installing : jsoncpp-1.9.5-3.fc38.ppc64le 59/87
Installing : gc-8.2.2-1.fc38.ppc64le 60/87
Installing : guile22-2.2.7-6.fc38.ppc64le 61/87
Installing : make-1:4.3-11.fc38.ppc64le 62/87
Installing : gcc-13.0.0-0.4.fc38.ppc64le 63/87
Running scriptlet: gcc-13.0.0-0.4.fc38.ppc64le 63/87
Installing : cmake-data-3.25.1-1.fc38.noarch 64/87
Installing : cmake-3.25.1-1.fc38.ppc64le 65/87
Installing : boost-test-1.78.0-9.fc38.ppc64le 66/87
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Installing : boost-random-1.78.0-9.fc38.ppc64le 69/87
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Installing : boost-nowide-1.78.0-9.fc38.ppc64le 71/87
Installing : boost-math-1.78.0-9.fc38.ppc64le 72/87
Installing : boost-iostreams-1.78.0-9.fc38.ppc64le 73/87
Installing : boost-contract-1.78.0-9.fc38.ppc64le 74/87
Installing : boost-1.78.0-9.fc38.ppc64le 75/87
Installing : boost-devel-1.78.0-9.fc38.ppc64le 76/87
Installing : boost-static-1.78.0-9.fc38.ppc64le 77/87
Installing : annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le 78/87
Running scriptlet: annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le 78/87
Installing : gcc-c++-13.0.0-0.4.fc38.ppc64le 79/87
Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le 80/87
Installing : sqlite-devel-3.40.0-1.fc38.ppc64le 81/87
Installing : tokyocabinet-devel-1.4.48-20.fc37.ppc64le 82/87
Installing : xsd-4.1.0-0.10.a11.fc37.ppc64le 83/87
Installing : xerces-c-devel-3.2.3-7.fc37.ppc64le 84/87
Installing : zlib-devel-1.2.13-1.fc38.ppc64le 85/87
Installing : libtirpc-devel-1.3.3-0.fc38.ppc64le 86/87
Installing : bzip2-devel-1.0.8-12.fc38.ppc64le 87/87
Running scriptlet: bzip2-devel-1.0.8-12.fc38.ppc64le 87/87
Verifying : boost-1.78.0-9.fc38.ppc64le 1/87
Verifying : boost-atomic-1.78.0-9.fc38.ppc64le 2/87
Verifying : boost-chrono-1.78.0-9.fc38.ppc64le 3/87
Verifying : boost-container-1.78.0-9.fc38.ppc64le 4/87
Verifying : boost-context-1.78.0-9.fc38.ppc64le 5/87
Verifying : boost-contract-1.78.0-9.fc38.ppc64le 6/87
Verifying : boost-coroutine-1.78.0-9.fc38.ppc64le 7/87
Verifying : boost-date-time-1.78.0-9.fc38.ppc64le 8/87
Verifying : boost-devel-1.78.0-9.fc38.ppc64le 9/87
Verifying : boost-fiber-1.78.0-9.fc38.ppc64le 10/87
Verifying : boost-filesystem-1.78.0-9.fc38.ppc64le 11/87
Verifying : boost-graph-1.78.0-9.fc38.ppc64le 12/87
Verifying : boost-iostreams-1.78.0-9.fc38.ppc64le 13/87
Verifying : boost-json-1.78.0-9.fc38.ppc64le 14/87
Verifying : boost-locale-1.78.0-9.fc38.ppc64le 15/87
Verifying : boost-log-1.78.0-9.fc38.ppc64le 16/87
Verifying : boost-math-1.78.0-9.fc38.ppc64le 17/87
Verifying : boost-nowide-1.78.0-9.fc38.ppc64le 18/87
Verifying : boost-numpy3-1.78.0-9.fc38.ppc64le 19/87
Verifying : boost-program-options-1.78.0-9.fc38.ppc64le 20/87
Verifying : boost-python3-1.78.0-9.fc38.ppc64le 21/87
Verifying : boost-random-1.78.0-9.fc38.ppc64le 22/87
Verifying : boost-regex-1.78.0-9.fc38.ppc64le 23/87
Verifying : boost-serialization-1.78.0-9.fc38.ppc64le 24/87
Verifying : boost-stacktrace-1.78.0-9.fc38.ppc64le 25/87
Verifying : boost-static-1.78.0-9.fc38.ppc64le 26/87
Verifying : boost-system-1.78.0-9.fc38.ppc64le 27/87
Verifying : boost-test-1.78.0-9.fc38.ppc64le 28/87
Verifying : boost-thread-1.78.0-9.fc38.ppc64le 29/87
Verifying : boost-timer-1.78.0-9.fc38.ppc64le 30/87
Verifying : boost-type_erasure-1.78.0-9.fc38.ppc64le 31/87
Verifying : boost-wave-1.78.0-9.fc38.ppc64le 32/87
Verifying : bzip2-devel-1.0.8-12.fc38.ppc64le 33/87
Verifying : cmake-3.25.1-1.fc38.ppc64le 34/87
Verifying : cmake-data-3.25.1-1.fc38.noarch 35/87
Verifying : cmake-filesystem-3.25.1-1.fc38.ppc64le 36/87
Verifying : cmake-rpm-macros-3.25.1-1.fc38.noarch 37/87
Verifying : expat-2.5.0-1.fc38.ppc64le 38/87
Verifying : gc-8.2.2-1.fc38.ppc64le 39/87
Verifying : guile22-2.2.7-6.fc38.ppc64le 40/87
Verifying : jsoncpp-1.9.5-3.fc38.ppc64le 41/87
Verifying : libb2-0.98.1-7.fc38.ppc64le 42/87
Verifying : libcutl-1.10.0-25.fc38.ppc64le 43/87
Verifying : libicu-71.1-2.fc38.ppc64le 44/87
Verifying : libicu-devel-71.1-2.fc38.ppc64le 45/87
Verifying : libmpc-1.2.1-5.fc38.ppc64le 46/87
Verifying : libtirpc-devel-1.3.3-0.fc38.ppc64le 47/87
Verifying : libuv-1:1.44.2-2.fc38.ppc64le 48/87
Verifying : libxcrypt-devel-4.4.33-5.fc38.ppc64le 49/87
Verifying : make-1:4.3-11.fc38.ppc64le 50/87
Verifying : mpdecimal-2.5.1-4.fc38.ppc64le 51/87
Verifying : python3-numpy-1:1.23.5-1.fc38.ppc64le 52/87
Verifying : annobin-docs-10.99-1.0.1.fc38.noarch 53/87
Verifying : annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le 54/87
Verifying : cpp-13.0.0-0.4.fc38.ppc64le 55/87
Verifying : gcc-13.0.0-0.4.fc38.ppc64le 56/87
Verifying : gcc-c++-13.0.0-0.4.fc38.ppc64le 57/87
Verifying : gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le 58/87
Verifying : libasan-13.0.0-0.4.fc38.ppc64le 59/87
Verifying : libatomic-13.0.0-0.4.fc38.ppc64le 60/87
Verifying : libgfortran-13.0.0-0.4.fc38.ppc64le 61/87
Verifying : libquadmath-13.0.0-0.4.fc38.ppc64le 62/87
Verifying : libstdc++-devel-13.0.0-0.4.fc38.ppc64le 63/87
Verifying : libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le 64/87
Verifying : libubsan-13.0.0-0.4.fc38.ppc64le 65/87
Verifying : emacs-filesystem-1:28.1-3.fc37.noarch 66/87
Verifying : flexiblas-3.2.1-3.fc38.ppc64le 67/87
Verifying : flexiblas-netlib-3.2.1-3.fc38.ppc64le 68/87
Verifying : flexiblas-openblas-openmp-3.2.1-3.fc38.ppc64le 69/87
Verifying : glibc-devel-2.36.9000-19.fc38.ppc64le 70/87
Verifying : kernel-headers-6.1.0-1.fc38.ppc64le 71/87
Verifying : openblas-0.3.21-4.fc38.ppc64le 72/87
Verifying : openblas-openmp-0.3.21-4.fc38.ppc64le 73/87
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 74/87
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 75/87
Verifying : python3-3.11.1-1.fc38.ppc64le 76/87
Verifying : python3-libs-3.11.1-1.fc38.ppc64le 77/87
Verifying : rhash-1.4.3-1.fc38.ppc64le 78/87
Verifying : sqlite-3.40.0-1.fc38.ppc64le 79/87
Verifying : sqlite-devel-3.40.0-1.fc38.ppc64le 80/87
Verifying : tokyocabinet-1.4.48-20.fc37.ppc64le 81/87
Verifying : tokyocabinet-devel-1.4.48-20.fc37.ppc64le 82/87
Verifying : vim-filesystem-2:9.0.1054-1.fc38.noarch 83/87
Verifying : xerces-c-3.2.3-7.fc37.ppc64le 84/87
Verifying : xerces-c-devel-3.2.3-7.fc37.ppc64le 85/87
Verifying : xsd-4.1.0-0.10.a11.fc37.ppc64le 86/87
Verifying : zlib-devel-1.2.13-1.fc38.ppc64le 87/87
Installed:
annobin-docs-10.99-1.0.1.fc38.noarch
annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le
boost-1.78.0-9.fc38.ppc64le
boost-atomic-1.78.0-9.fc38.ppc64le
boost-chrono-1.78.0-9.fc38.ppc64le
boost-container-1.78.0-9.fc38.ppc64le
boost-context-1.78.0-9.fc38.ppc64le
boost-contract-1.78.0-9.fc38.ppc64le
boost-coroutine-1.78.0-9.fc38.ppc64le
boost-date-time-1.78.0-9.fc38.ppc64le
boost-devel-1.78.0-9.fc38.ppc64le
boost-fiber-1.78.0-9.fc38.ppc64le
boost-filesystem-1.78.0-9.fc38.ppc64le
boost-graph-1.78.0-9.fc38.ppc64le
boost-iostreams-1.78.0-9.fc38.ppc64le
boost-json-1.78.0-9.fc38.ppc64le
boost-locale-1.78.0-9.fc38.ppc64le
boost-log-1.78.0-9.fc38.ppc64le
boost-math-1.78.0-9.fc38.ppc64le
boost-nowide-1.78.0-9.fc38.ppc64le
boost-numpy3-1.78.0-9.fc38.ppc64le
boost-program-options-1.78.0-9.fc38.ppc64le
boost-python3-1.78.0-9.fc38.ppc64le
boost-random-1.78.0-9.fc38.ppc64le
boost-regex-1.78.0-9.fc38.ppc64le
boost-serialization-1.78.0-9.fc38.ppc64le
boost-stacktrace-1.78.0-9.fc38.ppc64le
boost-static-1.78.0-9.fc38.ppc64le
boost-system-1.78.0-9.fc38.ppc64le
boost-test-1.78.0-9.fc38.ppc64le
boost-thread-1.78.0-9.fc38.ppc64le
boost-timer-1.78.0-9.fc38.ppc64le
boost-type_erasure-1.78.0-9.fc38.ppc64le
boost-wave-1.78.0-9.fc38.ppc64le
bzip2-devel-1.0.8-12.fc38.ppc64le
cmake-3.25.1-1.fc38.ppc64le
cmake-data-3.25.1-1.fc38.noarch
cmake-filesystem-3.25.1-1.fc38.ppc64le
cmake-rpm-macros-3.25.1-1.fc38.noarch
cpp-13.0.0-0.4.fc38.ppc64le
emacs-filesystem-1:28.1-3.fc37.noarch
expat-2.5.0-1.fc38.ppc64le
flexiblas-3.2.1-3.fc38.ppc64le
flexiblas-netlib-3.2.1-3.fc38.ppc64le
flexiblas-openblas-openmp-3.2.1-3.fc38.ppc64le
gc-8.2.2-1.fc38.ppc64le
gcc-13.0.0-0.4.fc38.ppc64le
gcc-c++-13.0.0-0.4.fc38.ppc64le
gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le
glibc-devel-2.36.9000-19.fc38.ppc64le
guile22-2.2.7-6.fc38.ppc64le
jsoncpp-1.9.5-3.fc38.ppc64le
kernel-headers-6.1.0-1.fc38.ppc64le
libasan-13.0.0-0.4.fc38.ppc64le
libatomic-13.0.0-0.4.fc38.ppc64le
libb2-0.98.1-7.fc38.ppc64le
libcutl-1.10.0-25.fc38.ppc64le
libgfortran-13.0.0-0.4.fc38.ppc64le
libicu-71.1-2.fc38.ppc64le
libicu-devel-71.1-2.fc38.ppc64le
libmpc-1.2.1-5.fc38.ppc64le
libquadmath-13.0.0-0.4.fc38.ppc64le
libstdc++-devel-13.0.0-0.4.fc38.ppc64le
libtirpc-devel-1.3.3-0.fc38.ppc64le
libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le
libubsan-13.0.0-0.4.fc38.ppc64le
libuv-1:1.44.2-2.fc38.ppc64le
libxcrypt-devel-4.4.33-5.fc38.ppc64le
make-1:4.3-11.fc38.ppc64le
mpdecimal-2.5.1-4.fc38.ppc64le
openblas-0.3.21-4.fc38.ppc64le
openblas-openmp-0.3.21-4.fc38.ppc64le
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-libs-3.11.1-1.fc38.ppc64le
python3-numpy-1:1.23.5-1.fc38.ppc64le
rhash-1.4.3-1.fc38.ppc64le
sqlite-3.40.0-1.fc38.ppc64le
sqlite-devel-3.40.0-1.fc38.ppc64le
tokyocabinet-1.4.48-20.fc37.ppc64le
tokyocabinet-devel-1.4.48-20.fc37.ppc64le
vim-filesystem-2:9.0.1054-1.fc38.noarch
xerces-c-3.2.3-7.fc37.ppc64le
xerces-c-devel-3.2.3-7.fc37.ppc64le
xsd-4.1.0-0.10.a11.fc37.ppc64le
zlib-devel-1.2.13-1.fc38.ppc64le
Complete!
Finish: build setup for percolator-3.05-10.fc38.src.rpm
Start: rpmbuild percolator-3.05-10.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658448000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.TCgmbz
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-05.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-05
+ /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
+ sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt
+ sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mLchBr
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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-3-05
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ mkdir -p percolator
~/build/BUILD/percolator-rel-3-05/percolator ~/build/BUILD/percolator-rel-3-05
+ pushd percolator
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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=ppc64le ..
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- 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 = ppc64le
-- TOOL CHAIN FILE =
-- PROFILING =
-- -------------------------------------------------------------------------------
--
-- Architecture:
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
-- : /usr/include
-- Version: 3.2.3
-- 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
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0")
-- Configuring done
-- Generating done
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-3-05/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 -j5 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05 -B/builddir/build/BUILD/percolator-rel-3-05/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
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[ 5%] Building C object src/blas/CMakeFiles/blas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/blas/daxpy.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/blas/ddot.c
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/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c: In function 'dgemv_':
/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c:59:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
59 | if (*m == 0 || *n == 0 || *alpha == 0.0 && *beta == 1.0) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/blas/dnrm2.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/MyException.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/Database.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable]
206 | Protein* protein = NULL;
| ^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 20%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/Peptide.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function]
375 | static bool equal_peptides(
| ^~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 14%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/PeptideConstraint.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/PeptideSrc.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/Protein.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
529 | switch(decoy_type){
| ^
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-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/picked_protein/Protein.cpp: In member function 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/ProteinPeptideIterator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 4%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 17%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 30%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 6%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/percolator/src/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 32%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/parser.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/parser.cxx:102:22: warning: 'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
102 | DOMImplementation& dom_impl_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning: when initialized here [-Wreorder]
144 | parser_impl::parser_impl() : clean_(true),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
178 | size_t n(s.size());
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
170 | int i(1);
| ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 34%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 24%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/picked_protein/PickedProteinCaller.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp: In member function 'bool PickedProteinCaller::getProteinFragmentsAndDuplicates(std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp:365:8: warning: unused variable 'success' [-Wunused-variable]
365 | bool success = true;
| ^~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/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
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/serializer.cxx
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/Vector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/BaseSpline.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PSMDescription.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/ResultHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -MF CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o.d -o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp:23:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning: when initialized here [-Wreorder]
26 | PSMDescriptionDOC::PSMDescriptionDOC() :
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning: when initialized here [-Wreorder]
30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
| ^~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 49%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 29%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 53%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 53%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/svm.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const std::string&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:158:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
158 | double a = reader.readDouble();
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector<OptionalField>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:18: warning: unused variable 'targetIdx' [-Wunused-variable]
290 | unsigned int targetIdx = 0u, decoyIdx = 0u;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:34: warning: unused variable 'decoyIdx' [-Wunused-variable]
290 | unsigned int targetIdx = 0u, decoyIdx = 0u;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector<double>&, Scores&, SanityCheck*&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:489:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
489 | if (hasDefaultValues && init_values.size() > numFeatures) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:29,
from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const std::string&, bool, bool, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder]
99 | bool reportUniquePeptides_;
| ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:93:8: warning: 'bool XMLInterface::printDecoys_' [-Wreorder]
93 | bool printDecoys_, printExpMass_;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:58:1: warning: when initialized here [-Wreorder]
58 | XMLInterface::XMLInterface(const std::string& outputFN,
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable]
257 | const unsigned int numFeatures = FeatureNames::getNumFeatures();
| ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()':
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder]
87 | bool concatenatedSearch_;
| ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:72:10: warning: 'double SanityCheck::test_fdr_' [-Wreorder]
72 | double test_fdr_, initial_train_fdr_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder]
31 | SanityCheck::SanityCheck() :
| ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:28,
from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39,
from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h: In constructor 'CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, int, bool, int, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:101:8: warning: 'CrossValidation::trainBestPositive_' will be initialized after [-Wreorder]
101 | bool trainBestPositive_;
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:90:16: warning: 'unsigned int CrossValidation::numThreads_' [-Wreorder]
90 | unsigned int numThreads_;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:32:1: warning: when initialized here [-Wreorder]
32 | CrossValidation::CrossValidation(bool quickValidation,
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:106:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
106 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:107:39: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
107 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:141:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
141 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:145:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
145 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:263:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
263 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:269:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
269 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:291:26: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
291 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:303:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
303 | for (int nestedFold = 0; nestedFold < nestedXvalBins_; ++nestedFold)
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:318:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<candidateCposCfrac>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
318 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::trainCpCnPair(candidateCposCfrac&, options*, AlgIn*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:343:16: warning: unused variable 'set' [-Wunused-variable]
343 | unsigned int set = cpCnFold.set;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:344:16: warning: unused variable 'nestedFold' [-Wunused-variable]
344 | unsigned int nestedFold = cpCnFold.nestedSet;
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:356:7: warning: unused variable 'tp' [-Wunused-variable]
356 | int tp = 0;
| ^~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/CrossValidation.cpp:399:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
399 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:439:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
439 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:474:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
474 | for (set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:483:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
483 | for (int set = 0; set < numFolds_; ++set) {
| ~~~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp: In member function 'void DataSet::print_features()':
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
69 | for (int i = 0; i < getSize(); i++) {
| ~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/percolator/src/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/LogisticRegression.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder]
238 | double pi0_, absenceRatio_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:10: warning: 'double ProteinProbEstimator::pi0_' [-Wreorder]
238 | double pi0_, absenceRatio_;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder]
25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder]
242 | unsigned int numberTargetProteins_;
| ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:237:8: warning: 'bool ProteinProbEstimator::usePi0_' [-Wreorder]
237 | bool usePi0_;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder]
25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder]
243 | std::string decoyPattern_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:240:10: warning: 'double ProteinProbEstimator::fdr_' [-Wreorder]
240 | double fdr_;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h: In constructor 'Caller::Caller()':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:103:48: warning: 'Caller::trainBestPositive_' will be initialized after [-Wreorder]
103 | bool reportEachIteration_, quickValidation_, trainBestPositive_,
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:101:59: warning: 'unsigned int Caller::numThreads_' [-Wreorder]
101 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:35:1: warning: when initialized here [-Wreorder]
35 | Caller::Caller() :
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp: In member function 'bool Caller::parseOptions(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:694:7: warning: label 'std' defined but not used [-Wunused-label]
694 | std:cerr << "Error: the --static option requires the --init-weights "
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/ssl.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'void cglsFun2(int, int*, const double*, double*, int, int, double*, double*, double*, double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:86:7: warning: unused variable 'ind' [-Wunused-variable]
86 | int ind = 0;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:87:10: warning: unused variable 'temp' [-Wunused-variable]
87 | double temp = 0.0;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int CGLS(const AlgIn&, double, int, double, const vector_int*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:117:19: warning: unused variable 'j' [-Wunused-variable]
117 | register int i, j;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int L2_SVM_MFN(const AlgIn&, options*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:251:10: warning: unused variable 't' [-Wunused-variable]
251 | double t = 0.0;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'double line_search(double*, double*, double, double*, double*, const double*, int, int, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:364:7: warning: unused variable 'inc' [-Wunused-variable]
364 | int inc = 1;
| ^~~
In function 'Clear(options*)',
inlined from 'Clear(options*)' at /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:440:6:
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:442:12: warning: pointer 'opt_2(D)' used after 'operator delete[](void*)' [-Wuse-after-free]
442 | delete[] opt;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:441:12: note: call to 'operator delete[](void*)' here
441 | delete[] opt;
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PackedVector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o -MF CMakeFiles/perclibrary.dir/EludeModel.cpp.o.d -o CMakeFiles/perclibrary.dir/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PackedMatrix.cpp
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[ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Logger.cpp
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[ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/MyException.cpp
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[ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder]
108 | bool isDecoy_;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:106:7: warning: 'int ProteinScoreHolder::groupId_' [-Wreorder]
106 | int groupId_;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder]
20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
| ^~~~~~~~~~~~~~~~~~
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[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PosteriorEstimator.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:468:21: warning: unused variable 'queue' [-Wunused-variable]
468 | int nP = 1, queue = 0;
| ^~~~~
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[ 90%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 82%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Matrix.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 86%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:20,
from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder]
110 | double mseThreshold_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:106:8: warning: 'bool FidoInterface::doGridSearch_' [-Wreorder]
106 | bool doGridSearch_;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:76:1: warning: when initialized here [-Wreorder]
76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable]
132 | double prior, prior2, prior3, prior4;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, const std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable]
556 | double prob = probabilities[k];
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable]
558 | unsigned fpChange = proteinNames[k].size() - tpChange;
| ^~~~~~~~
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:32:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp: In member function 'void Scores::populateWithPSMs(SetHandler&)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:292:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
292 | if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:295:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
295 | if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 89%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/PickedProteinInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34,
from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:27,
from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:86:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder]
86 | double maxPeptidePval_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:8: warning: 'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
85 | bool reportFragmentProteins_, reportDuplicateProteins_;
| ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder]
22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder]
85 | bool reportFragmentProteins_, reportDuplicateProteins_;
| ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:83:26: warning: 'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
83 | ProteinInferenceMethod protInferenceMethod_;
| ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder]
22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)':
/builddir/build/BUILD/percolator-rel-3-05/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()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:344:13: warning: unused variable 'significantPeptides' [-Wunused-variable]
344 | int significantPeptides = 0;
| ^~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 92%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/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/DescriptionOfCorrect.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.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/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/EludeModel.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
/usr/bin/ranlib libperclibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
[ 97%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/./PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/./BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/./LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/./PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 96%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
from /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 98%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-05/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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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 -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-3-05/percolator/src ../libperclibrary.a ../fido/libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-05/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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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 -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 -lstdc++
In function 'readRawSequence',
inlined from 'parseProteinFastaFile' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/picked_protein/Protein.cpp: In member function 'parseProteinFastaFile':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p fido
~/build/BUILD/percolator-rel-3-05/fido ~/build/BUILD/percolator-rel-3-05
+ pushd fido
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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=ppc64le ../src/fido
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- 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
-- Generating done
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-3-05/fido
+ /usr/bin/make -O -j5 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/fido -B/builddir/build/BUILD/percolator-rel-3-05/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/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-3-05/fido'
cd /builddir/build/BUILD/percolator-rel-3-05/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 37%] 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 50%] 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/Set.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/Vector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 62%] 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | 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:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 25%] 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | 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:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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-3-05/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:58:3: warning: when initialized here [-Wreorder]
58 | 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:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
55 | int label;
| ^~~~~
../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
54 | PSMDescription* pPSM;
| ^~~~
../src/Scores.h:59:3: warning: when initialized here [-Wreorder]
59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
| ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:4:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
39 | void Array<T>::add(const T & element)
| ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)'
14 | void add(int el);
| ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-05/converters ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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=ppc64le ../src/converters
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- 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 :
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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets'
188 | (void) ramp_fgets(buf, sizeof(buf) - 1, result);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread'
343 | ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets'
509 | (void) ramp_fgets(buf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets'
541 | (void) ramp_fgets(buf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets'
575 | (void) ramp_fgets(buf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets'
967 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets'
984 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets'
1056 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets'
1058 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread'
1479 | ramp_fread(pData + partial, (int)(peaksLen - partial), pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets'
1571 | (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets'
1573 | (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets'
1626 | (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread'
1658 | ramp_fread(pData + partial, peaksLen - partial, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets'
1792 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets'
1795 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets'
1816 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets'
1926 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets'
1933 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets'
1989 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
| ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:123:
In function '*strchr',
inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'rampSelfTest(char*)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
2054 | strncpy(buf, filename, sizeof(buf));
| ^
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/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/parser.cxx:102:22: warning: 'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
102 | DOMImplementation& dom_impl_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning: when initialized here [-Wreorder]
144 | parser_impl::parser_impl() : clean_(true),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
178 | size_t n(s.size());
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
170 | int i(1);
| ^
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
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[ 32%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/LazyMatrix.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
56 | *data_copies++;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:101:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
101 | for ( int i = 0 ; i < m.size() ; i++ ) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(value_type, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
115 | for ( int i = 0 ; i < m.size() ; i++ ) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector<float>&, int)':
/builddir/build/BUILD/percolator-rel-3-05/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[i]->begin();
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:313:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
313 | for ( uint i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:322:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
322 | for ( uint i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:331:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
331 | for ( uint i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
339 | for ( uint i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
351 | for ( uint i = 0 ; i < nrows ; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/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-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
393 | for ( uint i = shift; i < nrows; i++ ) {
| ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
412 | for ( uint i = nrows - offset ; i < nrows; i++ ) {
| ~~^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 34%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSConvertFile.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSObject.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:21:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
21 | for(i=0;i<m.vSpectrum->size();i++){
| ~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:36:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
36 | for(i=0;i<m.vSpectrum->size();i++){
| ~^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 5%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/converters/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 38%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeSqlite(const char*, MSObject&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/Spectrum.h:4,
from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.h:4,
from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: 'MSHeader::header' declared here
54 | char header[16][128];
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:916:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
916 | for(int i=0; i<chgs.size(); i++)
| ~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/MSReader.cpp:756:9: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
756 | uLong sizeM;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:757:9: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
757 | uLong sizeI;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::executeSqlStmt(Spectrum&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable 'charge' [-Wunused-variable]
1187 | int charge=-1;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeCompressSpec(FILE*, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/MSReader.cpp:1616:15: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
1616 | uLong sizeM;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1617:15: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
1617 | uLong sizeI;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'int MSReader::openFile(const char*, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:101:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
101 | fread(&iFType,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:102:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
102 | fread(&iVersion,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:103:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | fread(&header,sizeof(MSHeader),1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::readFile(const char*, bool, Spectrum&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:189:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
189 | fread(&i,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:191:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
191 | fread(&i,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:207:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
207 | fread(&z.z,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:208:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
208 | fread(&z.mz,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:213:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
213 | fread(&ez.z,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:214:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
214 | fread(&ez.mh,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:215:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
215 | fread(&ez.pRTime,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:216:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
216 | fread(&ez.pArea,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:239:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
239 | fread(&p.mz,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:240:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
240 | fread(&p.intensity,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:280:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
280 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:285:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
285 | fgets(tstr,256,fileIn);
| make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:297:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
297 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:347:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
347 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:374:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
374 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:377:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
377 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:400:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
400 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:405:21: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
405 | fscanf(fileIn,"%lf %f\n",&p.mz,&p.intensity);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:411:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
411 | fgets(tstr,256,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readCompressSpec(FILE*, MSScanInfo&, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1669:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1669 | fread(&i,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1671:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1671 | fread(&i,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1677:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1677 | fread(compr,mzLen,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1684:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1684 | fread(compr,intensityLen,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readSpecHeader(FILE*, MSScanInfo&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1882:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1882 | fread(&ms.scanNumber[0],4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1884:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1884 | fread(&ms.scanNumber[1],4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1885:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1885 | fread(&ms.mz,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1886:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1886 | fread(&ms.rTime,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1889:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1889 | fread(&ms.BPI,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1890:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1890 | fread(&ms.BPM,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1891:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1891 | fread(&ms.convA,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1892:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1892 | fread(&ms.convB,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1893:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1893 | fread(&ms.TIC,8,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1894:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1894 | fread(&ms.IIT,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1897:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1897 | fread(&ms.numZStates,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1899:24: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1899 | if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1902:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1902 | fread(&ms.numDataPoints,4,1,fileIn);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1952:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1952 | fread(&i,4,1,f);
| ~~~~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1953:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1953 | fread(&iVersion,4,1,f);
| ~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/13/cstdio:42,
from /usr/include/c++/13/parallel/compiletime_settings.h:33,
from /usr/include/c++/13/parallel/parallel.h:37,
from /usr/include/c++/13/parallel/base.h:40,
from /usr/include/c++/13/parallel/algobase.h:40,
from /usr/include/c++/13/bits/stl_algobase.h:2229,
from /usr/include/c++/13/vector:62,
from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:5:
In function '*__sprintfieee128',
inlined from 'MSReader::appendFile(Spectrum&)' at /builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:853:7: note: 'lastScanID' was declared here
853 | int lastScanID;
| ^~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 40%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 43%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 41%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:51:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
51 | for ( int i = 0 ; i < rts.size() ; i++ ) {
| ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
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[ 47%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:81:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
81 | for(i=0;i<s.vPeaks->size();i++){
| ~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:85:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<EZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
85 | for(i=0;i<s.vEZ->size();i++){
| ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:89:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
89 | for(i=0;i<s.vZ->size();i++){
| ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)':
/builddir/build/BUILD/percolator-rel-3-05/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)) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'float Spectrum::getTotalIntensity()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
389 | for(int i=0; i<vPeaks->size(); i++)
| ~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector<Peak_T>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:428:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
428 | for(int i=0; i<peaks.size(); i++)
| ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::printMe()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:453:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
453 | for(int i=0; i<vPeaks->size(); i++)
| ~^~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/MSWarper.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
517 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
519 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
600 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
703 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:87:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<const char*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
87 | for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
812 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
813 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
815 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
818 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: 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]
820 | 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-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
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/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/converters/percolator_out.cxx
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/usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/converters/tandem2011.12.01.1.cxx
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[ 52%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/msmat.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
517 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
519 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
600 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
703 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:37:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
37 | for ( int i = 0 ; i < precursors.size() ; i++ )
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor_idx(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:48:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
48 | for ( int i = 0 ; i < ti.size() ; i++ ) {
| ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector<transition_info>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:57:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
57 | for ( int i = 0 ; i < transitions.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:86:24: 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]
86 | for ( int i = 0 ; i < labels.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:119:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
119 | for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:120:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
120 | for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable]
117 | int num_chroms = this->get_num_mzs();
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable]
118 | int num_rts = this->get_num_rts();
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector<int>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:228:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
228 | for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/msmat.cpp:247:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
247 | for ( int i = 1 ; i < retain_range.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:255:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
255 | for ( int i = 0 ; i < delete_range.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable]
237 | int set_idx = 0;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:266:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
266 | for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:283:30: warning: comparison of integer expressions of different signedness: 'off64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
283 | if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:417:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
417 | if ( iter_delt == rts.size() - 1 )
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variable]
680 | int scan_idx, num_scans, scan_length;
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
1068 | matrix_dim dim = get_data_dim();
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1278:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1278 | for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1279:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1279 | for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1294:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1294 | if ( i < 0 || i >= get_num_rts() ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1325:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1325 | for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
| ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1327:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1327 | if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1350:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1350 | if ( i < 0 || i >= get_num_rts() ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable]
1368 | const msmat & self = *this;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable]
1422 | int foo = 5;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable]
1498 | msmat * volatile_this;
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1555:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1555 | for ( int i = 0 ; i < get_num_rts() ; i++ ) {
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1561:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1561 | for ( int i = 0 ; i < scram_cmds.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable]
1605 | FILE * o_file, *ti_file, *sg_file;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable]
1605 | FILE * o_file, *ti_file, *sg_file;
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1746 | for ( int i = 0 ; i < chroms.size() ; i++ ){
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1762:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1762 | for ( int i = 0 ; i < chroms.size() ; i++ ){
| ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1828:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1828 | new_cnt < mzs.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1858:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1858 | new_cnt < rts.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1880:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1880 | new_cnt < mzs.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1898:13: warning: comparisomake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
n of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1898 | new_cnt < rts.size() ;
| ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1921:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1921 | for ( int i = 0 ; i < get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1944:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
1944 | for ( int i = 0 ; i < get_num_rows() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable]
1941 | size_t nrows = get_num_rows();
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/msmat.cpp:2004:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
2004 | for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
2010 | for ( int i = 0 ; i < mzs_slice.size() ; i++ ) {
| ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2019:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
2019 | for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable]
1990 | const int num_mzs = get_num_mzs();
| ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2071:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
2071 | for ( int i = 0 ; i < s1.size() ;i++ ) {
| ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2095:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
2095 | for ( int i = 0 ; i < s1.size() ;i++ ) {
| ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable]
2109 | int start_rt_idx = this->rt_to_rtidx(start_rt);
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable]
2110 | int stop_rt_idx = this->rt_to_rtidx(stop_rt);
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
812 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
813 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1740:9: 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]
1740 | msmat * msmat_from_thevoid
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function]
1713 | void output_bp_chrom( msmat & m, char * fname ) {
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function]
1582 | msmat * test_msmat ( int argc , char ** argv ) {
| ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
[ 63%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/msmat_base.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp:16:
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 60%] 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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/Reader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp: In member function 'Reader::translateFileToXML(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:327:32: warning: 'tcd' may be used uninitialized [-Wmaybe-uninitialized]
327 | tmpDirs[lineNumber_par]=tcd;
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:302:22: note: 'tcd' was declared here
302 | char * tcd;
| ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 49%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/crawutils.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable]
261 | int start_idx = -1;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable]
262 | int stop_idx = -1;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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[i].first == last_val) ) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable]
346 | int last_rank = -1;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:944:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
944 | if (cumulative_area.size() == idx)
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/crawutils.cpp:990:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
990 | if (cumulative_area.size() == idx)
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable]
1121 | bool last_tryp = false;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector<std::pair<std::set<int>, std::set<int> > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable]
1214 | int g2_len = g2.size();
| ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 65%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
517 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
519 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
600 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
703 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable]
343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable]
343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable]
343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable]
367 | int key_data_idx;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::write_header_field_string_list(FILE*, const char*, const std::vector<std::__cxx11::basic_string<char> >&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable]
431 | int num_elements = s.size();
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
812 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
813 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
815 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
818 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: 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]
820 | 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-3-05/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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
314 | delete k;
| ^
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
315 | delete v;
| ^
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/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::almake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
locator<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-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:394:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
394 | delete values;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:389:37: note: returned from 'operator new[](unsigned long)'
389 | float * values = new float[val_len];
| ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 61%] 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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/SqtReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MSToolkit/msmat_test.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
517 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
519 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
600 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
703 | int a = 3;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable]
13 | msmat * m;
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
812 | static int test_msmat_time_interp( msmat * msmat_f );
| ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
813 | static int test_msmat_sg_test( msmat * msmat_fh);
| ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
815 | static msmat * test_msmat(int argc, char ** argv);
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
818 | static void output_bp_chrom( msmat & m , char * fname);
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
| ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: 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]
820 | 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-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
69 | const static char * valid_fields[] = {
| ^~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
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/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
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MzidentmlReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
97 | } catch (std::exception e) {
| ^
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/converters/mzIdentML1.1.0.cxx
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/src/converters/SequestReader.cpp:174:14: warning: unused variable 'peptide_length' [-Wunused-variable]
174 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
| ^~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp:80:19: warning: comparison of integer expressions of different signedness: 'const int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
80 | if (it->first <= peptideSeq.length()) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/MsgfplusReader.cpp:333:27: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
333 | else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
333 | else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
| ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable]
272 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:291:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable]
291 | double SpecEValue = 0.0;
| ^~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable]
165 | size_t valueSize(buf.size ());
| ^~~~~~~~~
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'virtual void TandemReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:274:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
274 | } catch (MyException e) {
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:277:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
277 | } catch (std::exception e) {
| ^
/builddir/build/BUILD/percolator-rel-3-05/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-3-05/src/converters/TandemReader.cpp:497:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
497 | f_seq.push_back( charge == c ? 1.0 : 0.0);
| ~~~~~~~^~~~
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In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h: In constructor 'Interface::Interface()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:50:14: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder]
50 | bool xmlOutput;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:47:21: warning: 'std::string Interface::outputFN' [-Wreorder]
47 | std::string outputFN;
| ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:21:1: warning: when initialized here [-Wreorder]
21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
| ^~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/Tandem2Pin.cpp
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -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-3-05/src/converters/Msgfplus2Pin.cpp
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/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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 -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-3-05/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 -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In function 'strchr',
inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/converters'
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In function 'strchr',
inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Linking CXX executable msgf2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -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 -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-3-05/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 -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl
In function 'strchr',
inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/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-3-05/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-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p elude
+ pushd elude
~/build/BUILD/percolator-rel-3-05/elude ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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 -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_PREFIX_PATH:STRING=/usr -DBoost_USE_STATIC_LIBS:BOOL=OFF -DCMAKE_USE_RELATIVE_PATHS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -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' -DTARGET_ARCH=ppc64le ../src/elude_tool
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- 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 ELUDE:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../..
-- CMAKE_PREFIX_PATH = /usr
-- GOOGLE_TEST =
-- GOOGLE_TEST_PATH =
-- TARGET_ARCH = ppc64le
-- PROFILING =
-- -------------------------------------------------------------------------------
--
-- Architecture:
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0")
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_Fortran_FLAGS_RELEASE
CMAKE_INSTALL_DO_STRIP
CMAKE_SKIP_INSTALL_RPATH
CMAKE_USE_RELATIVE_PATHS
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-3-05/elude
+ /usr/bin/make -O -j5 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 17%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o
/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeMain.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeMain.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o
/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -MF CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type]
284 | }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
204 | svr_parameters_.C = best_c;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
182 | double best_c, best_e;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
205 | svr_parameters_.p = best_e;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
182 | double best_c, best_e;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
240 | svr_parameters_.C = best_c;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
241 | svr_parameters_.p = best_e;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
242 | svr_parameters_.gamma = best_g;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
240 | svr_parameters_.C = best_c;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
241 | svr_parameters_.p = best_e;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
242 | svr_parameters_.gamma = best_g;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
213 | double best_c, best_e, best_g;
| ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
204 | svr_parameters_.C = best_c;
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
182 | double best_c, best_e;
| ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
205 | svr_parameters_.p = best_e;
| ~~~~~make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o
/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -MF CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp
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~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
182 | double best_c, best_e;
| ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
172 | int ret;
| ^~~
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/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const std::string&, const std::map<std::__cxx11::basic_string<char>, double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable]
304 | int end_position, len = peptide.size();
| ^~~
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[ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o
/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
17 | /*
|
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; }
| ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; }
| ^
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder]
99 | Normalizer *the_normalizer_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:95:14: warning: 'SVRModel* RetentionModel::svr_model_' [-Wreorder]
95 | SVRModel *svr_model_;
| ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:30:1: warning: when initialized here [-Wreorder]
30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm),
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:36:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
36 | delete svr_model_;
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
62 | for(int i = 0; i < vsub_.size(); ++i)
| ~~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::TrainRetentionModel(const std::set<std::__cxx11::basic_string<char> >&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:187:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
187 | delete svr_model_;
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:291:20: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
291 | if (vsub_.size() != number_features) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:356:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
356 | delete svr_model_;
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
363 | int number_features, ret;
| ^~~
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/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -MF CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o.d -o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
48 | for (int i = 0; i < x.size(); ++i) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair<double, double>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
84 | for (int i = 0; i < data.size(); ++i) {
| ~~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:168:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
168 | for (int i = 1; i < Q.size(); ++i)
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:177:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<dataPoint> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
177 | for (int j = 0; j < best10Subsets.size(); ++j) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector<dataPoint>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:209:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
209 | for (int i = 0; i < v.size(); ++i) {
| ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:220:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
220 | for (int i = h; i < data.size(); ++i) {
| ~~^~~~~~~~~~~~~
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/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning: when initialized here [-Wreorder]
26 | PSMDescriptionDOC::PSMDescriptionDOC() :
| ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
92 | double pI_, massDiff_, predictedTime_, retentionTime_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning: when initialized here [-Wreorder]
30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
| ^~~~~~~~~~~~~~~~~
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/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/DataManager.cpp.o -MF CMakeFiles/eludelibrary.dir/DataManager.cpp.o.d -o CMakeFiles/eludelibrary.dir/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<std::pair<PSMDescription*, std::__cxx11::basic_string<char> > > DataManager::RemoveInSourceFragments(const Enzyme*, const double&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:334:50: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PSMDescription*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
334 | if (!remove_from_test && (initial_train_size != train_psms.size())) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<PSMDescription*> DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector<PSMDescription*>&, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:354:7: warning: unused variable 'initial_size' [-Wunused-variable]
354 | int initial_size = psms.size();
| ^~~~~~~~~~~~
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/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
167 | bool remove_non_enzymatic_;
| ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning: 'bool EludeCaller::context_format_' [-Wreorder]
143 | bool context_format_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
189 | RetentionModel *rt_model_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning: 'bool EludeCaller::ignore_ptms_' [-Wreorder]
173 | bool ignore_ptms_;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
196 | bool supress_print_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning: 'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
175 | bool only_hydrophobicity_index_;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
519 | while (found != string::npos) {
| ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
639 | int ret = 1;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
940 | double corr = 0.0, d = 0.0, avg_rank, rank_p;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1026 | if ((pos1 = path.find_last_of("/")) == string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1027 | if ((pos1 = path.find_last_of("\\"))== string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1032 | if ((pos2 = file_name.find_last_of(".")) != string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
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[ 91%] Linking CXX static library libeludelibrary.a
/usr/bin/cmake -P CMakeFiles/eludelibrary.dir/cmake_clean_target.cmake
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/usr/bin/ar qc libeludelibrary.a CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o CMakeFiles/eludelibrary.dir/DataManager.cpp.o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/StdvNormalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp.o"
/usr/bin/ranlib libeludelibrary.a
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make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 91%] Built target eludelibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 95%] Building CXX object CMakeFiles/elude.dir/EludeCaller.cpp.o
/usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/elude.dir/EludeCaller.cpp.o -MF CMakeFiles/elude.dir/EludeCaller.cpp.o.d -o CMakeFiles/elude.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
167 | bool remove_non_enzymatic_;
| ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning: 'bool EludeCaller::context_format_' [-Wreorder]
143 | bool context_format_;
| ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
189 | RetentionModel *rt_model_;
| ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning: 'bool EludeCaller::ignore_ptms_' [-Wreorder]
173 | bool ignore_ptms_;
| ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
196 | bool supress_print_;
| ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning: 'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
175 | bool only_hydrophobicity_index_;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder]
44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
| ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
519 | while (found != string::npos) {
| ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
639 | int ret = 1;
| ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
940 | double corr = 0.0, d = 0.0, avg_rank, rank_p;
| ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1026 | if ((pos1 = path.find_last_of("/")) == string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1027 | if ((pos1 = path.find_last_of("\\"))== string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
1032 | if ((pos2 = file_name.find_last_of(".")) != string::npos) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Linking CXX executable elude
/usr/bin/cmake -E cmake_link_script CMakeFiles/elude.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/elude.dir/EludeCaller.cpp.o -o elude -L/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src libeludelibrary.a
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make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.aFSkng
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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-3-05
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 94%] 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-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 97%] 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-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 23%] 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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 27%] 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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/converters.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 56%] 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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 61%] 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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/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-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le 'INSTALL=/usr/bin/install -p' -C elude
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 91%] Built target eludelibrary
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/elude/models/Jupiter_120.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/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-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/lib64/percolator
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 3.05-10.fc38 --unique-debug-suffix -3.05-10.fc38.ppc64le --unique-debug-src-base percolator-3.05-10.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-05
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/bin/tandem2pin
original debug info size: 82816kB, size after compression: 67072kB
/usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
6052 blocks
+ /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
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/src/serializer.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/src/serializer.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/src/parser.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/src/parser.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/percolator/src/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/elude/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.ppc64le/converters/Globals.h is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.7gty8g
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,-z,now -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-3-05
+ mkdir -p test
+ cd test
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
Pin-converter version 3.05.0, Build Date Jul 22 2022 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 bfc36bf986b54119b7cf7fa00b96ec32
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Percolator version 3.05.0, Build Date Jul 22 2022 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 Mon Dec 26 08:29:11 2022
on bfc36bf986b54119b7cf7fa00b96ec32
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 0.693862 cpu seconds or 1 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 33.72 cpu seconds or 15 seconds wall clock time.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.05-10.fc38.ppc64le
Provides: percolator = 3.05-10.fc38 percolator(ppc-64) = 3.05-10.fc38
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_2.17)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) 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(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(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_3.4.15)(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_3.4.5)(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-3.05-10.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.WE2Y56
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-data
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nNS65W
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.05-10.fc38.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FYWsvM
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-static
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.3LfqSa
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.05-10.fc38 percolator-static(ppc-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.05-10.fc38.ppc64le
Provides: percolator-debugsource = 3.05-10.fc38 percolator-debugsource(ppc-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.05-10.fc38.ppc64le
Provides: debuginfo(build-id) = 146d6f583ae80e3fcca2aa12a19d65235e385f7e debuginfo(build-id) = 21595aef00690c7e6413446b935b5a82c10bc99c debuginfo(build-id) = 31c416021d179fd3524337aac8fbbb184f18e79d debuginfo(build-id) = 6230280fadb079d333ee13da7a6295f4c0bd05f5 debuginfo(build-id) = 93f0507ce5ba15c18229b77f2c54c8b4334b518e debuginfo(build-id) = c438aad60181733bb6caddac0252e2efa744bccb percolator-debuginfo = 3.05-10.fc38 percolator-debuginfo(ppc-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(ppc-64) = 3.05-10.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le
Wrote: /builddir/build/RPMS/percolator-debugsource-3.05-10.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/percolator-3.05-10.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.05-10.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.05-10.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.05-10.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Yi2PKF
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.xlCAOB
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05 percolator-rel-3-05.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.05-10.fc38.src.rpm
Finish: build phase for percolator-3.05-10.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1672042909.556246/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm) Config(child) 5 minutes 24 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