Sat Mar 8 09:39:01 UTC 2025 I: starting to build comet-ms/trixie/arm64 on jenkins on '2025-03-08 09:38'
Sat Mar 8 09:39:01 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/82727/console.log
Sat Mar 8 09:39:01 UTC 2025 I: Downloading source for trixie/comet-ms=2019015+cleaned1-4.1
--2025-03-08 09:39:02-- http://deb.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015%2bcleaned1-4.1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1484 (1.4K) [text/prs.lines.tag]
Saving to: ‘comet-ms_2019015+cleaned1-4.1.dsc’
0K . 100% 255M=0s
2025-03-08 09:39:02 (255 MB/s) - ‘comet-ms_2019015+cleaned1-4.1.dsc’ saved [1484/1484]
Sat Mar 8 09:39:02 UTC 2025 I: comet-ms_2019015+cleaned1-4.1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: comet-ms
Binary: comet-ms
Architecture: any
Version: 2019015+cleaned1-4.1
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Homepage: http://comet-ms.sourceforge.net
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/comet-ms
Vcs-Git: https://salsa.debian.org/debichem-team/comet-ms.git
Build-Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man
Package-List:
comet-ms deb science optional arch=any
Checksums-Sha1:
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a104367afb14167d5c6727a659ebabd93e414987 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz
Checksums-Sha256:
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Files:
fac4a9263c2b124cb0183dc9bf645f4b 1378100 comet-ms_2019015+cleaned1.orig.tar.gz
60aaa0e3839d39e2e84ce79171d188bf 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz
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Sat Mar 8 09:39:02 UTC 2025 I: Checking whether the package is not for us
Sat Mar 8 09:39:02 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sat Mar 8 09:39:02 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sat Mar 8 09:41:21 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 10 04:02:03 -12 2026
I: pbuilder-time-stamp: 1775836923
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [comet-ms_2019015+cleaned1-4.1.dsc]
I: copying [./comet-ms_2019015+cleaned1.orig.tar.gz]
I: copying [./comet-ms_2019015+cleaned1-4.1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-4.1.dsc: unsupported subcommand
dpkg-source: info: extracting comet-ms in comet-ms-2019015+cleaned1
dpkg-source: info: unpacking comet-ms_2019015+cleaned1.orig.tar.gz
dpkg-source: info: unpacking comet-ms_2019015+cleaned1-4.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile-to-handle-lib-debian-way-of-doing-things.patch
dpkg-source: info: applying cometsearch-makefile-to-handle-lib-debian-way-of-doing-things.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/388341/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='681f61ebf10f420f95f41533dd6f225c'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='388341'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/pbuilderrc_5nbK --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-4.1.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/388341/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19914 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on libmstoolkit-dev (>= 82); however:
Package libmstoolkit-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmstoolkit-dev (<< 83); however:
Package libmstoolkit-dev is not installed.
pbuilder-satisfydepends-dummy depends on docbook-to-man; however:
Package docbook-to-man is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libmstoolkit-dev{a} libmstoolkit82t64{a} libosp5{a} libpipeline1{a} libsqlite3-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} opensp{a} po-debconf{a} sensible-utils{a} sgml-base{a} sgml-data{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.3 MB of archives. After unpacking 96.9 MB will be used.
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Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 docbook all 4.5-11 [126 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libosp5 arm64 1.5.2-15.2 [922 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 opensp arm64 1.5.2-15.2 [442 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 docbook-to-man arm64 1:2.0.0-48 [71.1 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libmstoolkit82t64 arm64 82-7.2 [123 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 libsqlite3-dev arm64 3.46.1-1 [1058 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 libmstoolkit-dev arm64 82-7.2 [130 kB]
Fetched 24.3 MB in 0s (55.9 MB/s)
Preconfiguring packages ...
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(Reading database ... 19914 files and directories currently installed.)
Preparing to unpack .../00-sgml-base_1.31_all.deb ...
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Selecting previously unselected package libmstoolkit-dev.
Preparing to unpack .../42-libmstoolkit-dev_82-7.2_arm64.deb ...
Unpacking libmstoolkit-dev (82-7.2) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmstoolkit82t64 (82-7.2) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up libosp5 (1.5.2-15.2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libexpat1-dev:arm64 (2.6.4-1) ...
Setting up libsqlite3-dev:arm64 (3.46.1-1) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libmstoolkit-dev (82-7.2) ...
Setting up sgml-base (1.31) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up opensp (1.5.2-15.2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up xml-core (0.19) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Processing triggers for sgml-base (1.31) ...
Setting up sgml-data (2.0.11+nmu1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook (4.5-11) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-to-man (1:2.0.0-48) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
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-> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version (1.37-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../comet-ms_2019015+cleaned1-4.1_source.changes
dpkg-buildpackage: info: source package comet-ms
dpkg-buildpackage: info: source version 2019015+cleaned1-4.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sebastian Ramacher <sramacher@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
rm -f debian/comet-ms.1
make clean
make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
rm -f *.o comet-ms
cd CometSearch ; make clean
make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
rm -f *.o libcometsearch.a
make[3]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
make[2]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/comet-ms.substvars debian/files
rm -fr -- debian/comet-ms/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
make[1]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/comet-ms.substvars debian/files
rm -fr -- debian/comet-ms/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1
dh_auto_build
make -j12 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
cd CometSearch ; make
make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit Threading.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometInterfaces.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearch.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPreprocess.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPostAnalysis.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometMassSpecUtils.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteOut.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteSqt.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePepXML.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePercolator.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteTxt.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearchManager.cpp -c
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometCheckForUpdates.cpp -c
In file included from CometPreprocess.h:21,
from CometPreprocess.cpp:19:
ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = PreprocessThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometPreprocess.cpp:74:65: required from here
74 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)':
CometMassSpecUtils.cpp:136:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
136 | fread(&lSize, sizeof(long), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:141:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:148:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:155:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
155 | fscanf(fpdb, "%99s", szProteinName);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometCheckForUpdates.cpp: In static member function 'static void CometCheckForUpdates::SendAnalyticsHit()':
CometCheckForUpdates.cpp:161:11: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=]
161 | "%s\r\n", host, (int)strlen(postData), postData);
| ^~ ~~~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometCheckForUpdates.h:20,
from CometCheckForUpdates.cpp:17:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static void CometCheckForUpdates::SendAnalyticsHit()' at CometCheckForUpdates.cpp:156:12:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 129 and 1155 bytes into a destination of size 1024
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWritePepXML.cpp: In static member function 'static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)':
CometWritePepXML.cpp:100:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometWritePepXML.cpp:101:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CometSearch.cpp:19:
ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:138:66: required from here
138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CometPostAnalysis.cpp:19:
ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = PostAnalysisThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometPostAnalysis.cpp:46:38: required from here
46 | minNumThreads, maxNumThreads);
| ^
ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometWriteOut.cpp:124:32: warning: '%.5d' directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=]
124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out",
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometWriteOut.cpp:17:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometWriteOut.cpp:124:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 20 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometWriteOut.cpp:115:35: warning: '%s' directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=]
115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out",
| ^~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometWriteOut.cpp:115:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 26 and 1070 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometWriteOut.cpp:273:28: warning: '%+d' directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~
CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometWriteOut.cpp:273:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometWriteOut.cpp:151:59: warning: '%s' directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=]
151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput);
| ^~ ~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometWriteOut.cpp:151:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 33 and 1056 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
CometSearch.cpp:312:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
312 | fgets(szPeffLine, iLenSzLine, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:329:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:673:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
673 | fgets(szBuf, sizeof(szBuf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp: In member function 'void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)':
CometSearch.cpp:725:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
725 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:777:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
777 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()':
CometSearch.cpp:1159:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1166:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1166 | fread(&iMinMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1167:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1167 | fread(&iMaxMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1168:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1185:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1224:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1229:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1229 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1233:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1266:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1269:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1269 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1273:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1311:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1311 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1316:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1323:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In static member function 'static bool CometSearchManager::WriteIndexedDatabase()':
CometSearchManager.cpp:2756:28: warning: '.idx' directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=]
2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase);
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometSearchManager.cpp:17:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometSearchManager::WriteIndexedDatabase()' at CometSearchManager.cpp:2756:11:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:416:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~
In function 'void PrintOutfileHeader()',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1559:25:
CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void PrintOutfileHeader()' at CometSearchManager.cpp:416:14,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1559:25:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 18 bytes into a destination of size 16
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1597:71: warning: '%s' directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=]
1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1597:17:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 42 and 553 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:223:73: warning: '%s' directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=]
223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
| ^~ ~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'bool UpdateInputFile(InputFileInfo*)' at CometSearchManager.cpp:223:20,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1606:35:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1700:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT);
| ^~ ~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1700:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1675:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1675:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1763:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt);
| ^~ ~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1763:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1737:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1737:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1826:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML);
| ^~ ~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1826:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1800:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML);
| ^~ ~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1800:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1854:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator);
| ^~ ~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1854:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:1975:32: warning: '%s' directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=]
1975 | sprintf(szOut, "%s", szStatusMsg);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1975:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 256 bytes into a destination of size 128
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearchManager.cpp:364:66: warning: '%s' directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=]
364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void CalcRunTime(time_t)' at CometSearchManager.cpp:364:11,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:2111:24:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o
make[3]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch CometSearch/CometCheckForUpdates.cpp CometSearch/CometMassSpecUtils.cpp CometSearch/CometPreprocess.cpp CometSearch/CometSearchManager.cpp CometSearch/CometWritePepXML.cpp CometSearch/CometWriteSqt.cpp CometSearch/Threading.cpp CometSearch/CometInterfaces.cpp CometSearch/CometPostAnalysis.cpp CometSearch/CometSearch.cpp CometSearch/CometWriteOut.cpp CometSearch/CometWritePercolator.cpp CometSearch/CometWriteTxt.cpp Comet.cpp -c
CometSearch/CometCheckForUpdates.cpp: In static member function 'static void CometCheckForUpdates::SendAnalyticsHit()':
CometSearch/CometCheckForUpdates.cpp:146:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
146 | char *host = "www.google-analytics.com";
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometCheckForUpdates.cpp:161:11: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=]
161 | "%s\r\n", host, (int)strlen(postData), postData);
| ^~ ~~~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometCheckForUpdates.h:20,
from CometSearch/CometCheckForUpdates.cpp:17:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'static void CometCheckForUpdates::SendAnalyticsHit()' at CometSearch/CometCheckForUpdates.cpp:156:12:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 129 and 1155 bytes into a destination of size 1024
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)':
CometSearch/CometMassSpecUtils.cpp:136:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
136 | fread(&lSize, sizeof(long), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:141:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:148:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:155:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
155 | fscanf(fpdb, "%99s", szProteinName);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CometSearch/CometPreprocess.h:21,
from CometSearch/CometPreprocess.cpp:19:
CometSearch/ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = PreprocessThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometPreprocess.cpp:74:65: required from here
74 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In static member function 'static bool CometSearchManager::WriteIndexedDatabase()':
CometSearch/CometSearchManager.cpp:2756:28: warning: '.idx' directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=]
2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase);
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometSearchManager.cpp:17:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometSearchManager::WriteIndexedDatabase()' at CometSearch/CometSearchManager.cpp:2756:11:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:416:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~
In function 'void PrintOutfileHeader()',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1559:25:
CometSearch/CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void PrintOutfileHeader()' at CometSearch/CometSearchManager.cpp:416:14,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1559:25:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 18 bytes into a destination of size 16
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1597:71: warning: '%s' directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=]
1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1597:17:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 42 and 553 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:223:73: warning: '%s' directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=]
223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
| ^~ ~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'bool UpdateInputFile(InputFileInfo*)' at CometSearch/CometSearchManager.cpp:223:20,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1606:35:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1700:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT);
| ^~ ~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1700:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1675:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1675:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1763:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt);
| ^~ ~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1763:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1737:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1737:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1826:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML);
| ^~ ~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1826:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1800:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML);
| ^~ ~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1800:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1854:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=]
1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator);
| ^~ ~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1854:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:1975:32: warning: '%s' directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=]
1975 | sprintf(szOut, "%s", szStatusMsg);
| ^~ ~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1975:23:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 256 bytes into a destination of size 128
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()':
CometSearch/CometSearchManager.cpp:364:66: warning: '%s' directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=]
364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void CalcRunTime(time_t)' at CometSearch/CometSearchManager.cpp:364:11,
inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:2111:24:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp: In static member function 'static void CometWritePepXML::ReadInstrument(char*, char*)':
CometSearch/CometWritePepXML.cpp:910:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
910 | GetVal(szMsInstrumentElement, "\"msModel\" value", szModel);
| ^~~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp:911:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
911 | GetVal(szMsInstrumentElement, "\"msManufacturer\" value", szManufacturer);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp: In static member function 'static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)':
CometSearch/CometWritePepXML.cpp:100:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp:101:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CometSearch/CometPostAnalysis.cpp:19:
CometSearch/ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = PostAnalysisThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometPostAnalysis.cpp:46:38: required from here
46 | minNumThreads, maxNumThreads);
| ^
CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function 'int CometSearch::twiddle(int*, int*, int*, int*)':
CometSearch/CometSearch.cpp:4973:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
CometSearch/CometSearch.cpp:4973:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
CometSearch/CometSearch.cpp:4973:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
In file included from CometSearch/CometSearch.cpp:19:
CometSearch/ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]'
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:138:66: required from here
138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type]
257 | reinterpret_cast<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
CometSearch/CometSearch.cpp:312:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
312 | fgets(szPeffLine, iLenSzLine, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:329:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:673:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
673 | fgets(szBuf, sizeof(szBuf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function 'void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)':
CometSearch/CometSearch.cpp:725:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
725 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:777:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
777 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()':
CometSearch/CometSearch.cpp:1159:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1166:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1166 | fread(&iMinMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1167:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1167 | fread(&iMaxMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1168:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1185:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1224:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1229:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1229 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1233:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1266:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1269:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1269 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1273:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1311:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1311 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1316:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1323:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometSearch/CometWriteOut.cpp:124:32: warning: '%.5d' directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=]
124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out",
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometWriteOut.cpp:17:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometSearch/CometWriteOut.cpp:124:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 20 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometSearch/CometWriteOut.cpp:115:35: warning: '%s' directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=]
115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out",
| ^~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometSearch/CometWriteOut.cpp:115:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 26 and 1070 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometSearch/CometWriteOut.cpp:273:28: warning: '%+d' directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~
CometSearch/CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometSearch/CometWriteOut.cpp:273:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)':
CometSearch/CometWriteOut.cpp:151:59: warning: '%s' directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=]
151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput);
| ^~ ~~~~~~~~
In function 'int sprintf(char*, const char*, ...)',
inlined from 'static bool CometWriteOut::PrintResults(int, bool, FILE*)' at CometSearch/CometWriteOut.cpp:151:14:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 33 and 1056 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
Comet.cpp: In function 'void LoadParameters(char*, CometInterfaces::ICometSearchManager*)':
Comet.cpp:1143:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1143 | fgets(szParamBuf, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Comet.cpp:1196:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1196 | fgets(szParamBuf, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Comet.cpp: In function 'void ProcessCmdLine(int, char**, char*, std::vector<InputFileInfo*>&, CometInterfaces::ICometSearchManager*)':
Comet.cpp:1396:75: warning: '%s' directive writing up to 511 bytes into a region of size 235 [-Wformat-overflow=]
1396 | sprintf(szErrorMsg+strlen(szErrorMsg), " Error - input file \"%s\" not found.\n", pInputFileInfo->szFileName);
| ^~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from Comet.cpp:18:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void ProcessCmdLine(int, char**, char*, std::vector<InputFileInfo*>&, CometInterfaces::ICometSearchManager*)' at Comet.cpp:1396:20:
/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 35 and 546 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cd CometSearch ; make
make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o
make[3]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch'
g++ Comet.o CometSearch/CometCheckForUpdates.o CometSearch/CometMassSpecUtils.o CometSearch/CometPreprocess.o CometSearch/CometSearchManager.o CometSearch/CometWritePepXML.o CometSearch/CometWriteSqt.o CometSearch/Threading.o CometSearch/CometInterfaces.o CometSearch/CometPostAnalysis.o CometSearch/CometSearch.o CometSearch/CometWriteOut.o CometSearch/CometWritePercolator.o CometSearch/CometWriteTxt.o -o comet-ms -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -L/usr/lib -lmstoolkitlite -lm -lpthread
make[2]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
make[1]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-CPjfXgl2
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/comet-ms.substvars
rm -fr -- debian/.debhelper/generated/comet-ms/ debian/comet-ms/ debian/tmp/
dh_installdirs
install -m0755 -d debian/comet-ms/usr/bin
dh_auto_install --destdir=debian/comet-ms/
install -m0755 -d /build/reproducible-path/comet-ms-2019015\+cleaned1/debian/comet-ms
dh_install
install -m0755 -d debian/comet-ms/usr/bin
cp --reflink=auto -a ./comet-ms debian/comet-ms/usr/bin/
dh_installdocs
install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms
install -p -m0644 debian/copyright debian/comet-ms/usr/share/doc/comet-ms/copyright
dh_installchangelogs
install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms
install -p -m0644 debian/.debhelper/generated/comet-ms/dh_installchangelogs.dch.trimmed debian/comet-ms/usr/share/doc/comet-ms/changelog.Debian
dh_installman
install -m0755 -d debian/comet-ms/usr/share/man/man1/
install -p -m0644 ./debian/comet-ms.1 debian/comet-ms/usr/share/man/man1/comet-ms.1
man-recode --to-code UTF-8 --suffix .dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1
mv debian/comet-ms/usr/share/man/man1/comet-ms.1.dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1
chmod 0644 -- debian/comet-ms/usr/share/man/man1/comet-ms.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/comet-ms
chmod a-x usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1
gzip -9nf usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1
cd '/build/reproducible-path/comet-ms-2019015+cleaned1'
dh_fixperms
find debian/comet-ms ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/comet-ms/usr/share/doc -type f -a -true -a ! -regex 'debian/comet-ms/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/comet-ms/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/comet-ms/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/comet-ms -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/comet-ms/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/comet-ms/usr/bin/comet-ms
dh_strip -a
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/9c
objcopy --only-keep-debug --compress-debug-sections debian/comet-ms/usr/bin/comet-ms debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/9c/796dbd46aa1947174c0bbc2bb09ffb926e0d58.debug
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/9c/796dbd46aa1947174c0bbc2bb09ffb926e0d58.debug
strip --remove-section=.comment --remove-section=.note debian/comet-ms/usr/bin/comet-ms
objcopy --add-gnu-debuglink debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/9c/796dbd46aa1947174c0bbc2bb09ffb926e0d58.debug debian/comet-ms/usr/bin/comet-ms
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc
ln -s comet-ms debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc/comet-ms-dbgsym
install -m0755 -d debian/.debhelper/comet-ms
dh_makeshlibs -a
rm -f debian/comet-ms/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/comet-ms/DEBIAN
dpkg-shlibdeps -Tdebian/comet-ms.substvars debian/comet-ms/usr/bin/comet-ms
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
install -m0755 -d debian/comet-ms/DEBIAN
dh_gencontrol
install -m0755 -d debian/comet-ms/DEBIAN
echo misc:Depends= >> debian/comet-ms.substvars
echo misc:Pre-Depends= >> debian/comet-ms.substvars
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN
dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -cdebian/control -Pdebian/.debhelper/comet-ms/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=comet-ms-dbgsym "-DDepends=comet-ms (= \${binary:Version})" "-DDescription=debug symbols for comet-ms" -DBuild-Ids=9c796dbd46aa1947174c0bbc2bb09ffb926e0d58 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -cdebian/control -Pdebian/comet-ms
chmod 0644 -- debian/comet-ms/DEBIAN/control
dh_md5sums
install -m0755 -d debian/comet-ms/DEBIAN
cd debian/comet-ms >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/comet-ms/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN
cd debian/.debhelper/comet-ms/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/comet-ms ..
dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_arm64.deb'.
dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-4.1_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../comet-ms_2019015+cleaned1-4.1_arm64.buildinfo
dpkg-genchanges --build=binary -O../comet-ms_2019015+cleaned1-4.1_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/388341 and its subdirectories
I: Current time: Fri Apr 10 04:04:18 -12 2026
I: pbuilder-time-stamp: 1775837058
Sat Mar 8 09:41:22 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Sat Mar 8 09:41:22 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Sat Mar 8 09:43:01 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Sat Mar 8 09:43:02 UTC 2025 I: comet-ms_2019015+cleaned1-4.1_arm64.changes:
Format: 1.8
Date: Sat, 13 Apr 2024 22:27:15 +0200
Source: comet-ms
Binary: comet-ms comet-ms-dbgsym
Architecture: arm64
Version: 2019015+cleaned1-4.1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Changed-By: Sebastian Ramacher <sramacher@debian.org>
Description:
comet-ms - Tandem mass spectrometry (MS/MS) search engine
Closes: 1068221
Changes:
comet-ms (2019015+cleaned1-4.1) unstable; urgency=medium
.
* Non-maintainer upload.
* debian/control: Remove hard-coded dependency on libmstoolkit82. (Closes:
#1068221)
Checksums-Sha1:
6a9059c1e310b6b5c7d1a84f12102c6f803a55c1 1760964 comet-ms-dbgsym_2019015+cleaned1-4.1_arm64.deb
cb8ebe151f1e608c33a26719cb7ccf8497d8df51 5343 comet-ms_2019015+cleaned1-4.1_arm64.buildinfo
58cb1ea7e6f89d5ed9f19a99d0e88663b13882ba 801028 comet-ms_2019015+cleaned1-4.1_arm64.deb
Checksums-Sha256:
381d9a9710857872e2cb5b4bc69104267a348bc9e30c4f74a19a2f06ff276111 1760964 comet-ms-dbgsym_2019015+cleaned1-4.1_arm64.deb
ed10652d5bbdadb6024e640f93d735f90d409c6d2d6f7e8f77074396c684be53 5343 comet-ms_2019015+cleaned1-4.1_arm64.buildinfo
079a72cd94aed05f70104d1a1a974be8d83af9bc19a8c02424ed1c8ee7772529 801028 comet-ms_2019015+cleaned1-4.1_arm64.deb
Files:
860791eaf7c8761948bb3f7b94b6cd1f 1760964 debug optional comet-ms-dbgsym_2019015+cleaned1-4.1_arm64.deb
20c5df356eddbc4f5bf3b19e41ec0d11 5343 science optional comet-ms_2019015+cleaned1-4.1_arm64.buildinfo
c327fc5eb15b1389a6896f8600edb895 801028 science optional comet-ms_2019015+cleaned1-4.1_arm64.deb
Sat Mar 8 09:43:03 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_6-82727.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/comet-ms_2019015+cleaned1-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/comet-ms_2019015+cleaned1-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/comet-ms_2019015+cleaned1-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/b1/comet-ms_2019015+cleaned1-4.1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.PYvzfW5b/b2/comet-ms_2019015+cleaned1-4.1_arm64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 236ms
CPU time consumed: 237ms
Sat Mar 8 09:43:03 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sat Mar 8 09:43:03 UTC 2025 I: comet-ms from trixie built successfully and reproducibly on arm64.
Sat Mar 8 09:43:05 UTC 2025 I: Submitting .buildinfo files to external archives:
Sat Mar 8 09:43:05 UTC 2025 I: Submitting 8.0K b1/comet-ms_2019015+cleaned1-4.1_arm64.buildinfo.asc
Sat Mar 8 09:43:07 UTC 2025 I: Submitting 8.0K b2/comet-ms_2019015+cleaned1-4.1_arm64.buildinfo.asc
Sat Mar 8 09:43:10 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Mar 8 09:43:10 UTC 2025 I: Done submitting .buildinfo files.
Sat Mar 8 09:43:10 UTC 2025 I: Removing signed comet-ms_2019015+cleaned1-4.1_arm64.buildinfo.asc files:
removed './b1/comet-ms_2019015+cleaned1-4.1_arm64.buildinfo.asc'
removed './b2/comet-ms_2019015+cleaned1-4.1_arm64.buildinfo.asc'