I: pbuilder: network access will be disabled during build
I: Current time: Mon Feb 24 12:11:49 +14 2025
I: pbuilder-time-stamp: 1740348709
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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/369636/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 23 22:12 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/369636/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/369636/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=11c5e920103e4f55921d9e1043a1aed4
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=369636
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AijnyfHb/pbuilderrc_zxby --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AijnyfHb/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-4.1.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/369636/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: amd64
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 ... 19775 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 25.0 MB of archives. After unpacking 94.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15.2 [972 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15.2 [448 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-48 [74.2 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libmstoolkit82t64 amd64 82-7.2 [140 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB]
Fetched 25.0 MB in 0s (61.2 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sgml-base.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19775 files and directories currently installed.)
Preparing to unpack .../00-sgml-base_1.31_all.deb ...
Unpacking sgml-base (1.31) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.45-3+b1_amd64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.40.4-4_amd64.deb ...
Unpacking bsdextrautils (2.40.4-4) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.13.0-1_amd64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-5_amd64.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../22-libelf1t64_0.192-4_amd64.deb ...
Unpacking libelf1t64:amd64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:amd64.
Preparing to unpack .../24-libunistring5_1.3-1_amd64.deb ...
Unpacking libunistring5:amd64 (1.3-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../25-libicu72_72.1-6_amd64.deb ...
Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.23.1-1_amd64.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../31-xml-core_0.19_all.deb ...
Unpacking xml-core (0.19) ...
Selecting previously unselected package sgml-data.
Preparing to unpack .../32-sgml-data_2.0.11+nmu1_all.deb ...
Unpacking sgml-data (2.0.11+nmu1) ...
Selecting previously unselected package docbook.
Preparing to unpack .../33-docbook_4.5-11_all.deb ...
Unpacking docbook (4.5-11) ...
Selecting previously unselected package libosp5.
Preparing to unpack .../34-libosp5_1.5.2-15.2_amd64.deb ...
Unpacking libosp5 (1.5.2-15.2) ...
Selecting previously unselected package opensp.
Preparing to unpack .../35-opensp_1.5.2-15.2_amd64.deb ...
Unpacking opensp (1.5.2-15.2) ...
Selecting previously unselected package docbook-to-man.
Preparing to unpack .../36-docbook-to-man_1%3a2.0.0-48_amd64.deb ...
Unpacking docbook-to-man (1:2.0.0-48) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../37-libexpat1_2.6.4-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.4-1) ...
Selecting previously unselected package libexpat1-dev:amd64.
Preparing to unpack .../38-libexpat1-dev_2.6.4-1_amd64.deb ...
Unpacking libexpat1-dev:amd64 (2.6.4-1) ...
Selecting previously unselected package libmstoolkit82t64.
Preparing to unpack .../39-libmstoolkit82t64_82-7.2_amd64.deb ...
Unpacking libmstoolkit82t64 (82-7.2) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../40-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Selecting previously unselected package libsqlite3-dev:amd64.
Preparing to unpack .../41-libsqlite3-dev_3.46.1-1_amd64.deb ...
Unpacking libsqlite3-dev:amd64 (3.46.1-1) ...
Selecting previously unselected package libmstoolkit-dev.
Preparing to unpack .../42-libmstoolkit-dev_82-7.2_amd64.deb ...
Unpacking libmstoolkit-dev (82-7.2) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-4) ...
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:amd64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up libosp5 (1.5.2-15.2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libexpat1-dev:amd64 (2.6.4-1) ...
Setting up libsqlite3-dev:amd64 (3.46.1-1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:amd64 (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:amd64 (0.0.8-1+b2) ...
Setting up libmstoolkit-dev (82-7.2) ...
Setting up sgml-base (1.31) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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...
Building tag database...
-> 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: user script /srv/workspace/pbuilder/369636/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/369636/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 amd64
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 -j20 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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
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 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/x86_64-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 ());
| ~~~~~~~~~~~~~~~~~
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/x86_64-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/x86_64-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/x86_64-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/x86_64-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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 -fcf-protection -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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 -fcf-protection -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-0p2seu__
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/a4
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/a4/c5ceb211fe2dd80ad9ac2a276a7e8235d03ce6.debug
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/a4/c5ceb211fe2dd80ad9ac2a276a7e8235d03ce6.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/a4/c5ceb211fe2dd80ad9ac2a276a7e8235d03ce6.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
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=a4c5ceb211fe2dd80ad9ac2a276a7e8235d03ce6 -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/comet-ms ..
dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root ..
dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb'.
dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../comet-ms_2019015+cleaned1-4.1_amd64.buildinfo
dpkg-genchanges --build=binary -O../comet-ms_2019015+cleaned1-4.1_amd64.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: user script /srv/workspace/pbuilder/369636/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/369636/tmp/hooks/B01_cleanup finished
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/369636 and its subdirectories
I: Current time: Mon Feb 24 12:16:43 +14 2025
I: pbuilder-time-stamp: 1740349003