Running as unit: rb-build-amd64_34-36985.service ==================================================================================== Mon Nov 25 18:13:04 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_34) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Mon Nov 25 18:13:04 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-1R5X4CE2" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 18:13:04 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 18:13:04 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-6YRnMj' Mon Nov 25 18:13:05 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 18:13:05 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-gXbYuv' ok, let's check if comet-ms is building anywhere yet… ok, comet-ms is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of comet-ms in trixie on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Mon Nov 25 18:13:19 UTC 2024 I: starting to build comet-ms/trixie/amd64 on jenkins on '2024-11-25 18:13' Mon Nov 25 18:13:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/36985/console.log 1732558399 amd64 trixie comet-ms Mon Nov 25 18:13:19 UTC 2024 I: Downloading source for trixie/comet-ms=2019015+cleaned1-4.1 --2024-11-25 18:13:19-- http://deb.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015%2bcleaned1-4.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1484 (1.4K) [text/prs.lines.tag] Saving to: ‘comet-ms_2019015+cleaned1-4.1.dsc’ 0K . 100% 203M=0s 2024-11-25 18:13:19 (203 MB/s) - ‘comet-ms_2019015+cleaned1-4.1.dsc’ saved [1484/1484] --2024-11-25 18:13:19-- http://deb.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015%2bcleaned1-4.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1484 (1.4K) [text/prs.lines.tag] Saving to: ‘comet-ms_2019015+cleaned1-4.1.dsc’ 0K . 100% 203M=0s 2024-11-25 18:13:19 (203 MB/s) - ‘comet-ms_2019015+cleaned1-4.1.dsc’ saved [1484/1484] Mon Nov 25 18:13:19 UTC 2024 I: comet-ms_2019015+cleaned1-4.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: comet-ms Binary: comet-ms Architecture: any Version: 2019015+cleaned1-4.1 Maintainer: The Debichem Group Uploaders: Filippo Rusconi Homepage: http://comet-ms.sourceforge.net Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/comet-ms Vcs-Git: https://salsa.debian.org/debichem-team/comet-ms.git Build-Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man Package-List: comet-ms deb science optional arch=any Checksums-Sha1: e8ce6f80224671a82f5c9123546c621fba5df7d0 1378100 comet-ms_2019015+cleaned1.orig.tar.gz a104367afb14167d5c6727a659ebabd93e414987 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz Checksums-Sha256: 27a5c4b89b82d4570485cca98b27a45dd55a640ea297d8188c1c008a6b5234a3 1378100 comet-ms_2019015+cleaned1.orig.tar.gz 05004bda0b5db500dff1d6be91d477dc0b4d97b6bf1715b433b9cb15a787a8f9 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz Files: fac4a9263c2b124cb0183dc9bf645f4b 1378100 comet-ms_2019015+cleaned1.orig.tar.gz 60aaa0e3839d39e2e84ce79171d188bf 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYKAB0WIQRCYn6EHZln2oPh+pAhk2s2YA/NiQUCZhrrJgAKCRAhk2s2YA/N iRrkAQC9i579L3K2MmEuwFS591qWR4TQQq+RmB24pIS1vWdjIQEA1lHf0PSA5PjE Me0u1TUZP65SzjDJOdrzmplIM882DQI= =F6go -----END PGP SIGNATURE----- Mon Nov 25 18:13:19 UTC 2024 I: Checking whether the package is not for us Mon Nov 25 18:13:20 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Mon Nov 25 18:13:20 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Mon Nov 25 18:13:20 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 18:13:20 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-NSly9Q' ==================================================================================== Mon Dec 29 00:36:21 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 comet-ms trixie /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM 2019015+cleaned1-4.1" as arguments. Mon Dec 29 00:36:21 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-QMZAAZbG" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Dec 29 00:36:21 UTC 2025 I: Downloading source for trixie/comet-ms=2019015+cleaned1-4.1 Reading package lists... NOTICE: 'comet-ms' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/comet-ms.git Please use: git clone https://salsa.debian.org/debichem-team/comet-ms.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1386 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (dsc) [1484 B] Get:2 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (tar) [1378 kB] Get:3 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (diff) [6788 B] Fetched 1386 kB in 1s (2601 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'comet-ms' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/comet-ms.git Please use: git clone https://salsa.debian.org/debichem-team/comet-ms.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1386 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (dsc) [1484 B] Get:2 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (tar) [1378 kB] Get:3 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (diff) [6788 B] Fetched 1386 kB in 1s (2601 kB/s) Download complete and in download only mode ============================================================================= Building comet-ms in trixie on amd64 on infom02-amd64 now. Date: Mon Dec 29 00:36:22 UTC 2025 Date UTC: Mon Dec 29 00:36:22 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 12:36:22 -12 2025 I: pbuilder-time-stamp: 1766968582 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [comet-ms_2019015+cleaned1-4.1.dsc] I: copying [./comet-ms_2019015+cleaned1.orig.tar.gz] I: copying [./comet-ms_2019015+cleaned1-4.1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Apr 13 20:29:26 2024 gpgv: using EDDSA key 42627E841D9967DA83E1FA9021936B36600FCD89 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-4.1.dsc: no acceptable signature found 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/1643823/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='479e9620a95e4c2180ed386000a0119b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1643823' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/pbuilderrc_wbj4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-4.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1643823/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 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 ... 19969 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} 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, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB of archives. After unpacking 91.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 docbook all 4.5-11 [126 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libmstoolkit82t64 amd64 82-7.2 [140 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB] Fetched 24.2 MB in 1s (27.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19969 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... 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I: Building the package I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../comet-ms_2019015+cleaned1-4.1_source.changes dpkg-buildpackage: info: source package comet-ms dpkg-buildpackage: info: source version 2019015+cleaned1-4.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sebastian Ramacher dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' cd CometSearch ; make make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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 In file included from CometSearch.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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*)': 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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*)': 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&, 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&, 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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-O3lxwTGf create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/1c 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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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=1c5b1f21208155f5071c95005e3aeaad4bcca7cc -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/comet-ms .. dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root .. dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_amd64.deb'. dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_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: 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/1643823 and its subdirectories I: Current time: Sun Dec 28 12:38:15 -12 2025 I: pbuilder-time-stamp: 1766968695 Mon Dec 29 00:38:15 UTC 2025 I: Signing ./b1/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo as comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc Mon Dec 29 00:38:15 UTC 2025 I: Signed ./b1/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo as ./b1/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc Mon Dec 29 00:38:15 UTC 2025 - build #1 for comet-ms/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Mon Dec 29 00:38:15 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-QMZAAZbG, removing. /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 18:15 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 18:13 b2 -rw-r--r-- 1 jenkins jenkins 1484 Apr 13 2024 comet-ms_2019015+cleaned1-4.1.dsc -rw------- 1 jenkins jenkins 2656 Nov 25 18:13 rbuildlog.fW5RQHf /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1: total 2756 -rw-r--r-- 1 jenkins jenkins 110993 Nov 25 18:15 build.log -rw-r--r-- 1 jenkins jenkins 1823828 Nov 25 18:15 comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 6788 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1484 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1.dsc -rw-r--r-- 1 jenkins jenkins 5452 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6334 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 830192 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1425 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2: total 0 Mon Nov 25 18:15:16 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 12:36:22 -12 2025 I: pbuilder-time-stamp: 1766968582 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [comet-ms_2019015+cleaned1-4.1.dsc] I: copying [./comet-ms_2019015+cleaned1.orig.tar.gz] I: copying [./comet-ms_2019015+cleaned1-4.1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Apr 13 20:29:26 2024 gpgv: using EDDSA key 42627E841D9967DA83E1FA9021936B36600FCD89 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-4.1.dsc: no acceptable signature found 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/1643823/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='479e9620a95e4c2180ed386000a0119b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1643823' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/pbuilderrc_wbj4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-4.1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1643823/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 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 ... 19969 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} 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, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB of archives. After unpacking 91.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 docbook all 4.5-11 [126 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libmstoolkit82t64 amd64 82-7.2 [140 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB] Fetched 24.2 MB in 1s (27.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19969 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-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 .../26-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package xml-core. Preparing to unpack .../30-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../31-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../32-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../33-libosp5_1.5.2-15_amd64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../34-opensp_1.5.2-15_amd64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../35-docbook-to-man_1%3a2.0.0-47_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-47) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../36-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../37-libexpat1-dev_2.6.4-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.4-1) ... Selecting previously unselected package libmstoolkit82t64. Preparing to unpack .../38-libmstoolkit82t64_82-7.2_amd64.deb ... Unpacking libmstoolkit82t64 (82-7.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../39-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 .../40-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 .../41-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 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... 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 (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libosp5 (1.5.2-15) ... 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 autopoint (0.22.5-2) ... 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 (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up opensp (1.5.2-15) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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 (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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 (1:2.0.0-47) ... 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 (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../comet-ms_2019015+cleaned1-4.1_source.changes dpkg-buildpackage: info: source package comet-ms dpkg-buildpackage: info: source version 2019015+cleaned1-4.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sebastian Ramacher dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' cd CometSearch ; make make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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 In file included from CometSearch.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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*)': 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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*)': 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&, 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&, 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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-O3lxwTGf create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/1c 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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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=1c5b1f21208155f5071c95005e3aeaad4bcca7cc -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/comet-ms .. dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root .. dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_amd64.deb'. dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_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: 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/1643823 and its subdirectories I: Current time: Sun Dec 28 12:38:15 -12 2025 I: pbuilder-time-stamp: 1766968695 Mon Nov 25 18:15:17 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Mon Nov 25 18:15:17 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Mon Nov 25 18:15:17 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 18:15:17 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-xaV1Um' ==================================================================================== Mon Nov 25 18:15:18 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 comet-ms trixie /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM 2019015+cleaned1-4.1" as arguments. Mon Nov 25 18:15:18 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-1MWTNZJ7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 18:15:18 UTC 2024 I: Downloading source for trixie/comet-ms=2019015+cleaned1-4.1 Reading package lists... NOTICE: 'comet-ms' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/comet-ms.git Please use: git clone https://salsa.debian.org/debichem-team/comet-ms.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1386 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (dsc) [1484 B] Get:2 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (tar) [1378 kB] Get:3 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (diff) [6788 B] Fetched 1386 kB in 0s (6909 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'comet-ms' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/comet-ms.git Please use: git clone https://salsa.debian.org/debichem-team/comet-ms.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1386 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (dsc) [1484 B] Get:2 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (tar) [1378 kB] Get:3 http://deb.debian.org/debian trixie/main comet-ms 2019015+cleaned1-4.1 (diff) [6788 B] Fetched 1386 kB in 0s (6909 kB/s) Download complete and in download only mode ============================================================================= Re-Building comet-ms in trixie on amd64 on infom01-amd64 now. Date: Mon Nov 25 18:15:18 UTC 2024 Date UTC: Mon Nov 25 18:15:18 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/pbuilderrc_k4GS + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' comet-ms = debian-installer -o comet-ms = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' comet-ms = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.xhW9mLlM/pbuilderrc_k4GS --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-4.1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 26 08:15:19 +14 2024 I: pbuilder-time-stamp: 1732558519 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [comet-ms_2019015+cleaned1-4.1.dsc] I: copying [./comet-ms_2019015+cleaned1.orig.tar.gz] I: copying [./comet-ms_2019015+cleaned1-4.1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Apr 13 20:29:26 2024 gpgv: using EDDSA key 42627E841D9967DA83E1FA9021936B36600FCD89 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-4.1.dsc: no acceptable signature found 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/3916240/tmp/hooks/D01_modify_environment starting debug: Running on infom01-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 Nov 25 18:15 /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/3916240/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3916240/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(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=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=5e64046d38f04442ab997500461e1f44 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=3916240 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.xhW9mLlM/pbuilderrc_k4GS --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-4.1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3916240/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 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 ... 19969 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} 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, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB of archives. After unpacking 91.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 docbook all 4.5-11 [126 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libmstoolkit82t64 amd64 82-7.2 [140 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB] Fetched 24.2 MB in 0s (87.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19969 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... 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_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... 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 libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-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 .../26-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package xml-core. Preparing to unpack .../30-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../31-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../32-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../33-libosp5_1.5.2-15_amd64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../34-opensp_1.5.2-15_amd64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../35-docbook-to-man_1%3a2.0.0-47_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-47) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../36-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../37-libexpat1-dev_2.6.4-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.4-1) ... Selecting previously unselected package libmstoolkit82t64. Preparing to unpack .../38-libmstoolkit82t64_82-7.2_amd64.deb ... Unpacking libmstoolkit82t64 (82-7.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../39-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 .../40-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 .../41-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 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... 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 (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libosp5 (1.5.2-15) ... 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 autopoint (0.22.5-2) ... 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 (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up opensp (1.5.2-15) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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 (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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 (1:2.0.0-47) ... 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 (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3916240/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3916240/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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' cd CometSearch ; make make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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 In file included from CometSearch.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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*)': 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 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 ()); | ~~~~~~~~~~~~~~~~~ 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::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' 69 | new ThreadManager(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(ThreadManager::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*)': 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&, 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&, 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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-XUYZaG5M create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/1c 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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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=1c5b1f21208155f5071c95005e3aeaad4bcca7cc -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- 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 chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/comet-ms .. dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root .. dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_amd64.deb'. dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_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/3916240/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3916240/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/3916240 and its subdirectories I: Current time: Tue Nov 26 08:16:43 +14 2024 I: pbuilder-time-stamp: 1732558603 + false + set +x Mon Nov 25 18:16:43 UTC 2024 I: Signing ./b2/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo as comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc Mon Nov 25 18:16:43 UTC 2024 I: Signed ./b2/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo as ./b2/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc Mon Nov 25 18:16:43 UTC 2024 - build #2 for comet-ms/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Mon Nov 25 18:16:43 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-1MWTNZJ7, removing. /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM: total 128 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 18:15 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 18:16 b2 -rw-r--r-- 1 jenkins jenkins 1484 Apr 13 2024 comet-ms_2019015+cleaned1-4.1.dsc -rw------- 1 jenkins jenkins 113938 Nov 25 18:15 rbuildlog.fW5RQHf /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1: total 2756 -rw-r--r-- 1 jenkins jenkins 110993 Nov 25 18:15 build.log -rw-r--r-- 1 jenkins jenkins 1823828 Nov 25 18:15 comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 6788 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1484 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1.dsc -rw-r--r-- 1 jenkins jenkins 5452 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6334 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 830192 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1425 Nov 25 18:15 comet-ms_2019015+cleaned1-4.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2: total 2756 -rw-r--r-- 1 jenkins jenkins 112922 Nov 25 18:16 build.log -rw-r--r-- 1 jenkins jenkins 1823828 Nov 25 18:16 comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 6788 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1484 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1.dsc -rw-r--r-- 1 jenkins jenkins 5449 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6331 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 830192 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1425 Nov 25 18:16 comet-ms_2019015+cleaned1-4.1_source.changes Mon Nov 25 18:16:44 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Mon Nov 25 18:16:45 UTC 2024 I: comet-ms_2019015+cleaned1-4.1_amd64.changes: Format: 1.8 Date: Sat, 13 Apr 2024 22:27:15 +0200 Source: comet-ms Binary: comet-ms comet-ms-dbgsym Architecture: amd64 Version: 2019015+cleaned1-4.1 Distribution: unstable Urgency: medium Maintainer: The Debichem Group Changed-By: Sebastian Ramacher Description: comet-ms - Tandem mass spectrometry (MS/MS) search engine Closes: 1068221 Changes: comet-ms (2019015+cleaned1-4.1) unstable; urgency=medium . * Non-maintainer upload. * debian/control: Remove hard-coded dependency on libmstoolkit82. (Closes: #1068221) Checksums-Sha1: 78b9bfd1605859d82f58b999cdd3da219f976975 1823828 comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb 03e032098561fa981f7c7fd414ef98304e206d93 5452 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo 1b9a2142d0442f3ed6055c5f257eb92113dcd358 830192 comet-ms_2019015+cleaned1-4.1_amd64.deb Checksums-Sha256: 5a29905a3c7ba1b7b71848e55ffa4fbd2873da5a104c1865a224ae532249786e 1823828 comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb 0fd9e5d5a9023d9194e54dce490abf6a93ec496959d3007f80bbaa5c05284dab 5452 comet-ms_2019015+cleaned1-4.1_amd64.buildinfo 81f26e9b26f32aca3b40435977d96f2eb2f5e20e639d1d38427e8cb3595ad9b0 830192 comet-ms_2019015+cleaned1-4.1_amd64.deb Files: 78c6fc0f8ee68445aa3ec866c16d6571 1823828 debug optional comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb 32f27f5239082ec1eca3ab0ad1423779 5452 science optional comet-ms_2019015+cleaned1-4.1_amd64.buildinfo fc5c7c133c6b6f1ba083c2913e61e309 830192 science optional comet-ms_2019015+cleaned1-4.1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/comet-ms_2019015+cleaned1-4.1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/comet-ms_2019015+cleaned1-4.1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/comet-ms_2019015+cleaned1-4.1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/comet-ms_2019015+cleaned1-4.1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/comet-ms_2019015+cleaned1-4.1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-25 18:15:16.431357956 +0000 +++ b2/build.log 2024-11-25 18:16:44.123402861 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 28 12:36:22 -12 2025 -I: pbuilder-time-stamp: 1766968582 +I: Current time: Tue Nov 26 08:15:19 +14 2024 +I: pbuilder-time-stamp: 1732558519 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,51 +28,83 @@ 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/1643823/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3916240/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Nov 25 18:15 /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/3916240/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3916240/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='479e9620a95e4c2180ed386000a0119b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1643823' - PS1='# ' - PS2='> ' + INVOCATION_ID=5e64046d38f04442ab997500461e1f44 + 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=3916240 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/pbuilderrc_wbj4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-4.1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.xhW9mLlM/pbuilderrc_k4GS --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-4.1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1643823/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3916240/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -156,7 +188,7 @@ Get: 40 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB] -Fetched 24.2 MB in 1s (27.9 MB/s) +Fetched 24.2 MB in 0s (87.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19969 files and directories currently installed.) @@ -347,7 +379,11 @@ fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../comet-ms_2019015+cleaned1-4.1_source.changes +I: user script /srv/workspace/pbuilder/3916240/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3916240/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 @@ -1242,7 +1278,7 @@ 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-O3lxwTGf + rm -fr -- /tmp/dh-xdg-rundir-XUYZaG5M create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary @@ -1337,12 +1373,14 @@ 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/3916240/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3916240/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/1643823 and its subdirectories -I: Current time: Sun Dec 28 12:38:15 -12 2025 -I: pbuilder-time-stamp: 1766968695 +I: removing directory /srv/workspace/pbuilder/3916240 and its subdirectories +I: Current time: Tue Nov 26 08:16:43 +14 2024 +I: pbuilder-time-stamp: 1732558603 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/comet-ms_2019015+cleaned1-4.1.diff: 66.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/comet-ms_2019015+cleaned1-4.1.diff.gz b2/build.log: 87.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.8% -- replaced with stdout Mon Nov 25 18:16:47 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_comet-ms_trixie_amd64_1732558607 + touch /var/log/reproducible-builds/diffoscope_stamp_comet-ms_trixie_amd64_1732558607 + RESULT=0 + systemd-run '--description=diffoscope on comet-ms/2019015+cleaned1-4.1 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_34-36985 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM --run-session -c jenkins-reproducible-trixie-diffoscope-ea05c37c-3d1f-4c6b-9aea-2c735a00f197 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/dbd-tmp-0pkS0d7 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1/comet-ms_2019015+cleaned1-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2/comet-ms_2019015+cleaned1-4.1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_34-36985.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/comet-ms_2019015+cleaned1-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b1/comet-ms_2019015+cleaned1-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xhW9mLlM/b2/comet-ms_2019015+cleaned1-4.1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.460s) 0.460s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.110s) 0.110s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 787ms CPU time consumed: 701ms _ ___ ___ _ __ ___ ___| |_ _ __ ___ ___ / __/ _ \| '_ ` _ \ / _ \ __|____| '_ ` _ \/ __| | (_| (_) | | | | | | __/ ||_____| | | | | \__ \ \___\___/|_| |_| |_|\___|\__| |_| |_| |_|___/ Mon Nov 25 18:48:27 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 25 18:48:27 UTC 2024 I: comet-ms from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-25 18:48:29] INFO: Starting at 2024-11-25 18:48:29.465194 [2024-11-25 18:48:29] INFO: Generating the pages of 1 package(s) [2024-11-25 18:48:30] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/comet-ms didn't produce a buildlog, even though it has been built. [2024-11-25 18:48:31] INFO: Finished at 2024-11-25 18:48:31.061998, took: 0:00:01.596814 Mon Nov 25 18:48:31 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/comet-ms.html Mon Nov 25 18:48:31 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Nov 25 18:48:31 UTC 2024 I: Submitting 8.0K b1/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc https://buildinfo.debian.net/03e032098561fa981f7c7fd414ef98304e206d93/comet-ms_2019015+cleaned1-4.1_amd64 Mon Nov 25 18:48:48 UTC 2024 I: Submitting 8.0K b2/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc https://buildinfo.debian.net/b07f08ad5a1fdfe363eff9d57e36344ac77a44aa/comet-ms_2019015+cleaned1-4.1_amd64 Mon Nov 25 18:49:17 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 25 18:49:17 UTC 2024 I: Done submitting .buildinfo files. Mon Nov 25 18:49:17 UTC 2024 I: Removing signed comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc files: removed './b1/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc' removed './b2/comet-ms_2019015+cleaned1-4.1_amd64.buildinfo.asc' 1732560557 amd64 trixie comet-ms Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/comet-ms_2019015+cleaned1-4.1.rbuild.log: 86.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/comet-ms_2019015+cleaned1-4.1.rbuild.log.gz [2024-11-25 18:49:18] INFO: Starting at 2024-11-25 18:49:18.279475 [2024-11-25 18:49:18] INFO: Generating the pages of 1 package(s) [2024-11-25 18:49:18] INFO: Finished at 2024-11-25 18:49:18.801575, took: 0:00:00.522108 All cleanup done. Mon Nov 25 18:49:18 UTC 2024 - total duration: 0h 35m 23s. Mon Nov 25 18:49:18 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-1R5X4CE2, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 36min 14.204s CPU time consumed: 8.472s