Diff of the two buildlogs: -- --- b1/build.log 2024-07-18 20:33:58.760388022 +0000 +++ b2/build.log 2024-07-18 20:35:43.975915937 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 20 14:55:32 -12 2025 -I: pbuilder-time-stamp: 1755744932 +I: Current time: Fri Jul 19 10:34:02 +14 2024 +I: pbuilder-time-stamp: 1721334842 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./sortmerna_2.1-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.9qvuBh6S/trustedkeys.kbx': General error -gpgv: Signature made Fri Mar 20 10:03:57 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.8Lsog3NM/trustedkeys.kbx': General error +gpgv: Signature made Sat Mar 21 12:03:57 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,134 +30,165 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2306611/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1306703/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 Jul 19 10:34 /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/1306703/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1306703/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:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='aa79821dc68940a4a8134b478609e3c9' - 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='2306611' - PS1='# ' - PS2='> ' + INVOCATION_ID=358e71c50f094051998530f4b0d06411 + 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=1306703 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.kNal6wQQ/pbuilderrc_10zI --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kNal6wQQ/b1 --logfile b1/build.log sortmerna_2.1-5.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.kNal6wQQ/pbuilderrc_MRLB --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kNal6wQQ/b2 --logfile b2/build.log sortmerna_2.1-5.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 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-23-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 2024 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 2024 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2306611/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 00:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Jul 19 10:34 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1306703/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -224,7 +255,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] -Fetched 18.3 MB in 0s (64.5 MB/s) +Fetched 18.3 MB in 1s (12.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19711 files and directories currently installed.) @@ -364,7 +395,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/sortmerna-2.1/ && 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 > ../sortmerna_2.1-5_source.changes +I: user script /srv/workspace/pbuilder/1306703/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1306703/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sortmerna-2.1/ && 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 > ../sortmerna_2.1-5_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 2.1-5 dpkg-buildpackage: info: source distribution unstable @@ -486,6 +521,7 @@ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: @@ -505,6 +541,39 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ +src/indexdb.cpp: In function 'int main(int, char**)': +src/indexdb.cpp:1583:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1583 | if ( len < pread_gv ) + | ~~~~^~~~~~~~~~ +src/indexdb.cpp:1593:11: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1593 | len > maxlen ? maxlen = len : maxlen; + | ~~~~^~~~~~~~ +src/indexdb.cpp:1761:24: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] + 1761 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; + | ~~~^~~~~ +src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 1877 | for ( int shift = 0; shift < interval; shift++ ) + | ~~~~~~^~~~~~~~~~ +src/indexdb.cpp:2030:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] + 2030 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; + | ~~~^~~~~ +src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] + 2074 | for ( int shift = 0; shift < interval; shift++ ) + | ~~~~~~^~~~~~~~~~ +In file included from alp/sls_alp_data.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + 83 | static double dbl_max_log=log(DBL_MAX); + | ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); + | ^~~~~~~~~~ +In file included from alp/sls_pvalues.hpp:43, + from alp/gumbel_params.hpp:42, + from alp/sls_alp_data.hpp:69, + from alp/sls_alp_data.cpp:37: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: @@ -543,7 +612,6 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp In file included from alp/njn_localmaxstat.cpp:36: alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] @@ -579,69 +647,30 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c -src/indexdb.cpp: In function 'int main(int, char**)': -src/indexdb.cpp:1583:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1583 | if ( len < pread_gv ) - | ~~~~^~~~~~~~~~ -src/indexdb.cpp:1593:11: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1593 | len > maxlen ? maxlen = len : maxlen; - | ~~~~^~~~~~~~ -src/indexdb.cpp:1761:24: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] - 1761 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; - | ~~~^~~~~ -src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 1877 | for ( int shift = 0; shift < interval; shift++ ) - | ~~~~~~^~~~~~~~~~ -src/indexdb.cpp:2030:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] - 2030 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; - | ~~~^~~~~ -src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 2074 | for ( int shift = 0; shift < interval; shift++ ) - | ~~~~~~^~~~~~~~~~ -In file included from alp/njn_localmaxstatutil.cpp:44: -alp/sls_alp_data.hpp: At global scope: +In file included from alp/sls_alp.hpp:47, + from alp/sls_alp.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); - | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/njn_localmaxstatutil.cpp:44: + from alp/sls_alp.hpp:47, + from alp/sls_alp.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp -In file included from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: -alp/sls_alp_data.hpp: At global scope: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - 83 | static double dbl_max_log=log(DBL_MAX); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c +In file included from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - 83 | static double dbl_max_log=log(DBL_MAX); - | ^~~~~~~~~~~ -In file included from alp/sls_pvalues.hpp:43, - from alp/gumbel_params.hpp:42, - from alp/sls_alp_data.hpp:69, - from alp/sls_alp.hpp:47, - from alp/sls_alp.cpp:37: + from alp/sls_alp_sim.hpp:48, + from alp/sls_alp_sim.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -661,8 +690,8 @@ alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp -In file included from alp/sls_alp_data.cpp:37: +In file included from alp/njn_localmaxstatutil.cpp:44: +alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -672,23 +701,37 @@ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp_data.cpp:37: + from alp/njn_localmaxstatutil.cpp:44: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp +In file included from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: +alp/sls_alp_data.hpp: At global scope: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + 83 | static double dbl_max_log=log(DBL_MAX); + | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, - from alp/sls_alp_sim.hpp:48, - from alp/sls_alp_sim.cpp:37: + from alp/sls_alp.hpp:47, + from alp/gumbel_params.cpp:40: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp +In file included from alp/sls_pvalues.cpp:37: +alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] + 83 | static double dbl_max_log=log(DBL_MAX); + | ^~~~~~~~~~~ +alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] + 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); + | ^~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp src/outputformats.cpp: In function 'void report_blast(std::ofstream&, s_align*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, bool, double, double, uint32_t, uint32_t)': src/outputformats.cpp:176:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 176 | for ( int l = 0; l < user_opts.size(); l++ ) @@ -731,14 +774,6 @@ src/outputformats.cpp:692:30: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] 692 | if ( (i+2) < strs) end_read = reads[i+1]; | ~~~~~~^~~~~~ -g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp -In file included from alp/sls_pvalues.cpp:37: -alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] - 83 | static double dbl_max_log=log(DBL_MAX); - | ^~~~~~~~~~~ -alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] - 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); - | ^~~~~~~~~~ src/paralleltraversal.cpp: In function 'void traversetrie_align(NodeElement*, uint32_t, unsigned char, unsigned char*, unsigned char*, bool&, std::vector&, uint32_t, uint32_t, uint32_t)': src/paralleltraversal.cpp:387:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 387 | for ( int f = 0; f < id_hits.size(); f++ ) @@ -782,8 +817,7 @@ 4105 | if ( p+1 < num_best_hits_gv ) | ~~~~^~~~~~~~~~~~~~~~~~ In file included from src/../include/paralleltraversal.hpp:36, - from src/paralleltraversal.cpp:26: -src/../include/../alp/sls_alp_data.hpp: At global scope: + from src/main.cpp:26: src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -794,12 +828,13 @@ from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, - from src/paralleltraversal.cpp:26: + from src/main.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: + from src/paralleltraversal.cpp:26: +src/../include/../alp/sls_alp_data.hpp: At global scope: src/../include/../alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ @@ -810,7 +845,7 @@ from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, - from src/main.cpp:26: + from src/paralleltraversal.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -869,12 +904,14 @@ 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/1306703/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1306703/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/2306611 and its subdirectories -I: Current time: Wed Aug 20 14:56:57 -12 2025 -I: pbuilder-time-stamp: 1755745017 +I: removing directory /srv/workspace/pbuilder/1306703 and its subdirectories +I: Current time: Fri Jul 19 10:35:42 +14 2024 +I: pbuilder-time-stamp: 1721334942