Diff of the two buildlogs: -- --- b1/build.log 2020-12-19 19:30:08.221798057 +0000 +++ b2/build.log 2020-12-19 19:31:02.884104338 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 21 13:52:18 -12 2022 -I: pbuilder-time-stamp: 1642816338 +I: Current time: Sun Dec 20 09:30:10 +14 2020 +I: pbuilder-time-stamp: 1608406210 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Oct 9 03:29:01 2018 -12 +gpgv: Signature made Wed Oct 10 05:29:01 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking sortmerna_2.1-3.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/45607/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/6973/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/6973/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/6973/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + 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=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2a9cd596853f41ac9c7be29ec787975b' - 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='45607' - PS1='# ' - PS2='> ' + INVOCATION_ID=4df3ad99feed4da09144e007e8ebb33e + 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=6973 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/tmp.WLOFBoXtaC/pbuilderrc_UiKb --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WLOFBoXtaC/b1 --logfile b1/build.log sortmerna_2.1-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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/tmp.WLOFBoXtaC/pbuilderrc_KCkL --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WLOFBoXtaC/b2 --logfile b2/build.log sortmerna_2.1-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.9.0-0.bpo.2-amd64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/45607/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 20 09:30 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 7 22:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/6973/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +259,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 0s (70.1 MB/s) +Fetched 19.0 MB in 0s (52.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -380,7 +414,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/sortmerna-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/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 dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 2.1-3 dpkg-buildpackage: info: source distribution unstable @@ -465,7 +499,7 @@ make[1]: Entering directory '/build/sortmerna-2.1' touch index/.tobuild dh_auto_build - make -j16 + make -j15 make[2]: Entering directory '/build/sortmerna-2.1' gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz.o cmph/bdz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz_ph.o cmph/bdz_ph.c @@ -507,9 +541,28 @@ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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] + 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] + 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] + 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] + 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] + 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] + for ( int shift = 0; shift < interval; shift++ ) + ~~~~~~^~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, - from alp/gumbel_params.cpp:45: + from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; @@ -518,7 +571,7 @@ if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, - from alp/gumbel_params.cpp:45: + from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; @@ -545,17 +598,25 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 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 -ffile-prefix-map=/build/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 -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] - 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] - 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] - for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; - ~~~^~~~~ +In file included from alp/njn_matrix.hpp:43, + from alp/njn_localmaxstatutil.hpp:39, + from alp/gumbel_params.cpp:45: +alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': +alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + ^~ +alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; + ^~~~~~~~~~ +In file included from alp/njn_localmaxstatutil.hpp:39, + from alp/gumbel_params.cpp:45: +alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': +alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; + ^~ +alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; + ^~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: @@ -566,15 +627,6 @@ alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ -src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] - 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] - 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] - for ( int shift = 0; shift < interval; shift++ ) - ~~~~~~^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': @@ -584,8 +636,8 @@ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ -In file included from alp/sls_alp.hpp:47, - from alp/gumbel_params.cpp:40: +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/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] static double dbl_max_log=log(DBL_MAX); @@ -596,12 +648,13 @@ 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: + from alp/njn_localmaxstat.cpp:36: alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/njn_localmaxstat.cpp:36: +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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.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] static double dbl_max_log=log(DBL_MAX); @@ -612,7 +665,8 @@ 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_localmaxstat.cpp:36: + 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] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -631,40 +685,14 @@ alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_alp_data.cpp:37: +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] 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] 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] - 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_localmaxstatmatrix.cpp:37: -alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': -alp/njn_vector.hpp:334:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - ^~ -alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; - ^~~~~~~~~~ -In file included from alp/njn_localmaxstatutil.hpp:39, - from alp/njn_localmaxstatmatrix.cpp:37: -alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': -alp/njn_matrix.hpp:598:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; - ^~ -alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 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 -ffile-prefix-map=/build/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 +g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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_alp_regression.hpp:47, from alp/sls_alp_regression.cpp:37: alp/sls_alp_data.hpp:83:16: warning: 'Sls::dbl_max_log' defined but not used [-Wunused-variable] @@ -681,13 +709,33 @@ alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from alp/sls_pvalues.cpp:37: +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] + 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: +alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] + static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] 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] 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] + 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: alp/sls_alp_data.hpp:82:18: warning: 'Sls::small_long' defined but not used [-Wunused-variable] @@ -701,24 +749,10 @@ alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] 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 -ffile-prefix-map=/build/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] for ( int l = 0; l < user_opts.size(); l++ ) ~~^~~~~~~~~~~~~~~~~~ -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] - 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: -alp/sls_normal_distr_array.hpp:43:15: warning: 'Sls::normal_distr_array_for_P_values_calculation' defined but not used [-Wunused-variable] - static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/outputformats.cpp: In function 'void report_fasta(char*, char*, char*, char**, int32_t, std::vector&, uint32_t, char*)': src/outputformats.cpp:493:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] for ( uint32_t i = 1; i < strs; i+=4 ) @@ -876,20 +910,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_2.1-3_amd64.deb'. dpkg-deb: building package 'sortmerna' in '../sortmerna_2.1-3_amd64.deb'. +dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_2.1-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sortmerna_2.1-3_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) I: copying local configuration +I: user script /srv/workspace/pbuilder/6973/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6973/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/45607 and its subdirectories -I: Current time: Fri Jan 21 13:53:10 -12 2022 -I: pbuilder-time-stamp: 1642816390 +I: removing directory /srv/workspace/pbuilder/6973 and its subdirectories +I: Current time: Sun Dec 20 09:31:02 +14 2020 +I: pbuilder-time-stamp: 1608406262