Diff of the two buildlogs: -- --- b1/build.log 2021-06-25 14:14:48.453768619 +0000 +++ b2/build.log 2021-06-25 14:15:28.420238247 +0000 @@ -1,8 +1,6 @@ -unshare: unshare failed: Cannot allocate memory -W: pbuilder: unshare CLONE_NEWNET not available -I: pbuilder: network access is available during build! -I: Current time: Fri Jun 25 02:07:33 -12 2021 -I: pbuilder-time-stamp: 1624630053 +I: pbuilder: network access will be disabled during build +I: Current time: Fri Jul 29 10:37:49 +14 2022 +I: pbuilder-time-stamp: 1659040669 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -19,8 +17,8 @@ I: copying [./pirs_2.0.2+dfsg-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.ySBr4Bdt/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 4 23:14:30 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.UlMmMOmC/trustedkeys.kbx': General error +gpgv: Signature made Sun Dec 6 01:14:30 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,137 +33,171 @@ dpkg-source: info: applying Remove-mtune-compiler-flag.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4762/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/53482/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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/53482/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/53482/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='ae717e34051d434ca132a6a37e3c8312' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='4762' - PS1='# ' - PS2='> ' + INVOCATION_ID=90b2370541ff47d1812df8c10bfc809b + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=53482 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.RCDTyXttLg/pbuilderrc_NfbR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RCDTyXttLg/b1 --logfile b1/build.log pirs_2.0.2+dfsg-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.RCDTyXttLg/pbuilderrc_AJeF --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RCDTyXttLg/b2 --logfile b2/build.log --extrapackages usrmerge pirs_2.0.2+dfsg-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux I: ls -l /bin - total 5784 - -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 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 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 23 21:28 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/4762/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 29 10:37 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 28 05:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/53482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -243,7 +275,7 @@ Get: 34 http://deb.debian.org/debian bullseye/main i386 libgzstream0 i386 1.5+dfsg-5 [6896 B] Get: 35 http://deb.debian.org/debian bullseye/main i386 libgzstream-dev i386 1.5+dfsg-5 [7188 B] Get: 36 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] -Fetched 28.3 MB in 15s (1842 kB/s) +Fetched 28.3 MB in 0s (62.2 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 ... 19675 files and directories currently installed.) @@ -402,8 +434,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (5546 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 37101 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/pirs-2.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/pirs-2.0.2+dfsg/ && 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 pirs dpkg-buildpackage: info: source version 2.0.2+dfsg-9 dpkg-buildpackage: info: source distribution unstable @@ -452,7 +520,7 @@ cd src && ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-pirs-diploid --disable-sse2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -489,12 +557,12 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/pirs-2.0.2+dfsg' dh_auto_build - cd src && make -j10 + cd src && make -j18 make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src' -(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash '/build/pirs-2.0.2+dfsg/src/missing' autoheader) +(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/build/pirs-2.0.2+dfsg/src/missing' autoheader) rm -f stamp-h1 touch config.h.in -cd . && /bin/bash ./config.status config.h +cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive @@ -511,12 +579,8 @@ g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GCBiasProfile.o GCBiasProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IndelProfile.o IndelProfile.cpp g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskQvalsByEamss.o MaskQvalsByEamss.cpp -main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" - | ^~~~~~~~ -main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" - | ^~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp pirs_diploid.cpp:639:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 639 | info(" [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n", | ^ @@ -538,92 +602,100 @@ pirs_diploid.cpp:643:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] 643 | info(" %#"PRIx64"]\n", het_type_tab[6]); | ^ -In file included from SimulationParameters.h:6, - from BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -InputStream.h: In constructor 'InputStream::InputStream(const char*)': -InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -In file included from SimulationParameters.h:7, - from BaseCallingProfile.h:7, - from BaseCallingProfile.cpp:5: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Profile.o Profile.cpp -In file included from OutputStream.cpp:1: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -In file included from SimulationParameters.h:6, - from GCBiasProfile.h:5, - from GCBiasProfile.cpp:5: -InputStream.h: In constructor 'InputStream::InputStream()': -InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 50 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -InputStream.h: In constructor 'InputStream::InputStream(const char*)': -InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -InputStream.h:25:7: note: 'class InputStream' declared here - 25 | class InputStream { - | ^~~~~~~~~~~ -In file included from SimulationParameters.h:7, - from GCBiasProfile.h:5, - from GCBiasProfile.cpp:5: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -In file included from SimulationParameters.h:6, - from IndelProfile.cpp:2: +main.cpp:18:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" + | ^~~~~~~~ +main.cpp:18:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 18 | "Compile Date: " __DATE__ " time: " __TIME__ "\n" + | ^~~~~~~~ +pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 168 | " "DEFAULT_BASE_CALLING_PROFILE"\n" + | ^ +pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 174 | " "DEFAULT_INDEL_PROFILE"\n" + | ^ +pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 180 | " "DEFAULT_GC_BIAS_PROFILE_100",\n" + | ^ +pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 181 | " "DEFAULT_GC_BIAS_PROFILE_150",\n" + | ^ +pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n" + | ^ +pirs_simulate.cpp:672:18: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n", + | ^ +pirs_simulate.cpp:700:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 700 | info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t", + | ^ +pirs_simulate.cpp:1235:10: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", + | ^ +pirs_simulate.cpp:1235:29: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", + | ^ +pirs_simulate.cpp:1540:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second); + | ^ +pirs_simulate.cpp:1557:2: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1557 | "# The total number of read pairs that were simulated was %"PRIu64".\n" + | ^ +pirs_simulate.cpp:1574:20: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1574 | error_log.printf("%d\t%"PRIu64"\t%g\n", + | ^ +pirs_simulate.cpp:1579:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1579 | error_log.printf("total\t%"PRIu64"\t%g\n", + | ^ +pirs_simulate.cpp:1685:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1685 | log_parameter(info_log, "Random seed: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1713:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1713 | info("Program: "PROGRAM "\n"); + | ^ +pirs_simulate.cpp:1714:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1714 | info("Version: "VERSION "\n"); + | ^ +pirs_simulate.cpp:1715:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1715 | info("Author: "AUTHOR "\n"); + | ^ +pirs_simulate.cpp:1716:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1716 | info("Contact: "CONTACT "\n"); + | ^ +pirs_simulate.cpp:1717:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^ +pirs_simulate.cpp:1717:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^~~~~~~~ +pirs_simulate.cpp:1717:44: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); + | ^~~~~~~~ +pirs_simulate.cpp:1764:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1764 | info("Bases in reference sequences: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1766:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1766 | info("Read pairs simulated: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1768:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1768 | info("Bases in reads: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1773:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1773 | info("Substitution error count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1777:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1777 | info("Insertion count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1779:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1779 | info("Deletion count: %"PRIu64"\n", + | ^ +pirs_simulate.cpp:1795:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases); + | ^ +pirs_simulate.cpp:1856:8: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] + 1856 | info("Note: A random seed (%"PRIu64") was specified on the command line.\n", + | ^ +In file included from InputStream.cpp:1: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -638,23 +710,7 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -In file included from SimulationParameters.h:7, - from IndelProfile.cpp:2: -OutputStream.h: In constructor 'OutputStream::OutputStream()': -OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 54 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': -OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] - 58 | memset(this, 0, sizeof(*this)); - | ^ -OutputStream.h:33:7: note: 'class OutputStream' declared here - 33 | class OutputStream { - | ^~~~~~~~~~~~ -In file included from InputStream.cpp:1: +In file included from Profile.cpp:2: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -669,36 +725,6 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ -IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)': -IndelProfile.cpp:117:44: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] - 117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1) - | ~~^ ~~ - | | | - | | uint64_t* {aka long long unsigned int*} - | long unsigned int* - | %llu -IndelProfile.cpp:119:42: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] - 119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1) - | ~~^ ~~ - | | | - | | uint64_t* {aka long long unsigned int*} - | long unsigned int* - | %llu -IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)': -IndelProfile.cpp:165:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 165 | info(" read_1_count = %lu\n", read_1_count); - | ~~^ ~~~~~~~~~~~~ - | | | - | | uint64_t {aka long long unsigned int} - | long unsigned int - | %llu -IndelProfile.cpp:166:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 166 | info(" read_2_count = %lu\n", read_2_count); - | ~~^ ~~~~~~~~~~~~ - | | | - | | uint64_t {aka long long unsigned int} - | long unsigned int - | %llu In file included from util.cpp:18: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] @@ -730,8 +756,9 @@ | | size_t {aka unsigned int} | long unsigned int | %u -g++ -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR='"/usr/share/pirs"' -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pirs_simulate.o pirs_simulate.cpp -In file included from Profile.cpp:2: +In file included from SimulationParameters.h:6, + from GCBiasProfile.h:5, + from GCBiasProfile.cpp:5: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] 50 | memset(this, 0, sizeof(*this)); @@ -746,6 +773,23 @@ InputStream.h:25:7: note: 'class InputStream' declared here 25 | class InputStream { | ^~~~~~~~~~~ +In file included from SimulationParameters.h:7, + from GCBiasProfile.h:5, + from GCBiasProfile.cpp:5: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ In file included from pirs_diploid.cpp:11: InputStream.h: In constructor 'InputStream::InputStream()': InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] @@ -797,93 +841,21 @@ | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} -pirs_simulate.cpp:168:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 168 | " "DEFAULT_BASE_CALLING_PROFILE"\n" - | ^ -pirs_simulate.cpp:174:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 174 | " "DEFAULT_INDEL_PROFILE"\n" - | ^ -pirs_simulate.cpp:180:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 180 | " "DEFAULT_GC_BIAS_PROFILE_100",\n" - | ^ -pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 181 | " "DEFAULT_GC_BIAS_PROFILE_150",\n" - | ^ -pirs_simulate.cpp:182:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 182 | " "DEFAULT_GC_BIAS_PROFILE_200",\n" - | ^ -pirs_simulate.cpp:672:18: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 672 | out_file.printf("%cread_%d_%"PRIu64"/%d\n", - | ^ -pirs_simulate.cpp:700:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 700 | info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t", - | ^ -pirs_simulate.cpp:1235:10: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", - | ^ -pirs_simulate.cpp:1235:29: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1235 | info("Simulated %"PRIu64" of %"PRIu64" read pairs\n", - | ^ -pirs_simulate.cpp:1540:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1540 | insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second); - | ^ -pirs_simulate.cpp:1557:2: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1557 | "# The total number of read pairs that were simulated was %"PRIu64".\n" - | ^ -pirs_simulate.cpp:1574:20: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1574 | error_log.printf("%d\t%"PRIu64"\t%g\n", - | ^ -pirs_simulate.cpp:1579:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1579 | error_log.printf("total\t%"PRIu64"\t%g\n", - | ^ -pirs_simulate.cpp:1685:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1685 | log_parameter(info_log, "Random seed: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1713:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1713 | info("Program: "PROGRAM "\n"); - | ^ -pirs_simulate.cpp:1714:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1714 | info("Version: "VERSION "\n"); - | ^ -pirs_simulate.cpp:1715:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1715 | info("Author: "AUTHOR "\n"); - | ^ -pirs_simulate.cpp:1716:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1716 | info("Contact: "CONTACT "\n"); - | ^ -pirs_simulate.cpp:1717:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^ -pirs_simulate.cpp:1717:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^~~~~~~~ -pirs_simulate.cpp:1717:44: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 1717 | info("Compile Date: "__DATE__ " time: " __TIME__ "\n"); - | ^~~~~~~~ -pirs_simulate.cpp:1764:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1764 | info("Bases in reference sequences: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1766:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1766 | info("Read pairs simulated: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1768:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1768 | info("Bases in reads: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1773:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1773 | info("Substitution error count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1777:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1777 | info("Insertion count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1779:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1779 | info("Deletion count: %"PRIu64"\n", - | ^ -pirs_simulate.cpp:1795:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1795 | info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases); - | ^ -pirs_simulate.cpp:1856:8: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix] - 1856 | info("Note: A random seed (%"PRIu64") was specified on the command line.\n", - | ^ +In file included from OutputStream.cpp:1: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ In file included from SimulationParameters.h:6, from BaseCallingProfile.h:7, from pirs_simulate.cpp:14: @@ -918,6 +890,102 @@ OutputStream.h:33:7: note: 'class OutputStream' declared here 33 | class OutputStream { | ^~~~~~~~~~~~ +In file included from SimulationParameters.h:6, + from BaseCallingProfile.h:7, + from BaseCallingProfile.cpp:5: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +InputStream.h: In constructor 'InputStream::InputStream(const char*)': +InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +In file included from SimulationParameters.h:7, + from BaseCallingProfile.h:7, + from BaseCallingProfile.cpp:5: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +In file included from SimulationParameters.h:6, + from IndelProfile.cpp:2: +InputStream.h: In constructor 'InputStream::InputStream()': +InputStream.h:50:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 50 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +InputStream.h: In constructor 'InputStream::InputStream(const char*)': +InputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class InputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +InputStream.h:25:7: note: 'class InputStream' declared here + 25 | class InputStream { + | ^~~~~~~~~~~ +In file included from SimulationParameters.h:7, + from IndelProfile.cpp:2: +OutputStream.h: In constructor 'OutputStream::OutputStream()': +OutputStream.h:54:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 54 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +OutputStream.h: In constructor 'OutputStream::OutputStream(const char*, OutputType)': +OutputStream.h:58:32: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class OutputStream'; use assignment or value-initialization instead [-Wclass-memaccess] + 58 | memset(this, 0, sizeof(*this)); + | ^ +OutputStream.h:33:7: note: 'class OutputStream' declared here + 33 | class OutputStream { + | ^~~~~~~~~~~~ +IndelProfile.cpp: In function 'void load_indel_info_line(char*, Profile&)': +IndelProfile.cpp:117:44: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] + 117 | } else if (sscanf(line, "Read_1_Count = %lu", &n) == 1) + | ~~^ ~~ + | | | + | | uint64_t* {aka long long unsigned int*} + | long unsigned int* + | %llu +IndelProfile.cpp:119:42: warning: format '%lu' expects argument of type 'long unsigned int*', but argument 3 has type 'uint64_t*' {aka 'long long unsigned int*'} [-Wformat=] + 119 | else if (sscanf(line, "Read_2_Count = %lu", &n) == 1) + | ~~^ ~~ + | | | + | | uint64_t* {aka long long unsigned int*} + | long unsigned int* + | %llu +IndelProfile.cpp: In constructor 'IndelProfile::IndelProfile(const SimulationParameters&)': +IndelProfile.cpp:165:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 165 | info(" read_1_count = %lu\n", read_1_count); + | ~~^ ~~~~~~~~~~~~ + | | | + | | uint64_t {aka long long unsigned int} + | long unsigned int + | %llu +IndelProfile.cpp:166:30: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 166 | info(" read_2_count = %lu\n", read_2_count); + | ~~^ ~~~~~~~~~~~~ + | | | + | | uint64_t {aka long long unsigned int} + | long unsigned int + | %llu g++ -Wall -Wextra -fopenmp -g -O2 -fdebug-prefix-map=/build/pirs-2.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pirs InputStream.o OutputStream.o main.o util.o mt19937-64.o pirs_diploid.o BaseCallingProfile.o GCBiasProfile.o IndelProfile.o MaskQvalsByEamss.o Profile.o pirs_simulate.o -lz -lz make[4]: Leaving directory '/build/pirs-2.0.2+dfsg/src/pirs' make[4]: Entering directory '/build/pirs-2.0.2+dfsg/src' @@ -925,7 +993,7 @@ make[3]: Leaving directory '/build/pirs-2.0.2+dfsg/src' make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src' dh_auto_build --sourcedirectory=src/stator/gcContCvgBias -- CC='$(CXX)' - cd src/stator/gcContCvgBias && make -j10 "INSTALL=install --strip-program=true" CC=\$\(CXX\) + cd src/stator/gcContCvgBias && make -j18 "INSTALL=install --strip-program=true" CC=\$\(CXX\) make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal self_util.cpp self_util.h g++ -c -O3 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wfloat-equal main.cpp @@ -951,7 +1019,7 @@ make[2]: Leaving directory '/build/pirs-2.0.2+dfsg/src/stator/gcContCvgBias' make[1]: Leaving directory '/build/pirs-2.0.2+dfsg' dh_auto_test -O--sourcedirectory=src - cd src && make -j10 check VERBOSE=1 + cd src && make -j18 check VERBOSE=1 make[1]: Entering directory '/build/pirs-2.0.2+dfsg/src' Making check in pirs make[2]: Entering directory '/build/pirs-2.0.2+dfsg/src/pirs' @@ -1022,21 +1090,24 @@ dpkg-gencontrol: warning: package pirs: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-9_i386.deb'. -dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-9_all.deb'. dpkg-deb: building package 'pirs' in '../pirs_2.0.2+dfsg-9_i386.deb'. +dpkg-deb: building package 'pirs-dbgsym' in '../pirs-dbgsym_2.0.2+dfsg-9_i386.deb'. dpkg-deb: building package 'pirs-profiles' in '../pirs-profiles_2.0.2+dfsg-9_all.deb'. +dpkg-deb: building package 'pirs-examples' in '../pirs-examples_2.0.2+dfsg-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pirs_2.0.2+dfsg-9_i386.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/53482/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/53482/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/4762 and its subdirectories -I: Current time: Fri Jun 25 02:14:47 -12 2021 -I: pbuilder-time-stamp: 1624630487 +I: removing directory /srv/workspace/pbuilder/53482 and its subdirectories +I: Current time: Fri Jul 29 10:38:27 +14 2022 +I: pbuilder-time-stamp: 1659040707