Diff of the two buildlogs: -- --- b1/build.log 2021-08-15 12:49:15.644675022 +0000 +++ b2/build.log 2021-08-15 12:52:46.896724896 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 15 00:47:03 -12 2021 -I: pbuilder-time-stamp: 1629031623 +I: Current time: Sun Sep 18 09:12:19 +14 2022 +I: pbuilder-time-stamp: 1663441939 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./crac_2.5.2+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.IfHLDoal/trustedkeys.kbx': General error -gpgv: Signature made Wed Dec 23 05:09:37 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.RHCSh3NG/trustedkeys.kbx': General error +gpgv: Signature made Thu Dec 24 07:09:37 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -34,135 +34,169 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7362/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8562/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-arm64. +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/8562/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8562/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='arm64' - 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='7362' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=8562 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.oH1xRSdqXk/pbuilderrc_LNma --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.oH1xRSdqXk/b1 --logfile b1/build.log crac_2.5.2+dfsg-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.oH1xRSdqXk/pbuilderrc_Zgu2 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.oH1xRSdqXk/b2 --logfile b2/build.log --extrapackages usrmerge crac_2.5.2+dfsg-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink16-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 07:09 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more - -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 134808 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 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 13 21:24 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 07:09 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/7362/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 2021 more + -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount + -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 134808 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 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 18 09:12 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 18 05:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 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/8562/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +303,7 @@ Get: 55 http://deb.debian.org/debian bullseye/main arm64 libjellyfish-2.0-2 arm64 2.3.0-10 [61.0 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libjellyfish-2.0-dev arm64 2.3.0-10 [136 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] -Fetched 26.4 MB in 1s (36.1 MB/s) +Fetched 26.4 MB in 2s (12.2 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 ... 19646 files and directories currently installed.) @@ -515,8 +549,45 @@ 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 arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1352 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 ... 22000 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/crac-2.5.2+dfsg/ && 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 > ../crac_2.5.2+dfsg-4_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/crac-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../crac_2.5.2+dfsg-4_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -556,7 +627,7 @@ ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 @@ -584,10 +655,10 @@ checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking how to print strings... printf -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -606,8 +677,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for ANSI C header files... no @@ -779,17 +850,6 @@ samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | sam_hdr_write(out,h); | ~~~~~~~~~~~~~^~~~~~~ -In file included from /usr/include/string.h:495, - from /usr/include/htslib/kstring.h:31, - from /usr/include/htslib/hts.h:37, - from /usr/include/htslib/sam.h:31, - from samLine.h:59, - from samLine.cpp:52: -In function 'char* strncpy(char*, const char*, size_t)', - inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, @@ -805,6 +865,17 @@ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +In file included from /usr/include/string.h:495, + from /usr/include/htslib/kstring.h:31, + from /usr/include/htslib/hts.h:37, + from /usr/include/htslib/sam.h:31, + from samLine.h:59, + from samLine.cpp:52: +In function 'char* strncpy(char*, const char*, size_t)', + inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'char* strncpy(char*, const char*, size_t)', inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10, inlined from 'CharOptionalField::CharOptionalField(const char*, char)' at samLine.cpp:91:34: @@ -889,6 +960,7 @@ 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp +g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, @@ -905,7 +977,19 @@ ./seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] 1051 | typedef typename Value >::Type THostValue; | ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp +g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp +In file included from /usr/include/libGkArrays/readsReader.h:109, + from locateTags.h:60, + from locateTags.cpp:53: +/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' + 111 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from ./seqan/sequence.h:38, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: @@ -913,7 +997,6 @@ ./seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] 239 | typedef typename Value::Type TLeftValue; | ^~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp In file included from ./seqan/sequence.h:51, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: @@ -990,18 +1073,6 @@ ./seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] 1647 | typedef typename Id::Type TId; | ^~~ -In file included from /usr/include/libGkArrays/readsReader.h:109, - from locateTags.h:60, - from locateTags.cpp:53: -/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' - 111 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from ./seqan/index.h:82, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: @@ -1145,7 +1216,7 @@ ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libSSA.a -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader @@ -1177,7 +1248,6 @@ crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 213 | printf("\tCompiled on %s.\n\n",__DATE__); | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1326,6 +1396,7 @@ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ +g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1341,34 +1412,6 @@ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.cpp -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from Support.h:59, - from SupportBreak.cpp:55: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from classifyTags.h:53, - from classifyTags.cpp:52: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1512,7 +1555,34 @@ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from Support.h:59, + from SupportBreak.cpp:55: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from classifyTags.h:53, + from classifyTags.cpp:52: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from ./libReadsReader/readsReader.h:57, from ./Read.h:55, from ./ReadIndex.h:52, @@ -1527,16 +1597,16 @@ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp crac.cpp: In function 'int main(int, char**)': crac.cpp:1009:26: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] 1009 | } catch (bad_alloc e) { | ^ -g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, - from JellyReadIndex.h:59, - from JellyReadIndex.cpp:55: + from Support.h:59, + from Support.cpp:57: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -1546,11 +1616,12 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, - from Support.h:59, - from Support.cpp:57: + from JellyReadIndex.h:59, + from JellyReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -1575,6 +1646,16 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': +Classifier.cpp:203:33: warning: 'bioundetermined_type' may be used uninitialized in this function [-Wmaybe-uninitialized] + 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 204 | suppoBreak->getPositionStartBreak(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 205 | bioundetermined_type, + | ~~~~~~~~~~~~~~~~~~~~~ + 206 | message.c_str()); + | ~~~~~~~~~~~~~~~~ locateServer.cpp: In function 'void* launchSubServer(void*)': locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] 464 | uint threshold = indexTags->getFactorLength(); @@ -1601,19 +1682,9 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()': -Classifier.cpp:203:33: warning: 'bioundetermined_type' may be used uninitialized in this function [-Wmaybe-uninitialized] - 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 204 | suppoBreak->getPositionStartBreak(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 205 | bioundetermined_type, - | ~~~~~~~~~~~~~~~~~~~~~ - 206 | message.c_str()); - | ~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src -I/build/crac-2.5.2+dfsg/src/libSSA -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp ln -s -f /build/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index -/bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -fdebug-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/src' @@ -1752,8 +1823,8 @@ Making install in libSSA make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' @@ -1764,7 +1835,7 @@ make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' /usr/bin/install -c -m 644 kseq.h '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' make[5]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' @@ -1777,8 +1848,8 @@ make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src' @@ -1788,14 +1859,14 @@ make[2]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/man' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/man' Making install in scripts make[2]: Entering directory '/build/crac-2.5.2+dfsg/scripts' make[3]: Entering directory '/build/crac-2.5.2+dfsg/scripts' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' @@ -1878,12 +1949,14 @@ 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/8562/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8562/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/7362 and its subdirectories -I: Current time: Sun Aug 15 00:49:14 -12 2021 -I: pbuilder-time-stamp: 1629031754 +I: removing directory /srv/workspace/pbuilder/8562 and its subdirectories +I: Current time: Sun Sep 18 09:15:45 +14 2022 +I: pbuilder-time-stamp: 1663442145