Diff of the two buildlogs: -- --- b1/build.log 2021-07-11 11:22:30.557893047 +0000 +++ b2/build.log 2021-07-11 11:25:41.626719562 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jul 10 23:19:17 -12 2021 -I: pbuilder-time-stamp: 1626002357 +I: Current time: Mon Jul 12 01:22:43 +14 2021 +I: pbuilder-time-stamp: 1626002563 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.NJTVPErt/trustedkeys.kbx': General error -gpgv: Signature made Wed Dec 23 05:09:37 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.TuLyeGxZ/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/11625/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2269/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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/2269/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2269/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='3cad66efe2a442d9b7ad3136027dfd4f' - 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='11625' - PS1='# ' - PS2='> ' + INVOCATION_ID=f271060f3f2f465a9ef3eda47a96b0b8 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=2269 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.ZtnJCZRb12/pbuilderrc_p8P3 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZtnJCZRb12/b1 --logfile b1/build.log crac_2.5.2+dfsg-4.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.ZtnJCZRb12/pbuilderrc_Tzyn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZtnJCZRb12/b2 --logfile b2/build.log --extrapackages usrmerge crac_2.5.2+dfsg-4.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt64c 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 9 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 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/11625/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 12 01:23 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 10 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/2269/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 armhf libjellyfish-2.0-2 armhf 2.3.0-10 [57.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libjellyfish-2.0-dev armhf 2.3.0-10 [132 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] -Fetched 26.0 MB in 4s (7315 kB/s) +Fetched 26.0 MB in 3s (7706 kB/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 ... 19398 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (903 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 ... 21751 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: Name or service not known +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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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 @@ -749,7 +820,7 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/crac-2.5.2+dfsg/src' @@ -773,11 +844,27 @@ 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/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 libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp 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/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 libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp 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/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 libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp +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/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 libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp +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/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 libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp samHeader.cpp: In member function 'bam_hdr_t* SamHeader::writeBamHeader(samFile*)': 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); | ~~~~~~~~~~~~~^~~~~~~ -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/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 libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp +In file included from ../libReadsReader/readsReader.h:57, + from ../Read.h:55, + from ../ReadIndex.h:52, + from ../Support.h:59, + from tagInfo.h:71, + from tagInfo.cpp:53: +../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/string.h:495, from /usr/include/htslib/kstring.h:31, from /usr/include/htslib/hts.h:37, @@ -819,22 +906,6 @@ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, 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, - from ../Support.h:59, - from tagInfo.h:71, - from tagInfo.cpp:53: -../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) - | ^~~~~~~~~ -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/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 libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp 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, @@ -880,10 +951,12 @@ 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 cracIndex.o cracIndex.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 bitarray.o bitarray.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 bitrankw32int.o bitrankw32int.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 chrPosition.o chrPosition.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 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 chrPosition.o chrPosition.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 HuffAlphabetRank.o HuffAlphabetRank.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 Huffman_Codes.o Huffman_Codes.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, @@ -907,7 +980,6 @@ ./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 HuffAlphabetRank.o HuffAlphabetRank.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: @@ -959,6 +1031,7 @@ ./seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] 1293 | typedef String TTarget; | ^~~~~~~ +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 locateOnGenome.o locateOnGenome.cpp In file included from ./seqan/sequence.h:53, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: @@ -1025,7 +1098,6 @@ ./seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 415 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ -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 Huffman_Codes.o Huffman_Codes.cpp In file included from ./seqan/file.h:66, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, @@ -1099,6 +1171,7 @@ cracIndex.cpp:224:50: required from here ./seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] ./seqan/sequence/string_packed.h:294:37: warning: comparison between types 'seqan::BitsPerValue >::' and 'seqan::BitsPerValue::' [-Wsign-compare] +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 locateTags.o locateTags.cpp In file included from ./seqan/basic.h:101, from ./seqan/sequence.h:27, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, @@ -1124,9 +1197,8 @@ ./seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here 57 | struct SimpleType | ^~~~~~~~~~ -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 locateOnGenome.o locateOnGenome.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 locateTags.o locateTags.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 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 /usr/include/libGkArrays/readsReader.h:109, from locateTags.h:60, from locateTags.cpp:53: @@ -1139,13 +1211,12 @@ /usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | 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/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 rm -f libSSA.a 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 @@ -1166,6 +1237,7 @@ 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 Classifier.o Classifier.cpp 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 classifyTags.o classifyTags.cpp 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 GkReadIndex.o GkReadIndex.cpp +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 JellyReadIndex.o JellyReadIndex.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; | ^~~~~~~~ @@ -1331,7 +1403,10 @@ 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 JellyReadIndex.o JellyReadIndex.cpp +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 crac.o crac.cpp +crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 213 | printf("\tCompiled on %s.\n\n",__DATE__); + | ^~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1374,23 +1449,6 @@ 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 crac.o crac.cpp -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 Parameters.o Parameters.cpp -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 SupportBreak.o SupportBreak.cpp -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 BreakList.o BreakList.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, @@ -1534,24 +1592,21 @@ /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); | ^~~~~ +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()); + | ~~~~~~~~~~~~~~~~ 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) { | ^ -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) - | ^~~~~~~~~ +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 Parameters.o Parameters.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1567,14 +1622,14 @@ 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 SupportBreak.o SupportBreak.cpp +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 BreakList.o BreakList.cpp 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 -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 -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 Support.cpp:57: + 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) \ | ^~~~~~~~~ @@ -1584,6 +1639,8 @@ 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 Support.o Support.cpp +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 locateServer.cpp: In function 'void* launchSubServer(void*)': locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] 464 | uint threshold = indexTags->getFactorLength(); @@ -1598,6 +1655,20 @@ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, + 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) \ + | ^~~~~~~~~ +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 locateServer.cpp:59: libReadsReader/readsReader.h: At global scope: @@ -1613,7 +1684,7 @@ 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 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/arm-linux-gnueabihf/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' @@ -1880,12 +1951,14 @@ 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/2269/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2269/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/11625 and its subdirectories -I: Current time: Sat Jul 10 23:22:26 -12 2021 -I: pbuilder-time-stamp: 1626002546 +I: removing directory /srv/workspace/pbuilder/2269 and its subdirectories +I: Current time: Mon Jul 12 01:25:34 +14 2021 +I: pbuilder-time-stamp: 1626002734