Diff of the two buildlogs: -- --- b1/build.log 2021-06-22 08:14:45.718103539 +0000 +++ b2/build.log 2021-06-22 08:26:02.392611379 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 25 02:36:36 -12 2022 -I: pbuilder-time-stamp: 1658759796 +I: Current time: Tue Jun 22 22:14:56 +14 2021 +I: pbuilder-time-stamp: 1624349696 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./sibelia_3.0.7+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.HqoxPIlo/trustedkeys.kbx': General error -gpgv: Signature made Mon Apr 13 20:37:29 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.JrNSyUad/trustedkeys.kbx': General error +gpgv: Signature made Tue Apr 14 22:37:29 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key @@ -33,137 +33,171 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/62365/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27294/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27294/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27294/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e75559d83dd646d393c80ba36ea29ef0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='62365' - PS1='# ' - PS2='> ' + INVOCATION_ID=1952015f357647e9943ecd993f35238b + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27294 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.5NLHzcp3x6/pbuilderrc_yVqv --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.5NLHzcp3x6/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.5NLHzcp3x6/pbuilderrc_Vymx --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.5NLHzcp3x6/b2 --logfile b2/build.log --extrapackages usrmerge sibelia_3.0.7+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-1 (2021-06-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-686-pae #1 SMP Debian 4.19.194-1 (2021-06-10) i686 GNU/Linux I: ls -l /bin total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 23 03:46 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/62365/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 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 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 22 22:18 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 20 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 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/27294/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -275,7 +309,7 @@ Get: 62 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libseqan2-dev all 2.4.0+dfsg-14 [1220 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libtclap-dev i386 1.2.3-1 [143 kB] -Fetched 46.9 MB in 1s (92.0 MB/s) +Fetched 46.9 MB in 8s (5973 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 ... 19675 files and directories currently installed.) @@ -546,8 +580,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (291 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 ... 41446 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/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -586,57 +656,41 @@ -- Build files have been written to: /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu dh_auto_build -O--sourcedirectory=src - cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten cd /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= Dependee "/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake" is newer than depender "/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles/Sibelia.dir/depend.internal". 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp -[ 55%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp -[ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/sibelia-3.0.7+dfsg/src/blockinstance.cpp /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp -[ 65%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp /usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp -[ 70%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -[ 75%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/sibelia-3.0.7+dfsg/src/fasta.cpp -[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/sibelia-3.0.7+dfsg/src/synteny.cpp -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/sibelia-3.0.7+dfsg/src/serialization.cpp -[ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/sibelia-3.0.7+dfsg/src/platform.cpp -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/sibelia-3.0.7+dfsg/src/stranditerator.cpp -[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, @@ -648,28 +702,12 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, @@ -679,15 +717,6 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, @@ -698,14 +727,6 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: @@ -714,16 +735,10 @@ | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/platform.h:10, - from /build/sibelia-3.0.7+dfsg/src/platform.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -741,54 +756,11 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /build/sibelia-3.0.7+dfsg/src/test/../common.h:31, - from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, - from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -814,32 +786,6 @@ /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -In file included from /usr/include/c++/10/memory:83, - from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here - 57 | template class auto_ptr; - | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -869,7 +815,8 @@ 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -877,12 +824,14 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ @@ -890,13 +839,15 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -905,13 +856,15 @@ from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ @@ -920,12 +873,13 @@ from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -933,12 +887,12 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ @@ -946,14 +900,56 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ +[ 55%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o +[ 60%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/sibelia-3.0.7+dfsg/src/edge.cpp +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/sibelia-3.0.7+dfsg/src/fasta.cpp +[ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/sibelia-3.0.7+dfsg/src/serialization.cpp +[ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/sibelia-3.0.7+dfsg/src/synteny.cpp +[ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/sibelia-3.0.7+dfsg/src/platform.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -961,16 +957,12 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ @@ -978,37 +970,81 @@ from /build/sibelia-3.0.7+dfsg/src/common.h:20, from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/serialization.cpp:7: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +[ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/sibelia-3.0.7+dfsg/src/stranditerator.cpp +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: +/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from /usr/include/tclap/Arg.h:37, + from /usr/include/tclap/SwitchArg.h:32, + from /usr/include/tclap/CmdLine.h:27, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: +/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from /usr/include/tclap/Arg.h:37, + from /usr/include/tclap/SwitchArg.h:32, + from /usr/include/tclap/CmdLine.h:27, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: +/build/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/locale_conv.h:41, + from /usr/include/c++/10/locale:43, + from /usr/include/c++/10/iomanip:43, + from /usr/include/tclap/Arg.h:37, + from /usr/include/tclap/SwitchArg.h:32, + from /usr/include/tclap/CmdLine.h:27, + from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -In file included from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /build/sibelia-3.0.7+dfsg/src/common.h:20, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ @@ -1019,114 +1055,148 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o -/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/sibelia-3.0.7+dfsg/src/resource.cpp In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/resource.h:6, - from /build/sibelia-3.0.7+dfsg/src/resource.cpp:6: + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/test/../common.h:31, + from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, + from /build/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/platform.h:10, + from /build/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/sibelia-3.0.7+dfsg/src/common.h:31, from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from /usr/include/tclap/Arg.h:37, - from /usr/include/tclap/SwitchArg.h:32, - from /usr/include/tclap/CmdLine.h:27, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: +In file included from /usr/include/c++/10/memory:83, + from /build/sibelia-3.0.7+dfsg/src/common.h:20, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from /usr/include/tclap/Arg.h:37, - from /usr/include/tclap/SwitchArg.h:32, - from /usr/include/tclap/CmdLine.h:27, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: +In file included from /usr/include/c++/10/memory:83, + from /build/sibelia-3.0.7+dfsg/src/common.h:20, + from /build/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ -/build/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: -/build/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] - 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); +[ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o +/usr/bin/c++ -I/build/sibelia-3.0.7+dfsg/src/include -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/sibelia-3.0.7+dfsg/src/resource.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/bind.hpp:30, + from /build/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/sibelia-3.0.7+dfsg/src/resource.h:6, + from /build/sibelia-3.0.7+dfsg/src/resource.cpp:6: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/locale_conv.h:41, - from /usr/include/c++/10/locale:43, - from /usr/include/c++/10/iomanip:43, - from /usr/include/tclap/Arg.h:37, - from /usr/include/tclap/SwitchArg.h:32, - from /usr/include/tclap/CmdLine.h:27, - from /build/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: +In file included from /usr/include/c++/10/memory:83, + from /build/sibelia-3.0.7+dfsg/src/common.h:20, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here + 57 | template class auto_ptr; + | ^~~~~~~~ +In file included from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: +/build/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +In file included from /usr/include/c++/10/memory:83, + from /build/sibelia-3.0.7+dfsg/src/common.h:20, + from /build/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/sibelia-3.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles 0 -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird betreten dh_auto_test --no-parallel -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird verlassen create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src - cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/sibelia-3.0.7+dfsg/src -B/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten cd /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/src /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build -make[3]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. -make[3]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten +make[3]: Für das Ziel „CMakeFiles/Sibelia.dir/build“ ist nichts zu tun. +make[3]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen [100%] Built target Sibelia -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall -make[2]: Entering directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' -make[2]: Nothing to be done for 'preinstall'. -make[2]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird betreten +make[2]: Für das Ziel „preinstall“ ist nichts zu tun. +make[2]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" @@ -1142,65 +1212,65 @@ -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt +-- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf --- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg/obj-i686-linux-gnu“ wird verlassen debian/rules override_dh_install -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird betreten dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird verlassen dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch -make[1]: Entering directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird betreten dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py -make[1]: Leaving directory '/build/sibelia-3.0.7+dfsg' +make[1]: Verzeichnis „/build/sibelia-3.0.7+dfsg“ wird verlassen dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src @@ -1219,21 +1289,23 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-3_i386.deb'. -dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-3_i386.deb'. -dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-3_all.deb'. +dpkg-deb: Paket »sibelia-examples« wird in »../sibelia-examples_3.0.7+dfsg-3_all.deb« gebaut. +dpkg-deb: Paket »sibelia-dbgsym« wird in »../sibelia-dbgsym_3.0.7+dfsg-3_i386.deb« gebaut. +dpkg-deb: Paket »sibelia« wird in »../sibelia_3.0.7+dfsg-3_i386.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sibelia_3.0.7+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/27294/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27294/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/62365 and its subdirectories -I: Current time: Mon Jul 25 02:37:45 -12 2022 -I: pbuilder-time-stamp: 1658759865 +I: removing directory /srv/workspace/pbuilder/27294 and its subdirectories +I: Current time: Tue Jun 22 22:26:01 +14 2021 +I: pbuilder-time-stamp: 1624350361