Diff of the two buildlogs: -- --- b1/build.log 2021-06-16 21:34:57.030100940 +0000 +++ b2/build.log 2021-06-16 21:36:23.458813936 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 16 09:25:27 -12 2021 -I: pbuilder-time-stamp: 1623878727 +I: Current time: Wed Jul 20 17:57:58 +14 2022 +I: pbuilder-time-stamp: 1658289478 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 [./hinge_0.5.0-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.uVvg_HFY/trustedkeys.kbx': General error -gpgv: Signature made Thu Mar 19 05:26:36 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.qJ0iklbt/trustedkeys.kbx': General error +gpgv: Signature made Fri Mar 20 07:26:36 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,137 +34,171 @@ dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11331/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11950/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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/11950/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11950/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='451a191b89a141b0b6271cdf5e5559f0' - 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='11331' - PS1='# ' - PS2='> ' + INVOCATION_ID=a8684a95916f49389b37d455e23f932d + 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=11950 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.zdBDtGjGma/pbuilderrc_hlpC --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zdBDtGjGma/b1 --logfile b1/build.log hinge_0.5.0-6.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zdBDtGjGma/pbuilderrc_sqUl --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zdBDtGjGma/b2 --logfile b2/build.log --extrapackages usrmerge hinge_0.5.0-6.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5788 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 15 21:27 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/11331/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 20 17:58 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 19 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/11950/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -386,7 +420,7 @@ Get: 150 http://deb.debian.org/debian bullseye/main i386 python3-pysam i386 0.15.4+ds-3+b2 [1571 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 python3-pbcore all 1.7.1+git20200430.a127b1e+dfsg-1 [2881 kB] Get: 152 http://deb.debian.org/debian bullseye/main i386 python3-ujson i386 4.0.2-1 [23.3 kB] -Fetched 113 MB in 37s (3024 kB/s) +Fetched 113 MB in 1s (87.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) @@ -1014,8 +1048,44 @@ 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 (4645 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 ... 45929 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/hinge-0.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/hinge-0.5.0/ && 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 hinge dpkg-buildpackage: info: source version 0.5.0-6 dpkg-buildpackage: info: source distribution unstable @@ -1059,7 +1129,7 @@ -- Build files have been written to: /build/hinge-0.5.0/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-i686-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -1067,93 +1137,87 @@ make[2]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin /build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DB.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DB.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/depend.internal". Scanning dependencies of target ini -Scanning dependencies of target man +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/depend.internal". +Scanning dependencies of target PAF +Scanning dependencies of target DB make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". +Scanning dependencies of target kmer_lookup make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -Scanning dependencies of target PAF -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/depend.internal". make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -Scanning dependencies of target DB make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/depend.internal". -Scanning dependencies of target LA make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build Scanning dependencies of target DW_banded +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/depend.internal". make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -Scanning dependencies of target kmer_lookup +Scanning dependencies of target man make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 3%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c +make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +Scanning dependencies of target LA +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 6%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o +[ 3%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o +[ 6%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c -[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c -[ 13%] Generating hinge.1 -[ 17%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp +[ 10%] Generating hinge.1 +[ 13%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1 -[ 20%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c +[ 17%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +[ 24%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o +[ 24%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +[ 27%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c -[ 24%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -[ 27%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c [ 31%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c -/build/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': -/build/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 164 | { uint64 symbol = (uint64) (node->lft); - | ^ -/build/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': -/build/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 211 | node[value].lft = (HTree *) (uint64) i; - | ^ +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 31%] Built target man /build/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); @@ -1164,7 +1228,19 @@ /build/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': +/build/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 164 | { uint64 symbol = (uint64) (node->lft); + | ^ +/build/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': +/build/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 211 | node[value].lft = (HTree *) (uint64) i; + | ^ +[ 34%] Linking C static library libPAF.a +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 /build/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range': +/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /build/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1179,23 +1255,19 @@ /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -[ 34%] Linking C static library libPAF.a -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 -/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /usr/bin/ranlib libPAF.a -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' [ 37%] Linking C static library libDW_banded.a cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake -[ 37%] Built target PAF +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 +[ 37%] Built target PAF /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o -[ 41%] Linking C static library libkmer_lookup.a -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 37%] Built target DW_banded +[ 41%] Linking C static library libkmer_lookup.a +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 -[ 41%] Built target DW_banded /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' @@ -1211,8 +1283,6 @@ make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-0.5.0/src/lib/falcon.c -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 44%] Built target man [ 48%] Linking C static library libfalcon.a cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 @@ -1222,17 +1292,17 @@ [ 48%] Built target falcon [ 51%] Linking C static library libDB.a cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 [ 55%] Linking CXX static library libini.a cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake -/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 +/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o /usr/bin/ranlib libDB.a -/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o /usr/bin/ranlib libini.a -[ 55%] Built target DB make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 55%] Built target DB [ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake @@ -1281,9 +1351,9 @@ make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' @@ -1294,44 +1364,44 @@ cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/hinging.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/hinging.dir/depend.internal". -Scanning dependencies of target consensus Scanning dependencies of target Reads_filter -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' Scanning dependencies of target get_maximal_reads -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". +Scanning dependencies of target consensus +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' Scanning dependencies of target draft_assembly +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build -Scanning dependencies of target hinging -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +Scanning dependencies of target hinging +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 68%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 68%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp [ 72%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp -[ 79%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -[ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp +[ 75%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp +[ 79%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp +[ 82%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o +cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp /build/hinge-0.5.0/src/consensus/consensus.cpp: In function 'int main(int, char**)': /build/hinge-0.5.0/src/consensus/consensus.cpp:126:15: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 126 | printf("%lu\n", res.size()); @@ -1361,12 +1431,12 @@ [ 89%] Linking CXX executable get_maximal_reads cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 89%] Built target get_maximal_reads [ 93%] Linking CXX executable Reads_filter cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 93%] Built target get_maximal_reads -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' [ 93%] Built target Reads_filter [ 96%] Linking CXX executable draft_assembly cd /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1 @@ -1385,137 +1455,137 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-i686-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin /build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin /build/hinge-0.5.0/obj-i686-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'bin/CMakeFiles/man.dir/build'. -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'bin/lib/CMakeFiles/ini.dir/build'. +make[3]: Nothing to be done for 'bin/CMakeFiles/man.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DB.dir/build'. -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'bin/lib/CMakeFiles/PAF.dir/build'. +make[3]: Nothing to be done for 'bin/lib/CMakeFiles/ini.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LA.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'bin/lib/CMakeFiles/PAF.dir/build'. +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/kmer_lookup.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DW_banded.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -[ 10%] Built target ini -[ 13%] Built target man +[ 3%] Built target man +[ 13%] Built target ini [ 20%] Built target LA -[ 27%] Built target PAF -[ 37%] Built target DB -make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= +[ 31%] Built target DB +[ 37%] Built target PAF [ 44%] Built target DW_banded [ 51%] Built target kmer_lookup +make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib /build/hinge-0.5.0/obj-i686-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LAInterface.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/falcon.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' [ 58%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend +[ 65%] Built target falcon +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter /build/hinge-0.5.0/obj-i686-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-i686-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout /build/hinge-0.5.0/obj-i686-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= -[ 65%] Built target falcon -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'bin/maximal/CMakeFiles/get_maximal_reads.dir/build'. -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/filter/CMakeFiles/Reads_filter.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/layout/CMakeFiles/hinging.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build -[ 72%] Built target Reads_filter -[ 79%] Built target get_maximal_reads -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/consensus.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' -cd /build/hinge-0.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-i686-linux-gnu /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-i686-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= -[ 86%] Built target hinging -[ 93%] Built target consensus +make[3]: Nothing to be done for 'bin/maximal/CMakeFiles/get_maximal_reads.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-i686-linux-gnu' make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/draft_assembly.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' +[ 72%] Built target Reads_filter +[ 79%] Built target hinging +[ 86%] Built target consensus +[ 93%] Built target get_maximal_reads [100%] Built target draft_assembly make[2]: Leaving directory '/build/hinge-0.5.0/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-i686-linux-gnu/CMakeFiles 0 @@ -1527,61 +1597,61 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter @@ -1615,20 +1685,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'hinge' in '../hinge_0.5.0-6_i386.deb'. dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-6_i386.deb'. +dpkg-deb: building package 'hinge' in '../hinge_0.5.0-6_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hinge_0.5.0-6_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/11950/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11950/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/11331 and its subdirectories -I: Current time: Wed Jun 16 09:34:56 -12 2021 -I: pbuilder-time-stamp: 1623879296 +I: removing directory /srv/workspace/pbuilder/11950 and its subdirectories +I: Current time: Wed Jul 20 17:59:22 +14 2022 +I: pbuilder-time-stamp: 1658289562