Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 06:17:52.846727905 +0000 +++ b2/build.log 2023-06-06 06:18:51.192172452 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 8 00:39:35 -12 2024 -I: pbuilder-time-stamp: 1720442375 +I: Current time: Tue Jun 6 20:17:54 +14 2023 +I: pbuilder-time-stamp: 1686032274 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./kalign_3.3.5.orig.tar.gz] I: copying [./kalign_3.3.5-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 5 18:45:57 2023 -12 +gpgv: Signature made Mon Feb 6 20:45:57 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,137 +29,169 @@ dpkg-source: info: applying pass-proper-flags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30848/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10195/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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 6 20:18 /bin/sh -> /bin/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/10195/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10195/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 parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(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 parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9fd6f865144f4e90854ce78b3f5817d8' - 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='30848' - PS1='# ' - PS2='> ' + INVOCATION_ID=aa2a178179024eeea5d5ffd5e421b8d9 + 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=10195 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/r-b-build.jgPzSKSP/pbuilderrc_LWfI --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jgPzSKSP/b1 --logfile b1/build.log kalign_3.3.5-1.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/r-b-build.jgPzSKSP/pbuilderrc_qgmF --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jgPzSKSP/b2 --logfile b2/build.log --extrapackages usrmerge kalign_3.3.5-1.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 ionos6-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/30848/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 6 20:18 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/10195/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -248,7 +280,7 @@ Get: 47 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libsimde-dev all 0.7.4~rc2-2 [377 kB] -Fetched 34.2 MB in 1s (67.1 MB/s) +Fetched 34.2 MB in 1s (27.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19599 files and directories currently installed.) @@ -458,8 +490,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/kalign-3.3.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kalign_3.3.5-1_source.changes +I: user script /srv/workspace/pbuilder/10195/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/10195/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/kalign-3.3.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kalign_3.3.5-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3.5-1 dpkg-buildpackage: info: source distribution unstable @@ -527,7 +570,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_build - cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j7 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kalign-3.3.5/obj-i686-linux-gnu/CMakeFiles /build/kalign-3.3.5/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -535,117 +578,139 @@ make[3]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend -make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake --color= -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend +make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib 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'/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake --color= -make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering 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object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_ALPHABET -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c +[ 2%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +[ 4%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic 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lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -MF CMakeFiles/tldevel.dir/src/tldevel.c.o.d -o CMakeFiles/tldevel.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c +cd 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+/build/kalign-3.3.5/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kalign-3.3.5/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -c /build/kalign-3.3.5/lib/src/tlmisc.c -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -MF CMakeFiles/bpm_utest.dir/src/alphabet.c.o.d -o CMakeFiles/bpm_utest.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c -[ 21%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_ALPHABET -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c -make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build -make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -[ 22%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c -[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +[ 15%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c -[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +[ 17%] Linking C executable task_utest +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/task_utest.dir/src/tldevel.c.o CMakeFiles/task_utest.dir/src/tlrng.c.o CMakeFiles/task_utest.dir/src/task.c.o -o task_utest -lm +make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 17%] Built target task_utest +[ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -MF CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c -[ 27%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm.c.o -c /build/kalign-3.3.5/lib/src/bpm.c -[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +[ 20%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd 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-ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -c /build/kalign-3.3.5/lib/src/msa_op.c -[ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c -[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +[ 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lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c +[ 30%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -c /build/kalign-3.3.5/lib/src/msa_misc.c -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o +[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -c /build/kalign-3.3.5/lib/src/msa_check.c -[ 38%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +[ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c +[ 34%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -MF CMakeFiles/tldevel.dir/src/tlrng.c.o.d -o CMakeFiles/tldevel.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c +[ 35%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUTEST_EDIST -Wall -Wextra 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[-Wunused-variable] 58 | float d2; | ^~ -[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +[ 37%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c +[ 38%] Linking C executable alphabet_utest +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 38%] Built target alphabet_utest +[ 40%] Linking C executable edist_utest +[ 41%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/lib/src -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -MF CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/kalign-3.3.5/lib/src/esl_stopwatch.c +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/edist_utest.dir/src/tldevel.c.o CMakeFiles/edist_utest.dir/src/tlrng.c.o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -o edist_utest -lm +[ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/kalign-3.3.5/lib/src/msa_cmp.c +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -MF CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c -[ 42%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -MF CMakeFiles/task_utest.dir/src/tlrng.c.o.d -o CMakeFiles/task_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 45%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -MF CMakeFiles/bpm_utest.dir/src/alphabet.c.o.d -o CMakeFiles/bpm_utest.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c +[ 45%] Built target edist_utest +[ 47%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm.c.o -c /build/kalign-3.3.5/lib/src/bpm.c +[ 48%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm_test.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -c /build/kalign-3.3.5/lib/src/bpm_test.c +[ 50%] Linking C static library libtldevel.a +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +/usr/bin/ranlib libtldevel.a +make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 50%] Built target tldevel +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -MF CMakeFiles/kalign_OBJ.dir/src/task.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -c /build/kalign-3.3.5/lib/src/bisectingKmeans.c -[ 47%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DTASKWRITETEST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/task_utest.dir/src/task.c.o -MF CMakeFiles/task_utest.dir/src/task.c.o.d -o CMakeFiles/task_utest.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c -/build/kalign-3.3.5/lib/src/task.c: In function 'read_tasks': -/build/kalign-3.3.5/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kalign-3.3.5/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kalign-3.3.5/lib/src/task.c: In function 'read_tasks': /build/kalign-3.3.5/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 94 | fscanf( f_ptr, "%d", &n_tasks); @@ -653,178 +718,156 @@ /build/kalign-3.3.5/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -MF CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -c /build/kalign-3.3.5/lib/src/sequence_distance.c -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bpm.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -c /build/kalign-3.3.5/lib/src/bpm.c -[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +[ 57%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -MF CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -MF CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -c /build/kalign-3.3.5/lib/src/pick_anchor.c -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -c /build/kalign-3.3.5/lib/src/aln_param.c +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -c /build/kalign-3.3.5/lib/src/aln_wrap.c -[ 57%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -c /build/kalign-3.3.5/lib/src/aln_param.c +[ 62%] Linking C executable bpm_utest +cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bpm_utest.dir/src/tldevel.c.o CMakeFiles/bpm_utest.dir/src/tlrng.c.o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o CMakeFiles/bpm_utest.dir/src/alphabet.c.o CMakeFiles/bpm_utest.dir/src/bpm.c.o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -o bpm_utest -lm +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -c /build/kalign-3.3.5/lib/src/aln_run.c -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +[ 65%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp 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lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-i686-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -MF CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/kalign-3.3.5/lib/src/weave_alignment.c -[ 68%] Linking C executable bpm_utest -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic 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alphabet_utest -cd /build/kalign-3.3.5/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 -/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest -/usr/bin/ranlib libtldevel.a -make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -[ 74%] Built target tldevel -[ 74%] Built target alphabet_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' [ 74%] Built target kalign_OBJ make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend +make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib /build/kalign-3.3.5/obj-i686-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake --color= -make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/lib /build/kalign-3.3.5/obj-i686-linux-gnu /build/kalign-3.3.5/obj-i686-linux-gnu/lib 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-Wl,-Bstatic -lpthread -Wl,-Bdynamic make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 97%] Built target kalignfmt [ 98%] Linking C executable largebench -[ 98%] Built target kalign_lib_test -make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' cd /build/kalign-3.3.5/obj-i686-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 -[ 98%] Built target kalignfmt -[ 98%] Built target kalign-bin /usr/bin/cc -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' +[ 98%] Built target kalign-bin +make[4]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' [ 98%] Built target largebench /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] @@ -851,10 +894,10 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_test - cd obj-i686-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 + cd obj-i686-linux-gnu && make -j7 test ARGS\+=--verbose ARGS\+=-j7 make[2]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j16 +/usr/bin/ctest --force-new-ctest-process --verbose -j7 UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/kalign-3.3.5/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-i686-linux-gnu/DartConfiguration.tcl @@ -908,32 +951,8 @@ 7: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB11001_EOF.msf" 7: Working Directory: /build/kalign-3.3.5/tests 7: Test timeout computed to be: 1500 -test 8 - Start 8: kalign_itest_BB12006.msf - -8: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.msf" -8: Working Directory: /build/kalign-3.3.5/tests -8: Test timeout computed to be: 1500 -test 9 - Start 9: kalign_itest_BB12006.tfa - -9: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" -9: Working Directory: /build/kalign-3.3.5/tests -9: Test timeout computed to be: 1500 -test 10 - Start 10: kalign_itest_BB30014.msf - -10: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" -10: Working Directory: /build/kalign-3.3.5/tests -10: Test timeout computed to be: 1500 -test 11 - Start 11: kalign_itest_BB30014.tfa - -11: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB30014.tfa" -11: Working Directory: /build/kalign-3.3.5/tests -11: Test timeout computed to be: 1500 1: LEN: 256 -1: [2024-07-08 00:40:16] : LOG : Testing correctness of serial bpm. +1: [2023-06-06 20:18:33] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -1066,68 +1085,96 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2024-07-08 00:40:16] : LOG : Check for correctness. -3: [2024-07-08 00:40:16] : LOG : Timing serial -3: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -4: 584 995 981 610 327 -4: 910 849 68 355 714 -4: 498 572 755 948 26 -4: 802 482 998 770 377 -4: 696 1 98 17 553 -4: 220 125 242 989 813 -4: 629 360 767 552 874 -4: 487 412 308 375 322 -4: 918 225 405 484 175 -4: 483 783 717 67 943 -4: 919 656 693 343 16 -4: 431 48 762 909 237 -4: 881 786 91 214 489 -4: 610 999 984 861 26 -4: 186 956 564 56 942 -4: 404 777 739 416 541 -4: 96 661 161 526 820 -4: 40 251 964 351 623 -4: 440 273 432 829 127 -4: 190 220 241 99 556 -4: 656 785 388 130 562 -4: 849 17 392 364 357 -4: 31 741 440 95 165 -4: 96 192 531 773 316 -4: 467 229 677 438 235 -4: 927 31 343 708 444 -4: 666 18 506 451 537 -4: 516 807 996 426 100 -4: 688 671 354 358 690 -4: 155 740 754 516 432 -4: 695 542 505 632 836 -4: 511 877 721 90 482 -4: 721 517 763 19 845 -4: 154 560 406 516 827 -4: 221 141 393 4 795 -4: 168 585 37 339 884 -4: 104 874 487 251 796 -4: 79 7 178 793 737 -4: 866 303 999 336 711 -4: 397 604 798 511 742 -4: 858 555 374 929 150 -4: 351 762 366 451 944 -4: 325 380 514 56 636 -4: 375 275 966 136 202 -4: 891 590 925 302 566 -4: 669 316 611 126 726 -4: 329 543 107 616 416 -4: 451 282 978 262 154 -4: 868 737 362 844 731 -4: 36 286 910 292 903 -4: 725 83 388 388 157 -4: 827 750 115 735 60 -4: 773 16 284 11 130 -4: 637 909 443 231 357 +3: [2023-06-06 20:18:33] : LOG : Check for correctness. +3: [2023-06-06 20:18:33] : LOG : Timing serial +4: 56 601 514 170 717 +4: 660 253 784 61 407 +4: 47 499 890 728 696 +4: 190 718 549 761 318 +4: 416 87 183 573 815 +4: 266 168 153 422 201 +4: 172 338 720 395 60 +4: 558 585 728 267 239 +4: 424 501 735 402 242 +4: 338 697 1 953 668 +4: 962 343 121 232 654 +4: 134 527 127 60 542 +4: 247 208 840 607 991 +4: 241 382 292 920 871 +4: 434 659 452 537 866 +4: 545 466 721 197 775 +4: 303 517 472 351 203 +4: 882 910 869 275 541 +4: 191 13 110 102 280 +4: 971 984 596 664 124 +4: 775 914 472 482 990 +4: 772 953 207 828 702 +4: 923 379 528 851 432 +4: 135 913 430 875 243 +4: 675 887 674 906 125 +4: 324 920 665 924 854 +4: 521 338 810 544 603 +4: 2 444 853 988 760 +4: 57 836 814 730 323 +4: 219 191 243 244 46 +4: 446 956 712 631 93 +4: 274 987 786 904 430 +4: 25 605 79 122 39 +4: 645 883 409 269 315 +4: 750 533 733 60 373 +4: 538 210 442 746 89 +4: 910 563 871 473 339 +4: 646 404 81 581 646 +4: 484 324 647 986 653 +4: 758 123 217 612 416 +4: 559 291 78 841 164 +4: 144 149 255 887 598 +4: 361 54 798 178 981 +4: 79 207 645 906 887 +4: 684 5 409 658 232 +4: 849 1 37 490 849 +4: 417 729 392 594 347 +4: 388 430 197 968 871 +4: 99 355 272 477 110 +4: 204 671 779 522 296 +4: 134 472 195 180 369 +4: 653 538 368 34 47 +4: 819 152 762 146 42 +4: 263 16 71 475 22 5: Aligned: 5: ------GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP---------- 5: ------------MQDRVKRPMNAFIVWSRDQRRKMAL-EN-PRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK---YPNYKYRP- 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS--N-L-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNA--- 5: ----------------MHIKKPLNAFMLYMKEMRANV-VA-ESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY + 1/11 Test #2: alphabet_utest ................... Passed 0.01 sec +test 8 + Start 8: kalign_itest_BB12006.msf + +8: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.msf" +8: Working Directory: /build/kalign-3.3.5/tests +8: Test timeout computed to be: 1500 + 2/11 Test #4: task_utest ....................... Passed 0.02 sec +test 9 + Start 9: kalign_itest_BB12006.tfa + +9: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" +9: Working Directory: /build/kalign-3.3.5/tests +9: Test timeout computed to be: 1500 + 3/11 Test #5: C++Lib ........................... Passed 0.02 sec +test 10 + Start 10: kalign_itest_BB30014.msf + +10: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB12006.tfa" +10: Working Directory: /build/kalign-3.3.5/tests +10: Test timeout computed to be: 1500 +3: [2023-06-06 20:18:33] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 + 4/11 Test #3: edist_utest ...................... Passed 0.03 sec +test 11 + Start 11: kalign_itest_BB30014.tfa + +11: Test command: /build/kalign-3.3.5/obj-i686-linux-gnu/src/kalign "/build/kalign-3.3.5/tests/data/BB30014.tfa" +11: Working Directory: /build/kalign-3.3.5/tests +11: Test timeout computed to be: 1500 6: 6: Kalign (3.3.5) 6: @@ -1144,15 +1191,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -6: [2024-07-08 00:40:16] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. -6: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -6: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -6: [2024-07-08 00:40:16] : LOG : Building guide tree. -6: [2024-07-08 00:40:16] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -6: [2024-07-08 00:40:16] : LOG : Aligning -6: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +6: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +6: [2023-06-06 20:18:33] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. +6: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +6: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-06-06 20:18:33] : LOG : Building guide tree. +6: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-06-06 20:18:33] : LOG : Aligning +6: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -1165,6 +1212,7 @@ 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK + 5/11 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.03 sec 7: 7: Kalign (3.3.5) 7: @@ -1181,15 +1229,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -7: [2024-07-08 00:40:16] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. -7: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -7: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -7: [2024-07-08 00:40:16] : LOG : Building guide tree. -7: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -7: [2024-07-08 00:40:16] : LOG : Aligning -7: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +7: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +7: [2023-06-06 20:18:33] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. +7: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +7: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-06-06 20:18:33] : LOG : Building guide tree. +7: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-06-06 20:18:33] : LOG : Aligning +7: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -1202,6 +1250,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK + 6/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.03 sec 8: 8: Kalign (3.3.5) 8: @@ -1218,14 +1267,40 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -8: [2024-07-08 00:40:16] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. -8: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -8: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -8: [2024-07-08 00:40:16] : LOG : Building guide tree. -8: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -8: [2024-07-08 00:40:16] : LOG : Aligning +8: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +8: [2023-06-06 20:18:33] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. +8: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +8: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-06-06 20:18:33] : LOG : Building guide tree. +8: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-06-06 20:18:33] : LOG : Aligning +8: [2023-06-06 20:18:33] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +8: >1al2_ad +8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS +8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF +8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ +8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ +8: KA--- +8: >1bbt_ac +8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- +8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF +8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY +8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- +8: ----- +8: >1bev_ac +8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N +8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC +8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG +8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ +8: TAILQ +8: >1mec_ac +8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- +8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF +8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM +8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP +8: Q---- + 7/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.03 sec 9: 9: Kalign (3.3.5) 9: @@ -1242,66 +1317,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -9: [2024-07-08 00:40:16] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -9: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -9: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -9: [2024-07-08 00:40:16] : LOG : Building guide tree. -9: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-07-08 00:40:16] : LOG : Aligning -10: -10: Kalign (3.3.5) -10: -10: Copyright (C) 2006,2019,2020,2021 Timo Lassmann -10: -10: This program comes with ABSOLUTELY NO WARRANTY; for details type: -10: `kalign -showw'. -10: This is free software, and you are welcome to redistribute it -10: under certain conditions; consult the COPYING file for details. -10: -10: Please cite: -10: Lassmann, Timo. -10: "Kalign 3: multiple sequence alignment of large data sets." -10: Bioinformatics (2019) -10: https://doi.org/10.1093/bioinformatics/btz795 -10: -10: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -10: [2024-07-08 00:40:16] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -10: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -10: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -10: [2024-07-08 00:40:16] : LOG : Building guide tree. - 1/11 Test #2: alphabet_utest ................... Passed 0.10 sec - 2/11 Test #3: edist_utest ...................... Passed 0.08 sec - 3/11 Test #4: task_utest ....................... Passed 0.08 sec - 4/11 Test #5: C++Lib ........................... Passed 0.08 sec - 5/11 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.07 sec - 6/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.07 sec -10: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -10: [2024-07-08 00:40:16] : LOG : Aligning -11: -11: Kalign (3.3.5) -11: -11: Copyright (C) 2006,2019,2020,2021 Timo Lassmann -11: -11: This program comes with ABSOLUTELY NO WARRANTY; for details type: -11: `kalign -showw'. -11: This is free software, and you are welcome to redistribute it -11: under certain conditions; consult the COPYING file for details. -11: -11: Please cite: -11: Lassmann, Timo. -11: "Kalign 3: multiple sequence alignment of large data sets." -11: Bioinformatics (2019) -11: https://doi.org/10.1093/bioinformatics/btz795 -11: -11: [2024-07-08 00:40:16] : LOG : Detected protein sequences. -11: [2024-07-08 00:40:16] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. -11: [2024-07-08 00:40:16] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2024-07-08 00:40:16] : LOG : Calculating pairwise distances -8: [2024-07-08 00:40:16] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 -9: [2024-07-08 00:40:16] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +9: [2023-06-06 20:18:33] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +9: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +9: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-06-06 20:18:33] : LOG : Building guide tree. +9: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-06-06 20:18:33] : LOG : Aligning +9: [2023-06-06 20:18:33] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1326,31 +1350,31 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- -8: >1al2_ad -8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -8: KA--- -8: >1bbt_ac -8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -8: ----- -8: >1bev_ac -8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -8: TAILQ -8: >1mec_ac -8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -8: Q---- -10: [2024-07-08 00:40:16] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +10: +10: Kalign (3.3.5) +10: +10: Copyright (C) 2006,2019,2020,2021 Timo Lassmann +10: +10: This program comes with ABSOLUTELY NO WARRANTY; for details type: +10: `kalign -showw'. +10: This is free software, and you are welcome to redistribute it +10: under certain conditions; consult the COPYING file for details. +10: +10: Please cite: +10: Lassmann, Timo. +10: "Kalign 3: multiple sequence alignment of large data sets." +10: Bioinformatics (2019) +10: https://doi.org/10.1093/bioinformatics/btz795 +10: +10: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +10: [2023-06-06 20:18:33] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +10: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +10: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-06-06 20:18:33] : LOG : Building guide tree. +10: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-06-06 20:18:33] : LOG : Aligning +10: [2023-06-06 20:18:33] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1375,20 +1399,39 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- - 7/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.07 sec - 8/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.05 sec - 9/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.04 sec -11: [2024-07-08 00:40:16] : LOG : CPU Time: 0.06u 00:00:00.06 Elapsed: 00:00:00.00 -11: [2024-07-08 00:40:16] : LOG : Building guide tree. + 8/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.02 sec + 9/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.02 sec +11: +11: Kalign (3.3.5) +11: +11: Copyright (C) 2006,2019,2020,2021 Timo Lassmann +11: +11: This program comes with ABSOLUTELY NO WARRANTY; for details type: +11: `kalign -showw'. +11: This is free software, and you are welcome to redistribute it +11: under certain conditions; consult the COPYING file for details. +11: +11: Please cite: +11: Lassmann, Timo. +11: "Kalign 3: multiple sequence alignment of large data sets." +11: Bioinformatics (2019) +11: https://doi.org/10.1093/bioinformatics/btz795 +11: +11: [2023-06-06 20:18:33] : LOG : Detected protein sequences. +11: [2023-06-06 20:18:33] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. +11: [2023-06-06 20:18:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2023-06-06 20:18:33] : LOG : Calculating pairwise distances +11: [2023-06-06 20:18:33] : LOG : CPU Time: 0.07u 00:00:00.07 Elapsed: 00:00:00.00 +11: [2023-06-06 20:18:33] : LOG : Building guide tree. +11: [2023-06-06 20:18:33] : LOG : CPU Time: 0.13u 00:00:00.13 Elapsed: 00:00:00.00 +11: [2023-06-06 20:18:33] : LOG : Aligning 1: 0 6300 0 0 1: 0 0 6300 6300 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2024-07-08 00:40:16] : LOG : Testing correctness of AVX bpm. -11: [2024-07-08 00:40:16] : LOG : CPU Time: 0.08u 00:00:00.07 Elapsed: 00:00:00.00 -11: [2024-07-08 00:40:16] : LOG : Aligning -11: [2024-07-08 00:40:16] : LOG : CPU Time: 0.10u 00:00:00.09 Elapsed: 00:00:00.00 +1: [2023-06-06 20:18:33] : LOG : Testing correctness of AVX bpm. +11: [2023-06-06 20:18:33] : LOG : CPU Time: 0.11u 00:00:00.10 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -1697,29 +1740,29 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -10/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.21 sec +10/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.18 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: Dyn AVX DYN/AVX -1: [2024-07-08 00:40:26] : LOG : Timing DYN 256 -1: [2024-07-08 00:40:30] : LOG : 2.099120 - dyn -1: [2024-07-08 00:40:30] : LOG : 0.000000 - bpm -1: [2024-07-08 00:40:30] : LOG : 0.295933 - bpm_block2 -1: [2024-07-08 00:40:30] : LOG : 0.315698 - bpm_block -11/11 Test #1: bpm_utest ........................ Passed 14.40 sec +1: [2023-06-06 20:18:41] : LOG : Timing DYN 256 +1: [2023-06-06 20:18:43] : LOG : 1.871134 - dyn +1: [2023-06-06 20:18:43] : LOG : 0.000000 - bpm +1: [2023-06-06 20:18:43] : LOG : 0.422984 - bpm_block2 +1: [2023-06-06 20:18:43] : LOG : 0.437296 - bpm_block +11/11 Test #1: bpm_utest ........................ Passed 10.33 sec 100% tests passed, 0 tests failed out of 11 -Total Test time (real) = 14.41 sec +Total Test time (real) = 10.33 sec make[2]: Leaving directory '/build/kalign-3.3.5/obj-i686-linux-gnu' make[1]: Leaving directory '/build/kalign-3.3.5' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ - cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/kalign-3.3.5/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j7 install DESTDIR=/build/kalign-3.3.5/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kalign-3.3.5/obj-i686-linux-gnu' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1764,8 +1807,8 @@ dpkg-gencontrol: warning: Built-Using field of package kalign: substitution variable ${simde:Built-Using} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3.5-1_i386.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.3.5-1_i386.deb'. +dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3.5-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.3.5-1_i386.buildinfo dpkg-genchanges --build=binary -O../kalign_3.3.5-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1773,12 +1816,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/10195/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10195/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/30848 and its subdirectories -I: Current time: Mon Jul 8 00:40:48 -12 2024 -I: pbuilder-time-stamp: 1720442449 +I: removing directory /srv/workspace/pbuilder/10195 and its subdirectories +I: Current time: Tue Jun 6 20:18:50 +14 2023 +I: pbuilder-time-stamp: 1686032330