Diff of the two buildlogs: -- --- b1/build.log 2023-04-20 03:19:27.196622325 +0000 +++ b2/build.log 2023-04-20 03:20:58.000592079 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 21 21:41:02 -12 2024 -I: pbuilder-time-stamp: 1716370862 +I: Current time: Thu Apr 20 17:19:28 +14 2023 +I: pbuilder-time-stamp: 1681960768 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ 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 @@ -28,135 +28,167 @@ 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/653814/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2612308/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 Apr 20 17:19 /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/2612308/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2612308/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='faa4f1ec46a54e6295113513614aba34' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='653814' - PS1='# ' - PS2='> ' + INVOCATION_ID=127989c198254242b9a77852237d9239 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2612308 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.iWqMN2Xv/pbuilderrc_jkAp --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.iWqMN2Xv/b1 --logfile b1/build.log kalign_3.3.5-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.iWqMN2Xv/pbuilderrc_BsGH --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.iWqMN2Xv/b2 --logfile b2/build.log --extrapackages usrmerge kalign_3.3.5-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 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 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 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 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 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 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 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 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 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 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 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/653814/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 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 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 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 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 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 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 20 17:19 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 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/2612308/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -245,7 +277,7 @@ Get: 47 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] -Fetched 32.7 MB in 0s (90.6 MB/s) +Fetched 32.7 MB in 1s (46.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (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 ... 19596 files and directories currently installed.) @@ -455,8 +487,19 @@ 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/2612308/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/2612308/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 @@ -680,7 +723,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kalign-3.3.5/obj-x86_64-linux-gnu/CMakeFiles /build/kalign-3.3.5/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -697,63 +740,79 @@ make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make -f lib/CMakeFiles/alphabet_utest.dir/build.make 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-I/build/kalign-3.3.5/obj-x86_64-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/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/kalign-3.3.5/lib/src/test.c +cd /build/kalign-3.3.5/obj-x86_64-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 +[ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +cd 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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 +[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-x86_64-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 +[ 27%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-linux-gnu/lib -I/build/kalign-3.3.5/lib/include -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong 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-DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 +[ 34%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/kalign-3.3.5/obj-x86_64-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); @@ -761,46 +820,32 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c -[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -cd /build/kalign-3.3.5/obj-x86_64-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 -[ 27%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -cd /build/kalign-3.3.5/obj-x86_64-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 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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 +[ 38%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +cd /build/kalign-3.3.5/obj-x86_64-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 +[ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-x86_64-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 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/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/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c -[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_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 +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 /build/kalign-3.3.5/lib/src/euclidean_dist.c: In function 'main': /build/kalign-3.3.5/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/kalign-3.3.5/lib/src/msa_alloc.c -[ 38%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_io.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -c /build/kalign-3.3.5/lib/src/msa_io.c -[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -[ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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/kalign_OBJ.dir/src/task.c.o +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 [ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 /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); @@ -808,11 +853,9 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_wrap.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 @@ -826,79 +869,73 @@ cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/kalign-3.3.5/lib/src/aln_setup.c [ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/kalign-3.3.5/lib/src/aln_controller.c -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_seqprofile.c -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -[ 65%] Linking C executable bpm_utest +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/kalign-3.3.5/lib/src/aln_seqseq.c -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -[ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 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Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-x86_64-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 alphabet_utest +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +[ 70%] Linking C executable edist_utest +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_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 +/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 +[ 71%] Linking C executable task_utest +cd /build/kalign-3.3.5/obj-x86_64-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 +[ 72%] Linking C executable bpm_utest +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' /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 -[ 70%] Linking C static library libtldevel.a +make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +[ 74%] Linking C static library libtldevel.a cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -[ 71%] Linking C executable edist_utest -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +[ 74%] Built target alphabet_utest +[ 74%] Built target edist_utest cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.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/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 +make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' /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 -[ 72%] Linking C executable task_utest -make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +[ 74%] Built target task_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -[ 74%] Linking C executable alphabet_utest -[ 74%] Built target edist_utest -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 [ 74%] Built target tldevel -/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 [ 74%] Built target bpm_utest -/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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -[ 74%] Built target task_utest -[ 74%] Built target alphabet_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-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-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build -make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -[ 75%] Linking C static library libkalign_static.a -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake -[ 77%] Linking C static library libkalign.a +make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' +[ 75%] Linking C static library libkalign.a +[ 77%] Linking C static library libkalign_static.a cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 -/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +cd /build/kalign-3.3.5/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 /usr/bin/ar qc libkalign.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -/usr/bin/ranlib libkalign_static.a +/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a +/usr/bin/ranlib libkalign_static.a make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -[ 77%] Built target kalign_static -make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend -make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/src /build/kalign-3.3.5/obj-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/src /build/kalign-3.3.5/obj-x86_64-linux-gnu/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake --color= [ 77%] Built target kalign -make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend -make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' -cd /build/kalign-3.3.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/tests /build/kalign-3.3.5/obj-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/tests /build/kalign-3.3.5/obj-x86_64-linux-gnu/tests/CMakeFiles/largebench.dir/DependInfo.cmake --color= make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend +[ 77%] Built target kalign_static make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' cd /build/kalign-3.3.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/src /build/kalign-3.3.5/obj-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/src /build/kalign-3.3.5/obj-x86_64-linux-gnu/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake --color= @@ -908,73 +945,79 @@ cd /build/kalign-3.3.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/tests /build/kalign-3.3.5/obj-x86_64-linux-gnu /build/kalign-3.3.5/obj-x86_64-linux-gnu/tests 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/build/kalign-3.3.5/lib/src/esl_stopwatch.c +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 20%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -: warning: ISO C99 requires whitespace after the macro name -[ 21%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 22%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/kalign-3.3.5/lib/src/test.c +[ 14%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c +[ 15%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +[ 17%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o : warning: ISO C99 requires whitespace after the macro name +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +[ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o : warning: ISO C99 requires whitespace after the macro name +[ 20%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c : warning: ISO C99 requires whitespace after the macro name -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/kalign-3.3.5/lib/src/test.c +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c : warning: ISO C99 requires whitespace after the macro name +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +[ 21%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name -[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +/build/kalign-3.3.5/lib/src/euclidean_dist.c: In function 'main': +/build/kalign-3.3.5/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] + 58 | float d2; + | ^~ +[ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 25%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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CMakeFiles/task_utest.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c -: warning: ISO C99 requires whitespace after the macro name -[ 28%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c -: warning: ISO C99 requires whitespace after the macro name -[ 30%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 /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); @@ -1112,52 +1144,52 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -: warning: ISO C99 requires whitespace after the macro name -[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name -[ 34%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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-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 -msse4.1 -DHAVE_SSE4.1 -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 cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/kalign-3.3.5/lib/src/msa_alloc.c -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o : warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name +[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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/alphabet_utest.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat 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/build/kalign-3.3.5/lib/src/msa_io.c -[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o : warning: ISO C99 requires whitespace after the macro name +[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -c /build/kalign-3.3.5/lib/src/msa_io.c +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/lib -I/build/kalign-3.3.5/lib/include -g -O2 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42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o +[ 40%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +: warning: ISO C99 requires whitespace after the macro name +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 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Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 -: warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name -: warning: ISO C99 requires whitespace after the macro name -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 /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); @@ -1165,16 +1197,27 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +: warning: ISO C99 requires whitespace after the macro name +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +: warning: ISO C99 requires whitespace after the macro name +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +[ 50%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +: warning: ISO C99 requires whitespace after the macro name : warning: ISO C99 requires whitespace after the macro name [ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +: warning: ISO C99 requires whitespace after the macro name [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name -: warning: ISO C99 requires whitespace after the macro name [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 [ 57%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o @@ -1183,169 +1226,179 @@ : warning: ISO C99 requires whitespace after the macro name [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/kalign-3.3.5/lib/src/aln_mem.c -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.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 -msse4.1 -DHAVE_SSE4.1 -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 +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_seqprofile.c : warning: ISO C99 requires whitespace after the macro name -[ 65%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +make[4]: Leaving directory '/build/kalign-3.3.5/obj-sse4.1' +[ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_profileprofile.c -[ 67%] Linking C executable edist_utest +[ 68%] Linking C executable edist_utest cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 -[ 68%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o : warning: ISO C99 requires whitespace after the macro name -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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%] Built target task_utest +[ 70%] Linking C executable bpm_utest /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 -msse4.1 -DHAVE_SSE4.1 -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 -[ 70%] Linking C executable alphabet_utest -cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 -[ 71%] Linking C executable bpm_utest +[ 71%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-sse4.1/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 -msse4.1 -DHAVE_SSE4.1 -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 +/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 -msse4.1 -DHAVE_SSE4.1 -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 : warning: ISO C99 requires whitespace after the macro name +make[4]: Leaving directory '/build/kalign-3.3.5/obj-sse4.1' +make[4]: Leaving directory '/build/kalign-3.3.5/obj-sse4.1' +[ 71%] Built target edist_utest +[ 71%] Built target bpm_utest [ 72%] Linking C static library libtldevel.a cd /build/kalign-3.3.5/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -/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 -msse4.1 -DHAVE_SSE4.1 -fPIC -Wl,-z,relro -Wl,-z,now -rdynamic 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lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' cd /build/kalign-3.3.5/obj-avx && /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-avx /build/kalign-3.3.5/obj-avx/lib /build/kalign-3.3.5/obj-avx/lib/CMakeFiles/task_utest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' 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-avx' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -make -f 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-o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/kalign-3.3.5/lib/src/msa_cmp.c -[ 41%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 -[ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 34%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 37%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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); @@ -1493,16 +1522,10 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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-avx/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 -mavx -DHAVE_AVX -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 -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 38%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.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); @@ -1510,6 +1533,26 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 44%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 45%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 48%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +/build/kalign-3.3.5/lib/src/euclidean_dist.c: In function 'main': +/build/kalign-3.3.5/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] + 58 | float d2; + | ^~ +[ 51%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 [ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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_wrap.c.o @@ -1518,64 +1561,59 @@ cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 [ 57%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 +[ 58%] Linking C executable edist_utest +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_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 -mavx -DHAVE_AVX -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 +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/kalign-3.3.5/lib/src/aln_mem.c -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +[ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/kalign-3.3.5/lib/src/aln_controller.c +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -MF 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-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 -mavx -DHAVE_AVX -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/kalign-3.3.5/lib/src/aln_controller.c -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' +[ 65%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -fPIC -Wall -Wextra -pedantic -fopenmp 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lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +[ 67%] Built target edist_utest +[ 68%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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-avx/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 -mavx -DHAVE_AVX -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 -[ 70%] Linking C executable alphabet_utest -cd /build/kalign-3.3.5/obj-avx/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 -mavx -DHAVE_AVX -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 -[ 71%] Linking C static library libtldevel.a -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -[ 72%] Linking C executable task_utest +[ 70%] Linking C executable task_utest cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' /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 -mavx -DHAVE_AVX -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-avx' +[ 71%] Linking C static library libtldevel.a +cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 -[ 72%] Built target bpm_utest -[ 72%] Built target alphabet_utest +[ 72%] Linking C executable alphabet_utest +cd /build/kalign-3.3.5/obj-avx/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 +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' /usr/bin/ranlib libtldevel.a +/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 -mavx -DHAVE_AVX -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-avx' +[ 72%] Built target task_utest [ 72%] Built target tldevel make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -[ 74%] Linking C executable edist_utest -cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_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 -mavx -DHAVE_AVX -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 -[ 74%] Built target task_utest -make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -[ 74%] Built target edist_utest +[ 72%] Built target alphabet_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -[ 74%] Built target kalign_OBJ +[ 72%] 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 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lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' -[ 75%] Linking C static library libkalign.a +make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' +[ 74%] Linking C static library libkalign.a +[ 75%] Linking C static library libkalign_static.a cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -[ 77%] Linking C static library libkalign_static.a cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/kalign-3.3.5/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 @@ -1585,83 +1623,88 @@ /usr/bin/ranlib libkalign_static.a make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' -[ 77%] Built target kalign -[ 77%] Built target kalign_static +[ 75%] Built target kalign make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend +[ 75%] Built target kalign_static make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' cd /build/kalign-3.3.5/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/src /build/kalign-3.3.5/obj-avx /build/kalign-3.3.5/obj-avx/src /build/kalign-3.3.5/obj-avx/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake --color= make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend +make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-avx' cd /build/kalign-3.3.5/obj-avx && /usr/bin/cmake -E cmake_depends "Unix 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -mavx -DHAVE_AVX -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' +[ 94%] Built target kalign_cmp_test +[ 94%] Built target kalign_io_test +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' +[ 94%] Built target kalign_lib_test [ 95%] Linking C executable kalignfmt cd /build/kalign-3.3.5/obj-avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.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 -mavx -DHAVE_AVX -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic @@ -1672,6 +1715,10 @@ /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 -mavx -DHAVE_AVX -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic [ 98%] Linking C executable largebench cd /build/kalign-3.3.5/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.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 -mavx -DHAVE_AVX -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-avx' +[ 98%] Built target kalign-bin +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' /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] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", @@ -1685,10 +1732,6 @@ /build/kalign-3.3.5/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 -mavx -DHAVE_AVX -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-avx' -[ 98%] Built target kalign-bin -make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx' [ 98%] Built target largebench [100%] Linking CXX executable kaligncpp cd /build/kalign-3.3.5/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 @@ -1699,7 +1742,7 @@ /usr/bin/cmake -E cmake_progress_start /build/kalign-3.3.5/obj-avx/CMakeFiles 0 make[2]: Leaving directory '/build/kalign-3.3.5/obj-avx' dh_auto_build --builddirectory obj-avx2 - cd obj-avx2 && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-avx2 && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/kalign-3.3.5/obj-avx2' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kalign-3.3.5/obj-avx2/CMakeFiles /build/kalign-3.3.5/obj-avx2//CMakeFiles/progress.marks @@ -1708,83 +1751,87 @@ 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 -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= +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-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/tldevel.dir/DependInfo.cmake --color= -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake --color= -make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake --color= +cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' +cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake --color= -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-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/task_utest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build -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-avx2' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build +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-avx2' make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' 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-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 -mavx2 -DHAVE_AVX2 -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 +[ 8%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +[ 10%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +[ 11%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +[ 14%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC 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/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c +cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/kalign-3.3.5/lib/src/tldevel.c +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/kalign-3.3.5/lib/src/tlmisc.c cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 20%] 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lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 22%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 24%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 25%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/kalign-3.3.5/obj-avx2/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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -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/msa_alloc.c.o +[ 27%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/kalign-3.3.5/lib/src/msa_alloc.c -[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 27%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 [ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 30%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 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/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o +cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 /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); @@ -1792,23 +1839,15 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -[ 34%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o +[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 37%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 38%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 40%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c -[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +[ 38%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/lib -I/build/kalign-3.3.5/lib/include -g -O2 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CMakeFiles/kalign_OBJ.dir/src/task.c.o -c /build/kalign-3.3.5/lib/src/task.c -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 /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] @@ -1817,71 +1856,70 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 42%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +[ 47%] Linking C executable task_utest +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 -[ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +[ 48%] Built target task_utest +[ 50%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/kalign-3.3.5/lib/src/tlrng.c +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra 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/build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/kalign-3.3.5/lib/src/aln_mem.c -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp 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CMakeFiles/tldevel.dir/link.txt --verbose=1 +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +/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 +cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/kalign-3.3.5/lib/src/aln_mem.c [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/kalign-3.3.5/lib/src/aln_setup.c +/usr/bin/ranlib libtldevel.a [ 61%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wall -Wextra -pedantic -fopenmp -std=gnu11 -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF 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lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/kalign-3.3.5/lib/src/alphabet.c +[ 65%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -DUTEST_EDIST -Wall -Wextra -pedantic -std=gnu11 -MD -MT lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/kalign-3.3.5/lib/src/euclidean_dist.c +[ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/lib -I/build/kalign-3.3.5/lib/include -g -O2 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-MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/kalign-3.3.5/lib/src/aln_profileprofile.c cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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 alphabet_utest -cd /build/kalign-3.3.5/obj-avx2/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 -mavx2 -DHAVE_AVX2 -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-avx2' -[ 70%] Linking C static library libtldevel.a -cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -[ 70%] Built target alphabet_utest -cd /build/kalign-3.3.5/obj-avx2/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 -[ 71%] Linking C executable task_utest -cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script 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--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 -mavx2 -DHAVE_AVX2 -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 make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' -[ 74%] Built target edist_utest +[ 72%] Built target alphabet_utest make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' -[ 74%] Built target kalign_OBJ +[ 72%] 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-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/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-avx2' cd /build/kalign-3.3.5/obj-avx2 && /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-avx2 /build/kalign-3.3.5/obj-avx2/lib /build/kalign-3.3.5/obj-avx2/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' @@ -1890,107 +1928,112 @@ make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -[ 75%] Linking C static library libkalign.a +[ 74%] Linking C static library libkalign.a cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -[ 77%] Linking C static library libkalign_static.a +[ 75%] Linking C static library libkalign_static.a cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake -cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 -/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +cd /build/kalign-3.3.5/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 /usr/bin/ar qc libkalign.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -/usr/bin/ranlib libkalign_static.a /usr/bin/ranlib libkalign.a +/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' +/usr/bin/ranlib libkalign_static.a make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' -[ 77%] Built target kalign_static -make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend -[ 77%] Built target kalign -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -cd /build/kalign-3.3.5/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/src /build/kalign-3.3.5/obj-avx2 /build/kalign-3.3.5/obj-avx2/src /build/kalign-3.3.5/obj-avx2/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake --color= -make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend -make[4]: Entering directory '/build/kalign-3.3.5/obj-avx2' -cd /build/kalign-3.3.5/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kalign-3.3.5 /build/kalign-3.3.5/tests /build/kalign-3.3.5/obj-avx2 /build/kalign-3.3.5/obj-avx2/tests /build/kalign-3.3.5/obj-avx2/tests/CMakeFiles/largebench.dir/DependInfo.cmake --color= +[ 75%] Built target kalign make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend +make -f 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-I/build/kalign-3.3.5/lib/src -I/build/kalign-3.3.5/lib/include -I/build/kalign-3.3.5/obj-avx2/lib -g -O2 -ffile-prefix-map=/build/kalign-3.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wall -Wextra -pedantic -std=gnu11 -MD -MT tests/CMakeFiles/largebench.dir/large_benchmark.c.o -MF CMakeFiles/largebench.dir/large_benchmark.c.o.d -o CMakeFiles/largebench.dir/large_benchmark.c.o -c /build/kalign-3.3.5/tests/large_benchmark.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 -mavx2 -DHAVE_AVX2 -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 +make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' +[ 91%] Linking C executable kalign_io_test cd /build/kalign-3.3.5/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 -[ 94%] Linking C executable kalign_cmp_test -/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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic +[ 92%] Linking C executable kalign_cmp_test cd /build/kalign-3.3.5/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 +[ 92%] Built target edist_utest +[ 94%] Linking C executable kalign_lib_test /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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -rdynamic 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make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' [ 94%] Built target kalign_io_test +[ 94%] Built target kalign_cmp_test make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' [ 94%] Built target kalign_lib_test [ 95%] Linking C executable kalignfmt cd /build/kalign-3.3.5/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -[ 95%] Built target kalign_cmp_test +/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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic [ 97%] Linking C executable kalign cd /build/kalign-3.3.5/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic /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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic -[ 98%] Linking C executable largebench make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' +[ 97%] Built target kalignfmt +[ 98%] Linking C executable largebench cd /build/kalign-3.3.5/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 -[ 98%] Built target kalignfmt -/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 -mavx2 -DHAVE_AVX2 -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-avx2' +/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 -mavx2 -DHAVE_AVX2 -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 [ 98%] Built target kalign-bin make[4]: Leaving directory '/build/kalign-3.3.5/obj-avx2' [ 98%] Built target largebench @@ -2019,10 +2062,10 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/kalign-3.3.5' dh_auto_test - cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 + cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 make[2]: Entering directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j16 +/usr/bin/ctest --force-new-ctest-process --verbose -j15 UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/kalign-3.3.5/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -2101,7 +2144,7 @@ 11: Working Directory: /build/kalign-3.3.5/tests 11: Test timeout computed to be: 1500 1: LEN: 256 -1: [2024-05-21 21:41:55] : LOG : Testing correctness of serial bpm. +1: [2023-04-20 17:20:26] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -2234,63 +2277,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2024-05-21 21:41:55] : LOG : Check for correctness. -3: [2024-05-21 21:41:55] : LOG : Timing serial -3: [2024-05-21 21:41:55] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -4: 27 789 117 466 571 -4: 541 263 246 586 92 -4: 695 446 77 304 954 -4: 780 28 694 473 461 -4: 136 461 263 552 479 -4: 358 770 903 536 370 -4: 565 367 459 890 945 -4: 884 51 687 810 736 -4: 399 650 501 910 252 -4: 173 387 496 201 131 -4: 142 918 650 36 991 -4: 166 104 212 628 30 -4: 526 392 765 295 152 -4: 879 726 195 921 443 -4: 52 898 302 528 865 -4: 582 897 317 844 749 -4: 827 617 328 840 684 -4: 302 342 473 787 289 -4: 200 803 630 423 614 -4: 643 785 556 981 15 -4: 278 79 151 215 63 -4: 53 523 46 370 363 -4: 533 32 551 384 670 -4: 22 858 997 311 432 -4: 357 256 515 748 114 -4: 821 791 413 338 384 -4: 133 875 880 751 336 -4: 473 752 859 988 709 -4: 421 111 552 471 335 -4: 845 453 329 370 661 -4: 70 736 960 462 471 -4: 804 476 634 146 561 -4: 436 840 384 764 409 -4: 617 20 203 387 498 -4: 579 289 32 674 465 -4: 590 651 798 571 185 -4: 217 551 438 26 318 -4: 49 539 953 969 367 -4: 232 640 219 684 91 -4: 329 644 773 408 170 -4: 862 190 246 29 29 -4: 46 534 443 919 360 -4: 54 745 230 274 157 -4: 800 962 869 481 560 -4: 952 620 657 497 91 -4: 440 534 17 588 682 -4: 833 492 304 549 868 -4: 361 688 844 287 946 -4: 553 522 519 445 291 -4: 601 646 384 471 290 -4: 525 672 843 620 971 -4: 637 22 268 77 911 -4: 860 962 133 688 886 -4: 780 615 180 914 228 +3: [2023-04-20 17:20:26] : LOG : Check for correctness. +3: [2023-04-20 17:20:26] : LOG : Timing serial +3: [2023-04-20 17:20:26] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +4: 430 927 128 628 450 +4: 54 487 689 550 684 +4: 113 245 150 628 370 +4: 364 73 281 120 937 +4: 398 932 889 841 175 +4: 682 872 544 394 195 +4: 814 329 554 951 813 +4: 145 946 969 725 677 +4: 165 296 48 82 962 +4: 143 855 585 284 963 +4: 929 109 529 422 771 +4: 821 708 379 692 704 +4: 827 541 687 608 622 +4: 286 497 910 783 483 +4: 820 905 350 769 605 +4: 987 895 191 282 113 +4: 602 63 459 690 92 +4: 467 548 266 759 71 +4: 857 28 881 997 305 +4: 387 438 992 217 607 +4: 250 508 74 407 606 +4: 605 389 92 164 888 +4: 483 946 394 140 745 +4: 431 700 429 231 626 +4: 521 771 672 235 15 +4: 75 506 390 560 608 +4: 911 805 415 471 449 +4: 923 157 467 695 833 +4: 431 770 161 931 9 +4: 664 301 536 100 492 +4: 768 733 511 779 210 +4: 618 325 205 125 892 +4: 332 483 47 305 798 +4: 804 633 238 900 353 +4: 624 146 921 211 243 +4: 269 810 921 291 579 +4: 485 403 34 618 655 +4: 431 655 504 886 304 +4: 207 99 776 730 173 +4: 189 10 724 840 34 +4: 6 549 43 417 730 +4: 881 272 401 925 886 +4: 17 827 658 293 379 +4: 676 969 517 456 483 +4: 981 194 537 14 700 +4: 87 8 886 440 467 +4: 808 260 203 741 853 +4: 276 624 846 738 28 +4: 900 292 572 398 783 +4: 724 160 618 130 780 +4: 971 794 915 295 728 +4: 267 527 143 230 813 +4: 943 882 20 578 169 +4: 598 656 467 90 889 5: Aligned: 5: ------GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP---------- 5: ------------MQDRVKRPMNAFIVWSRDQRRKMAL-EN-PRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK---YPNYKYRP- @@ -2312,15 +2355,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -6: [2024-05-21 21:41:55] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. -6: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances -6: [2024-05-21 21:41:55] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -6: [2024-05-21 21:41:55] : LOG : Building guide tree. -6: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:41:55] : LOG : Aligning -6: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +6: [2023-04-20 17:20:26] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. +6: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances +6: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:26] : LOG : Building guide tree. +6: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:26] : LOG : Aligning +6: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2349,15 +2392,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -7: [2024-05-21 21:41:55] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. -7: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances -7: [2024-05-21 21:41:55] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:41:55] : LOG : Building guide tree. -7: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:41:55] : LOG : Aligning -7: [2024-05-21 21:41:55] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +7: [2023-04-20 17:20:26] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. +7: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances +7: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:26] : LOG : Building guide tree. +7: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:26] : LOG : Aligning +7: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2386,15 +2429,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -8: [2024-05-21 21:41:55] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. -8: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances -8: [2024-05-21 21:41:55] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:41:55] : LOG : Building guide tree. -8: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:41:55] : LOG : Aligning -8: [2024-05-21 21:41:55] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +8: [2023-04-20 17:20:26] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. +8: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances +8: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:26] : LOG : Building guide tree. +8: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:26] : LOG : Aligning +8: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2435,46 +2478,10 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -9: [2024-05-21 21:41:55] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -9: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances -9: [2024-05-21 21:41:55] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -9: [2024-05-21 21:41:55] : LOG : Building guide tree. -9: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:41:55] : LOG : Aligning - 1/11 Test #2: alphabet_utest ................... Passed 0.07 sec - 2/11 Test #3: edist_utest ...................... Passed 0.07 sec - 3/11 Test #4: task_utest ....................... Passed 0.06 sec - 4/11 Test #5: C++Lib ........................... Passed 0.06 sec - 5/11 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.05 sec - 6/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.05 sec - 7/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.04 sec -9: [2024-05-21 21:41:55] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -9: >1al2_ad -9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -9: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -9: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -9: KA--- -9: >1bbt_ac -9: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -9: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -9: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -9: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -9: ----- -9: >1bev_ac -9: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -9: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -9: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -9: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -9: TAILQ -9: >1mec_ac -9: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -9: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -9: Q---- +9: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +9: [2023-04-20 17:20:26] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +9: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances 10: 10: Kalign (3.3.5) 10: @@ -2491,38 +2498,22 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -10: [2024-05-21 21:41:55] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -10: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances -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: [2024-05-21 21:41:55] : LOG : Detected protein sequences. -11: [2024-05-21 21:41:55] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. -11: [2024-05-21 21:41:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2024-05-21 21:41:55] : LOG : Calculating pairwise distances - 8/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.03 sec -10: [2024-05-21 21:41:55] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 -10: [2024-05-21 21:41:55] : LOG : Building guide tree. -11: [2024-05-21 21:41:55] : LOG : CPU Time: 0.06u 00:00:00.05 Elapsed: 00:00:00.00 -11: [2024-05-21 21:41:55] : LOG : Building guide tree. -10: [2024-05-21 21:41:55] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -10: [2024-05-21 21:41:55] : LOG : Aligning -10: [2024-05-21 21:41:55] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +10: [2023-04-20 17:20:26] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +10: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances +10: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:26] : LOG : Building guide tree. +10: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:26] : LOG : Aligning + 1/11 Test #2: alphabet_utest ................... Passed 0.02 sec + 2/11 Test #3: edist_utest ...................... Passed 0.02 sec + 3/11 Test #4: task_utest ....................... Passed 0.02 sec + 4/11 Test #5: C++Lib ........................... Passed 0.02 sec + 5/11 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.02 sec + 6/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec + 7/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec +10: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2547,16 +2538,62 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- - 9/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.07 sec -1: 0 0 0 0 -1: 0 0 0 0 -1: 0 0 0 0 -1: 0 0 0 0 -1: -1: [2024-05-21 21:41:55] : LOG : Testing correctness of AVX bpm. -11: [2024-05-21 21:41:55] : LOG : CPU Time: 0.10u 00:00:00.09 Elapsed: 00:00:00.00 -11: [2024-05-21 21:41:55] : LOG : Aligning -11: [2024-05-21 21:41:55] : LOG : CPU Time: 0.09u 00:00:00.09 Elapsed: 00:00:00.00 +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: [2023-04-20 17:20:26] : LOG : Detected protein sequences. +11: [2023-04-20 17:20:26] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. +11: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:26] : LOG : Calculating pairwise distances + 8/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec +11: [2023-04-20 17:20:26] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:26] : LOG : Building guide tree. +9: [2023-04-20 17:20:26] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:26] : LOG : Building guide tree. +9: [2023-04-20 17:20:26] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:26] : LOG : Aligning +9: [2023-04-20 17:20:26] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +9: >1al2_ad +9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS +9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF +9: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ +9: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ +9: KA--- +9: >1bbt_ac +9: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- +9: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF +9: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY +9: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- +9: ----- +9: >1bev_ac +9: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N +9: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC +9: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG +9: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ +9: TAILQ +9: >1mec_ac +9: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- +9: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF +9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM +9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP +9: Q---- + 9/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.03 sec +11: [2023-04-20 17:20:26] : LOG : CPU Time: 0.08u 00:00:00.08 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:26] : LOG : Aligning +11: [2023-04-20 17:20:26] : LOG : CPU Time: 0.07u 00:00:00.07 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -2865,23 +2902,29 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -10/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.12 sec +10/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.09 sec +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: +1: [2023-04-20 17:20:26] : LOG : Testing correctness of AVX bpm. 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: [2024-05-21 21:42:00] : LOG : Timing DYN 256 -1: [2024-05-21 21:42:02] : LOG : 1.617024 - dyn -1: [2024-05-21 21:42:02] : LOG : 0.000000 - bpm -1: [2024-05-21 21:42:02] : LOG : 0.185869 - bpm_block2 -1: [2024-05-21 21:42:02] : LOG : 0.194446 - bpm_block -11/11 Test #1: bpm_utest ........................ Passed 7.58 sec +1: [2023-04-20 17:20:31] : LOG : Timing DYN 256 +1: [2023-04-20 17:20:34] : LOG : 1.757801 - dyn +1: [2023-04-20 17:20:34] : LOG : 0.000000 - bpm +1: [2023-04-20 17:20:34] : LOG : 0.206632 - bpm_block2 +1: [2023-04-20 17:20:34] : LOG : 0.191153 - bpm_block +11/11 Test #1: bpm_utest ........................ Passed 8.03 sec 100% tests passed, 0 tests failed out of 11 -Total Test time (real) = 7.58 sec +Total Test time (real) = 8.03 sec make[2]: Leaving directory '/build/kalign-3.3.5/obj-x86_64-linux-gnu' set -e ; for SIMD in avx2 avx sse4.1 ; do \ if lscpu | grep -q ${SIMD} ; then \ @@ -2908,25 +2951,25 @@ 1: Working Directory: /build/kalign-3.3.5/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2024-05-21 21:42:02] : LOG : Testing correctness of serial bpm. +1: [2023-04-20 17:20:34] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2024-05-21 21:42:02] : LOG : Testing correctness of AVX bpm. +1: [2023-04-20 17:20:34] : LOG : Testing correctness of AVX bpm. 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: [2024-05-21 21:42:08] : LOG : Timing DYN 256 -1: [2024-05-21 21:42:11] : LOG : 1.714962 - dyn -1: [2024-05-21 21:42:11] : LOG : 0.000000 - bpm -1: [2024-05-21 21:42:11] : LOG : 0.204183 - bpm_block2 -1: [2024-05-21 21:42:11] : LOG : 0.203386 - bpm_block - 1/11 Test #1: bpm_utest ........................ Passed 8.34 sec +1: [2023-04-20 17:20:39] : LOG : Timing DYN 256 +1: [2023-04-20 17:20:42] : LOG : 1.746022 - dyn +1: [2023-04-20 17:20:42] : LOG : 0.000000 - bpm +1: [2023-04-20 17:20:42] : LOG : 0.192094 - bpm_block2 +1: [2023-04-20 17:20:42] : LOG : 0.192526 - bpm_block + 1/11 Test #1: bpm_utest ........................ Passed 7.91 sec test 2 Start 2: alphabet_utest @@ -3065,77 +3108,77 @@ 2: ] -1 2: ^ -1 2: _ -1 - 2/11 Test #2: alphabet_utest ................... Passed 0.01 sec + 2/11 Test #2: alphabet_utest ................... Passed 0.00 sec test 3 Start 3: edist_utest 3: Test command: /build/kalign-3.3.5/obj-avx/lib/edist_utest 3: Working Directory: /build/kalign-3.3.5/obj-avx/lib 3: Test timeout computed to be: 1500 -3: [2024-05-21 21:42:11] : LOG : Check for correctness. -3: [2024-05-21 21:42:11] : LOG : Timing serial -3: [2024-05-21 21:42:11] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 - 3/11 Test #3: edist_utest ...................... Passed 0.02 sec +3: [2023-04-20 17:20:42] : LOG : Check for correctness. +3: [2023-04-20 17:20:42] : LOG : Timing serial +3: [2023-04-20 17:20:42] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 + 3/11 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest 4: Test command: /build/kalign-3.3.5/obj-avx/lib/task_utest 4: Working Directory: /build/kalign-3.3.5/obj-avx/lib 4: Test timeout computed to be: 1500 -4: 829 583 912 509 956 -4: 115 355 851 73 980 -4: 764 721 458 122 993 -4: 28 461 647 4 429 -4: 895 430 579 772 769 -4: 614 759 605 817 682 -4: 885 296 483 70 767 -4: 231 201 499 742 880 -4: 528 866 610 656 995 -4: 954 882 183 207 836 -4: 519 198 499 256 19 -4: 66 270 618 267 197 -4: 142 697 240 237 220 -4: 56 523 724 906 308 -4: 510 398 102 324 756 -4: 537 337 517 514 110 -4: 501 67 608 872 557 -4: 280 653 694 631 189 -4: 625 540 837 835 274 -4: 206 376 617 413 890 -4: 867 30 757 50 213 -4: 775 286 482 294 23 -4: 271 802 96 92 564 -4: 889 57 839 466 620 -4: 489 370 467 189 42 -4: 860 779 415 722 838 -4: 595 122 365 908 422 -4: 470 524 697 93 384 -4: 209 36 761 735 943 -4: 633 796 554 59 75 -4: 839 830 464 656 858 -4: 157 81 256 121 3 -4: 900 597 762 299 590 -4: 320 670 384 156 654 -4: 998 712 465 680 878 -4: 412 579 671 188 307 -4: 577 933 618 788 173 -4: 238 496 612 196 350 -4: 135 377 133 312 712 -4: 629 307 761 800 527 -4: 345 72 118 732 834 -4: 375 279 823 598 174 -4: 388 833 333 920 829 -4: 589 108 878 260 875 -4: 448 41 518 701 225 -4: 348 990 189 524 177 -4: 251 914 723 119 774 -4: 177 632 938 509 828 -4: 980 671 251 226 554 -4: 908 905 658 386 101 -4: 389 89 333 316 623 -4: 460 477 254 437 430 -4: 683 618 708 329 928 -4: 69 546 11 390 624 +4: 103 730 254 231 406 +4: 521 627 454 471 698 +4: 600 574 145 620 465 +4: 673 246 570 143 759 +4: 932 317 730 283 838 +4: 891 615 635 579 408 +4: 215 175 739 37 347 +4: 582 814 447 132 486 +4: 725 322 121 639 882 +4: 574 891 344 499 873 +4: 196 842 92 353 314 +4: 877 964 336 394 679 +4: 130 926 564 474 343 +4: 253 861 980 59 625 +4: 135 29 937 761 710 +4: 763 792 311 962 786 +4: 746 674 870 362 129 +4: 879 24 613 675 902 +4: 922 821 142 547 759 +4: 813 620 437 225 901 +4: 439 788 153 388 998 +4: 632 468 233 280 932 +4: 154 904 623 488 83 +4: 966 522 813 384 950 +4: 371 52 275 625 63 +4: 4 600 707 666 15 +4: 571 409 63 464 173 +4: 873 920 47 410 220 +4: 181 46 890 76 872 +4: 390 594 675 740 482 +4: 851 16 493 220 864 +4: 364 324 446 773 684 +4: 381 997 96 707 553 +4: 8 858 505 998 664 +4: 824 148 581 718 174 +4: 251 657 774 565 438 +4: 736 277 799 485 31 +4: 690 959 568 696 811 +4: 845 727 760 642 800 +4: 726 154 559 922 898 +4: 452 589 438 432 705 +4: 584 371 819 724 132 +4: 539 951 251 701 343 +4: 585 222 806 619 514 +4: 591 183 11 791 553 +4: 107 619 864 357 985 +4: 958 237 842 523 946 +4: 867 381 52 980 861 +4: 643 230 226 756 937 +4: 232 253 284 179 980 +4: 386 263 466 902 374 +4: 587 750 273 513 319 +4: 546 702 109 896 171 +4: 80 633 627 968 957 4/11 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -3148,7 +3191,7 @@ 5: ------------MQDRVKRPMNAFIVWSRDQRRKMAL-EN-PRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK---YPNYKYRP- 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS--N-L-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNA--- 5: ----------------MHIKKPLNAFMLYMKEMRANV-VA-ESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY - 5/11 Test #5: C++Lib ........................... Passed 0.01 sec + 5/11 Test #5: C++Lib ........................... Passed 0.00 sec test 6 Start 6: kalign_itest_BB11001.tfa @@ -3171,15 +3214,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -6: [2024-05-21 21:42:11] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. -6: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -6: [2024-05-21 21:42:11] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:11] : LOG : Building guide tree. -6: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:11] : LOG : Aligning -6: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +6: [2023-04-20 17:20:42] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. +6: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +6: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:42] : LOG : Building guide tree. +6: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:42] : LOG : Aligning +6: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3215,15 +3258,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -7: [2024-05-21 21:42:11] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. -7: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -7: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:11] : LOG : Building guide tree. -7: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:11] : LOG : Aligning -7: [2024-05-21 21:42:11] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +7: [2023-04-20 17:20:42] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. +7: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +7: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:42] : LOG : Building guide tree. +7: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:42] : LOG : Aligning +7: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3236,7 +3279,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 7/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.02 sec + 7/11 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec test 8 Start 8: kalign_itest_BB12006.msf @@ -3259,15 +3302,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -8: [2024-05-21 21:42:11] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. -8: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -8: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:11] : LOG : Building guide tree. -8: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:11] : LOG : Aligning -8: [2024-05-21 21:42:11] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +8: [2023-04-20 17:20:42] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. +8: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +8: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:42] : LOG : Building guide tree. +8: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:42] : LOG : Aligning +8: [2023-04-20 17:20:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3292,7 +3335,7 @@ 8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 8: Q---- - 8/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.02 sec + 8/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa @@ -3315,15 +3358,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -9: [2024-05-21 21:42:11] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -9: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -9: [2024-05-21 21:42:11] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:11] : LOG : Building guide tree. -9: [2024-05-21 21:42:11] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:11] : LOG : Aligning -9: [2024-05-21 21:42:11] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +9: [2023-04-20 17:20:42] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +9: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +9: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:42] : LOG : Building guide tree. +9: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:42] : LOG : Aligning +9: [2023-04-20 17:20:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3348,7 +3391,7 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- - 9/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.04 sec + 9/11 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec test 10 Start 10: kalign_itest_BB30014.msf @@ -3371,15 +3414,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -10: [2024-05-21 21:42:11] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -10: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -10: [2024-05-21 21:42:11] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:11] : LOG : Building guide tree. -10: [2024-05-21 21:42:11] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:11] : LOG : Aligning -10: [2024-05-21 21:42:11] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +10: [2023-04-20 17:20:42] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +10: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +10: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:42] : LOG : Building guide tree. +10: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:42] : LOG : Aligning +10: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3404,7 +3447,7 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- -10/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.06 sec +10/11 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec test 11 Start 11: kalign_itest_BB30014.tfa @@ -3427,15 +3470,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2024-05-21 21:42:11] : LOG : Detected protein sequences. -11: [2024-05-21 21:42:11] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. -11: [2024-05-21 21:42:11] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:11] : LOG : Calculating pairwise distances -11: [2024-05-21 21:42:11] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:11] : LOG : Building guide tree. -11: [2024-05-21 21:42:11] : LOG : CPU Time: 0.10u 00:00:00.10 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:11] : LOG : Aligning -11: [2024-05-21 21:42:11] : LOG : CPU Time: 0.08u 00:00:00.08 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:42] : LOG : Detected protein sequences. +11: [2023-04-20 17:20:42] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. +11: [2023-04-20 17:20:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:42] : LOG : Calculating pairwise distances +11: [2023-04-20 17:20:42] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:42] : LOG : Building guide tree. +11: [2023-04-20 17:20:42] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:42] : LOG : Aligning +11: [2023-04-20 17:20:42] : LOG : CPU Time: 0.07u 00:00:00.06 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -3744,11 +3787,11 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -11/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.13 sec +11/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.08 sec 100% tests passed, 0 tests failed out of 11 -Total Test time (real) = 8.67 sec +Total Test time (real) = 8.06 sec UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/kalign-3.3.5/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/kalign-3.3.5/obj-sse4.1/DartConfiguration.tcl @@ -3767,25 +3810,25 @@ 1: Working Directory: /build/kalign-3.3.5/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2024-05-21 21:42:11] : LOG : Testing correctness of serial bpm. +1: [2023-04-20 17:20:42] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2024-05-21 21:42:11] : LOG : Testing correctness of AVX bpm. +1: [2023-04-20 17:20:42] : LOG : Testing correctness of AVX bpm. 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: [2024-05-21 21:42:17] : LOG : Timing DYN 256 -1: [2024-05-21 21:42:19] : LOG : 1.694913 - dyn -1: [2024-05-21 21:42:19] : LOG : 0.000000 - bpm -1: [2024-05-21 21:42:19] : LOG : 0.204223 - bpm_block2 -1: [2024-05-21 21:42:19] : LOG : 0.198647 - bpm_block - 1/11 Test #1: bpm_utest ........................ Passed 7.81 sec +1: [2023-04-20 17:20:48] : LOG : Timing DYN 256 +1: [2023-04-20 17:20:50] : LOG : 1.750629 - dyn +1: [2023-04-20 17:20:50] : LOG : 0.000000 - bpm +1: [2023-04-20 17:20:50] : LOG : 0.208283 - bpm_block2 +1: [2023-04-20 17:20:50] : LOG : 0.214998 - bpm_block + 1/11 Test #1: bpm_utest ........................ Passed 8.06 sec test 2 Start 2: alphabet_utest @@ -3931,9 +3974,9 @@ 3: Test command: /build/kalign-3.3.5/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/kalign-3.3.5/obj-sse4.1/lib 3: Test timeout computed to be: 1500 -3: [2024-05-21 21:42:19] : LOG : Check for correctness. -3: [2024-05-21 21:42:19] : LOG : Timing serial -3: [2024-05-21 21:42:19] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +3: [2023-04-20 17:20:50] : LOG : Check for correctness. +3: [2023-04-20 17:20:50] : LOG : Timing serial +3: [2023-04-20 17:20:50] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 3/11 Test #3: edist_utest ...................... Passed 0.02 sec test 4 Start 4: task_utest @@ -3941,60 +3984,60 @@ 4: Test command: /build/kalign-3.3.5/obj-sse4.1/lib/task_utest 4: Working Directory: /build/kalign-3.3.5/obj-sse4.1/lib 4: Test timeout computed to be: 1500 -4: 332 135 393 452 385 -4: 226 605 417 881 545 -4: 562 322 489 502 957 -4: 834 484 115 393 42 -4: 832 85 153 704 998 -4: 501 442 250 726 829 -4: 583 787 320 526 562 -4: 973 560 601 51 536 -4: 142 332 360 716 182 -4: 236 555 460 428 171 -4: 930 385 959 418 794 -4: 991 121 109 391 580 -4: 748 732 232 582 304 -4: 670 631 213 139 366 -4: 51 626 940 254 974 -4: 204 420 973 452 288 -4: 655 178 989 517 510 -4: 373 603 203 745 598 -4: 822 163 515 4 324 -4: 626 456 684 290 903 -4: 234 17 488 802 999 -4: 61 235 816 332 799 -4: 728 992 557 920 787 -4: 947 677 864 486 859 -4: 370 507 621 640 760 -4: 112 612 248 467 551 -4: 689 778 944 602 938 -4: 91 986 183 850 207 -4: 32 141 979 218 509 -4: 86 170 56 286 172 -4: 521 295 236 580 247 -4: 716 988 534 221 921 -4: 795 329 155 972 937 -4: 662 409 397 585 734 -4: 336 717 58 620 570 -4: 495 251 939 522 732 -4: 983 988 753 757 961 -4: 340 491 452 919 242 -4: 215 658 292 401 134 -4: 134 677 568 640 354 -4: 432 874 406 666 36 -4: 741 981 44 552 671 -4: 770 3 87 355 133 -4: 457 393 223 105 920 -4: 179 356 765 88 532 -4: 769 687 611 886 351 -4: 254 645 5 778 863 -4: 840 841 799 350 353 -4: 923 619 481 416 896 -4: 210 659 739 21 998 -4: 428 41 255 214 652 -4: 398 255 569 450 795 -4: 769 155 854 800 669 -4: 560 156 136 215 396 +4: 758 252 401 981 265 +4: 143 452 216 640 350 +4: 105 495 583 426 935 +4: 202 762 823 612 557 +4: 537 378 974 852 348 +4: 967 293 464 60 585 +4: 402 879 194 507 20 +4: 627 543 908 891 268 +4: 410 77 418 769 460 +4: 730 364 586 735 155 +4: 718 734 95 54 701 +4: 553 979 373 699 169 +4: 282 289 155 321 577 +4: 963 245 401 482 950 +4: 203 755 921 283 720 +4: 994 901 602 447 996 +4: 754 897 980 462 73 +4: 441 768 963 92 70 +4: 703 415 382 504 136 +4: 857 100 120 791 893 +4: 351 773 821 349 629 +4: 746 684 293 222 402 +4: 333 814 158 898 566 +4: 287 795 808 332 184 +4: 801 894 1 593 541 +4: 160 549 795 420 534 +4: 723 93 510 585 340 +4: 682 685 463 881 759 +4: 929 872 261 742 577 +4: 402 636 72 795 17 +4: 333 973 555 806 137 +4: 441 897 280 917 537 +4: 343 831 341 670 496 +4: 112 916 99 212 840 +4: 272 270 838 114 470 +4: 79 279 960 379 863 +4: 874 383 480 982 469 +4: 580 230 245 108 37 +4: 962 900 753 758 423 +4: 186 855 352 267 24 +4: 563 563 634 647 245 +4: 79 560 332 393 842 +4: 816 98 97 271 888 +4: 104 976 133 861 254 +4: 29 844 426 874 229 +4: 959 580 596 162 105 +4: 286 95 621 999 204 +4: 498 381 933 469 532 +4: 830 508 2 805 462 +4: 477 158 468 341 300 +4: 954 977 713 828 698 +4: 571 8 642 463 802 +4: 524 958 320 675 305 +4: 365 430 781 264 846 4/11 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -4030,15 +4073,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -6: [2024-05-21 21:42:19] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. -6: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -6: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:19] : LOG : Building guide tree. -6: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2024-05-21 21:42:19] : LOG : Aligning -6: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +6: [2023-04-20 17:20:50] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001.tfa. +6: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +6: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:50] : LOG : Building guide tree. +6: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2023-04-20 17:20:50] : LOG : Aligning +6: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4074,15 +4117,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -7: [2024-05-21 21:42:19] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. -7: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -7: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:19] : LOG : Building guide tree. -7: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2024-05-21 21:42:19] : LOG : Aligning -7: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +7: [2023-04-20 17:20:50] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB11001_EOF.msf. +7: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +7: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:50] : LOG : Building guide tree. +7: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2023-04-20 17:20:50] : LOG : Aligning +7: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4118,15 +4161,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -8: [2024-05-21 21:42:19] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. -8: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -8: [2024-05-21 21:42:19] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:19] : LOG : Building guide tree. -8: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2024-05-21 21:42:19] : LOG : Aligning -8: [2024-05-21 21:42:19] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +8: [2023-04-20 17:20:50] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.msf. +8: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +8: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:50] : LOG : Building guide tree. +8: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2023-04-20 17:20:50] : LOG : Aligning +8: [2023-04-20 17:20:50] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4151,7 +4194,7 @@ 8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 8: Q---- - 8/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.02 sec + 8/11 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec test 9 Start 9: kalign_itest_BB12006.tfa @@ -4174,15 +4217,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -9: [2024-05-21 21:42:19] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -9: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -9: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:19] : LOG : Building guide tree. -9: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2024-05-21 21:42:19] : LOG : Aligning -9: [2024-05-21 21:42:19] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +9: [2023-04-20 17:20:50] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +9: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +9: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:50] : LOG : Building guide tree. +9: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2023-04-20 17:20:50] : LOG : Aligning +9: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4230,15 +4273,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -10: [2024-05-21 21:42:19] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. -10: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -10: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:19] : LOG : Building guide tree. -10: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2024-05-21 21:42:19] : LOG : Aligning -10: [2024-05-21 21:42:19] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +10: [2023-04-20 17:20:50] : LOG : Read 4 sequences from /build/kalign-3.3.5/tests/data/BB12006.tfa. +10: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +10: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:50] : LOG : Building guide tree. +10: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2023-04-20 17:20:50] : LOG : Aligning +10: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4286,15 +4329,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2024-05-21 21:42:19] : LOG : Detected protein sequences. -11: [2024-05-21 21:42:19] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. -11: [2024-05-21 21:42:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:19] : LOG : Calculating pairwise distances -11: [2024-05-21 21:42:19] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:19] : LOG : Building guide tree. -11: [2024-05-21 21:42:19] : LOG : CPU Time: 0.09u 00:00:00.08 Elapsed: 00:00:00.00 -11: [2024-05-21 21:42:19] : LOG : Aligning -11: [2024-05-21 21:42:19] : LOG : CPU Time: 0.09u 00:00:00.08 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:50] : LOG : Detected protein sequences. +11: [2023-04-20 17:20:50] : LOG : Read 44 sequences from /build/kalign-3.3.5/tests/data/BB30014.tfa. +11: [2023-04-20 17:20:50] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:50] : LOG : Calculating pairwise distances +11: [2023-04-20 17:20:50] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:50] : LOG : Building guide tree. +11: [2023-04-20 17:20:50] : LOG : CPU Time: 0.07u 00:00:00.07 Elapsed: 00:00:00.00 +11: [2023-04-20 17:20:50] : LOG : Aligning +11: [2023-04-20 17:20:50] : LOG : CPU Time: 0.07u 00:00:00.07 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -4603,16 +4646,16 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -11/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.09 sec +11/11 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.08 sec 100% tests passed, 0 tests failed out of 11 -Total Test time (real) = 8.00 sec +Total Test time (real) = 8.22 sec 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-x86_64-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-x86_64-linux-gnu && make -j15 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/kalign-3.3.5 -B/build/kalign-3.3.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -4680,12 +4723,14 @@ 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/2612308/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2612308/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/653814 and its subdirectories -I: Current time: Tue May 21 21:42:28 -12 2024 -I: pbuilder-time-stamp: 1716370948 +I: removing directory /srv/workspace/pbuilder/2612308 and its subdirectories +I: Current time: Thu Apr 20 17:20:57 +14 2023 +I: pbuilder-time-stamp: 1681960857