Diff of the two buildlogs: -- --- b1/build.log 2023-05-05 04:43:03.420222547 +0000 +++ b2/build.log 2023-05-05 04:59:10.277782365 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 4 16:34:28 -12 2023 -I: pbuilder-time-stamp: 1683261268 +I: Current time: Fri May 5 18:45:24 +14 2023 +I: pbuilder-time-stamp: 1683261924 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 [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Oct 25 01:36:26 2022 -12 +gpgv: Signature made Wed Oct 26 03:36:26 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-7.dsc: no acceptable signature found @@ -33,135 +33,167 @@ dpkg-source: info: applying exe_suffix I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9287/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 May 5 18:46 /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/7076/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7076/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='0a115c79d5fa4d3fa47ebaf043567ec3' - 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='9287' - PS1='# ' - PS2='> ' + INVOCATION_ID=d4d837000122456ebced6b64d63cbe17 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=7076 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.masyQHVx/pbuilderrc_QNFU --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.masyQHVx/b1 --logfile b1/build.log hhsuite_3.3.0+ds-7.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.masyQHVx/pbuilderrc_z6iG --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.masyQHVx/b2 --logfile b2/build.log --extrapackages usrmerge hhsuite_3.3.0+ds-7.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1c 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/9287/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 5 18:46 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/7076/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -293,7 +325,7 @@ Get: 86 http://deb.debian.org/debian bookworm/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.6 [338 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.6 [122 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libsimde-dev all 0.7.4~rc2-2 [377 kB] -Fetched 39.8 MB in 12s (3379 kB/s) +Fetched 39.8 MB in 1s (30.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) @@ -682,8 +714,19 @@ 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/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-7_source.changes +I: user script /srv/workspace/pbuilder/7076/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/7076/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-7_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-7 dpkg-buildpackage: info: source distribution unstable @@ -765,7 +808,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild - cd mybuild && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd mybuild && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-3.3.0+ds/mybuild//CMakeFiles/progress.marks @@ -775,27 +818,35 @@ make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/data /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake --color= -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 3%] Generating ../generated/context_data.crf.h -[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -[ 3%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 2%] Generating ../generated/context_data.crf.h cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c +[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c: In function 'ffindex_index_parse': /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c:291:43: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 291 | fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes); @@ -803,82 +854,59 @@ | | | | long int size_t {aka unsigned int} | %d -[ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c -[ 5%] Linking C static library libffindex.a +[ 6%] Linking C static library libffindex.a cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 5%] Built target ffindex -[ 6%] Generating ../generated/context_data.lib.h -cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated -cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h -[ 7%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 7%] Built target hhviterbialgorithm_with_celloff -[ 8%] Generating ../generated/cs219.lib.h -cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated -cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h -cd /build/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp -cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 9%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -cd /build/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp -cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h -cd /build/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp +[ 6%] Built target ffindex make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 10%] Built target generated -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src/cs /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src/cs /build/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/aa.cc -[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/as.cc -[ 13%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a +[ 8%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 +[ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake +/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 13%] Built target hhviterbialgorithm_with_celloff_and_ss -[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 9%] Built target hhviterbialgorithm_with_celloff_and_ss +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src/cs /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src/cs /build/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= +[ 9%] Built target hhviterbialgorithm_with_celloff make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 9%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp -[ 15%] Linking CXX static library libhhviterbialgorithm_and_ss.a +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/aa.cc +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp +[ 11%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); @@ -894,30 +922,17 @@ /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 15%] Built target hhviterbialgorithm_and_ss -[ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -[ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc -[ 18%] Linking CXX static library libA3M_COMPRESS.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 -/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -/usr/bin/ranlib libA3M_COMPRESS.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 18%] Built target A3M_COMPRESS -[ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/log.cc +[ 11%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color= +[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/as.cc make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o +[ 13%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:42: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] @@ -932,199 +947,227 @@ | | | | long int size_t {aka unsigned int} | %d -[ 21%] Linking C executable ffindex_apply +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +[ 14%] Linking C executable ffindex_apply cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 21%] Built target ffindex_apply -[ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/application.cc +[ 14%] Built target ffindex_apply make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o +[ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 24%] Built target ffindex_reduce +[ 17%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c +[ 20%] Linking CXX static library libA3M_COMPRESS.a +[ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT 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CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c -[ 27%] Linking C executable ffindex_from_fasta -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a -[ 28%] Linking C executable ffindex_build +[ 22%] Linking C executable ffindex_build cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 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lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o +[ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c -[ 29%] Built target ffindex_build -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c -[ 31%] Linking C executable ffindex_get +[ 24%] Linking C executable ffindex_from_fasta +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a +[ 25%] Linking C executable ffindex_get cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 32%] Linking C executable ffindex_modify -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -[ 32%] Built target ffindex_get +[ 25%] Built target ffindex_from_fasta +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend +[ 25%] Built target ffindex_get +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild 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lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o +[ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c +[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c +[ 28%] Linking C executable ffindex_unpack +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 33%] Built target ffindex_modify +[ 28%] Built target ffindex_unpack make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c -[ 35%] Linking C executable ffindex_unpack -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a +[ 30%] Linking C executable ffindex_modify +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 35%] Built target ffindex_unpack +[ 30%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color= -[ 36%] Linking C executable ffindex_order -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a -[ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o +[ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c +[ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +[ 33%] Linking C executable ffindex_order +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a +[ 34%] Linking C executable ffindex_from_fasta_with_split +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 37%] Built target ffindex_order +[ 34%] Built target ffindex_from_fasta_with_split make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o +[ 35%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_extract.cpp -[ 39%] Linking C executable ffindex_from_fasta_with_split -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 39%] Built target ffindex_from_fasta_with_split +[ 35%] Built target ffindex_order make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_reduce.cpp -[ 41%] Linking CXX static library libCS_OBJECTS.a -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 -/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o -/usr/bin/ranlib libCS_OBJECTS.a +[ 37%] Linking CXX executable a3m_extract +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 41%] Built target CS_OBJECTS +[ 37%] Built target a3m_extract make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 42%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o +[ 38%] Linking CXX executable a3m_reduce +[ 39%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -[ 43%] Linking CXX executable a3m_extract -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 43%] Built target a3m_extract +[ 39%] Built target a3m_reduce make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 44%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o +[ 40%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -[ 45%] Linking CXX executable a3m_reduce -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +[ 41%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h +[ 42%] Generating ../generated/cs219.lib.h +cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated +[ 43%] Linking CXX executable a3m_database_reduce +cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 45%] Built target a3m_reduce +[ 43%] Built target generated make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 46%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o +[ 44%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -[ 47%] Linking CXX executable a3m_database_reduce -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 47%] Built target a3m_database_reduce +[ 44%] Built target a3m_database_reduce +[ 45%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/log.cc +[ 46%] Linking CXX executable a3m_database_extract +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 46%] Built target a3m_database_extract +[ 47%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/application.cc +[ 48%] Linking CXX executable a3m_database_filter +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 48%] Built target a3m_database_filter +[ 49%] Linking CXX static library libCS_OBJECTS.a +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 +/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o +/usr/bin/ranlib libCS_OBJECTS.a +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 49%] Built target CS_OBJECTS make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o +[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits.cpp -[ 49%] Linking CXX executable a3m_database_extract -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 49%] Built target a3m_database_extract -[ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhdecl.cpp -[ 51%] Linking CXX executable a3m_database_filter -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 51%] Built target a3m_database_filter [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhit.cpp [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o @@ -1139,6 +1182,8 @@ cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhutil.cpp +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-3.3.0+ds/src/util.cpp In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/hhhit.h:14, from /build/hhsuite-3.3.0+ds/src/hhhitlist.h:16, @@ -1153,8 +1198,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/hhsuite-3.3.0+ds/src/util.cpp [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhalignment.cpp [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o @@ -1163,6 +1206,10 @@ cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhmm.cpp [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp +[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfullalignment.cpp /build/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -1188,10 +1235,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfullalignment.cpp [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o @@ -1208,6 +1251,10 @@ cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp +[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp +[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhdatabase.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/hhsuite-3.3.0+ds/lib/simd/simd.h:9, @@ -1219,17 +1266,15 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp +[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/hhprefilter.h:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -1281,10 +1326,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp 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CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfunc.cpp In file included from /usr/include/c++/12/vector:70, from /build/hhsuite-3.3.0+ds/src/util.h:20, from /build/hhsuite-3.3.0+ds/src/hhhmm.h:8, @@ -1312,6 +1353,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfunc.cpp [ 79%] Linking CXX static library libHH_OBJECTS.a cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 @@ -1328,99 +1371,107 @@ cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake --color= +make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build -make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 82%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o +[ 81%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o +[ 81%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_app.cpp +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde 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-ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfilter.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp 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83%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhfilter.cpp +[ 84%] Linking CXX executable hhblits cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 85%] Linking CXX executable hhsearch +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 83%] Built target hhblits -make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 84%] Building CXX object src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_app.cpp -[ 85%] Linking CXX executable hhfilter -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -[ 86%] Linking CXX executable hhmake -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 86%] Built target hhfilter +[ 85%] Built target hhblits make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 87%] Building 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libhhviterbialgorithm_with_celloff_and_ss.a +[ 89%] Linking CXX executable hhfilter +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 89%] Built target hhsearch +[ 89%] Built target hhmake make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 90%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc -[ 91%] Linking CXX executable hhalign -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 91%] Built target hhalign +[ 90%] Built target hhfilter make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 92%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o +[ 91%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp -[ 93%] Linking CXX executable hhconsensus -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 92%] Linking CXX executable hhalign +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 93%] Built target hhconsensus +[ 92%] Built target hhalign make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 94%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o +[ 93%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF 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src/CMakeFiles/hhalign_omp.dir/depend +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 95%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1448,19 +1499,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 95%] Linking CXX executable hhblits_omp +[ 96%] Linking CXX executable hhblits_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 95%] Built target hhblits_omp -make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend +[ 96%] Built target hhblits_omp +make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color= +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build +make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 96%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +[ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1488,19 +1539,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable hhsearch_omp +[ 98%] Linking CXX executable hhsearch_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 97%] Built target hhsearch_omp -make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 98%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp +[ 98%] Built target hhsearch_omp /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1576,7 +1619,7 @@ debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data - cd mybuild/data && make -j3 "INSTALL=install --strip-program=true" + cd mybuild/data && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks @@ -1598,179 +1641,179 @@ debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/hhsuite-3.3.0+ds' cd /build/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-3.3.0+ds/mybuild/src:/build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh -- 16:39:31.622 INFO: query.a3m is in A2M, A3M or FASTA format +- 18:53:41.883 INFO: query.a3m is in A2M, A3M or FASTA format -- 16:39:33.180 INFO: Alternative alignment: 0 +- 18:53:43.345 INFO: Alternative alignment: 0 -- 16:39:33.301 INFO: 1 alignments done +- 18:53:43.545 INFO: 1 alignments done -- 16:39:33.464 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm +- 18:53:43.684 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 -Date Thu May 4 16:39:33 2023 +Date Fri May 5 18:53:44 2023 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) -query.a3m 0 32127 1138 0 -query.a3m 0 32666 11 0 -query.a3m 0 32666 245 0 +query.a3m 0 32127 1257 0 +query.a3m 0 32666 9 0 +query.a3m 0 32666 313 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... -- 16:39:37.562 INFO: Searching 1 column state sequences. +- 18:53:48.870 INFO: Searching 1 column state sequences. -- 16:39:37.728 INFO: query.a3m is in A2M, A3M or FASTA format +- 18:53:49.077 INFO: query.a3m is in A2M, A3M or FASTA format -- 16:39:37.781 INFO: Iteration 1 +- 18:53:49.164 INFO: Iteration 1 -- 16:39:39.101 INFO: Prefiltering database +- 18:53:50.403 INFO: Prefiltering database -- 16:39:40.436 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 18:53:51.640 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 16:39:40.447 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 18:53:51.651 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 16:39:40.447 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 18:53:51.651 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 16:39:40.447 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 18:53:51.651 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 16:39:40.617 INFO: Alternative alignment: 0 +- 18:53:51.851 INFO: Alternative alignment: 0 -- 16:39:40.735 INFO: 1 alignments done +- 18:53:52.050 INFO: 1 alignments done -- 16:39:40.735 INFO: Alternative alignment: 1 +- 18:53:52.051 INFO: Alternative alignment: 1 -- 16:39:40.858 INFO: 1 alignments done +- 18:53:52.243 INFO: 1 alignments done -- 16:39:40.858 INFO: Alternative alignment: 2 +- 18:53:52.243 INFO: Alternative alignment: 2 -- 16:39:40.858 INFO: Alternative alignment: 3 +- 18:53:52.243 INFO: Alternative alignment: 3 -- 16:39:42.448 INFO: Premerge done +- 18:53:53.727 INFO: Premerge done -- 16:39:42.448 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 18:53:53.727 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 16:39:42.575 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 18:53:53.883 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.27431 Searched_HMMs 1 -Date Thu May 4 16:39:42 2023 +Date Fri May 5 18:53:53 2023 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) -- 16:39:42.663 INFO: Searching 1 column state sequences. +- 18:53:53.972 INFO: Searching 1 column state sequences. -- 16:39:42.808 INFO: Thread 0 query.a3m +- 18:53:54.145 INFO: Thread 0 query.a3m -- 16:39:42.852 INFO: query.a3m is in A2M, A3M or FASTA format +- 18:53:54.196 INFO: query.a3m is in A2M, A3M or FASTA format -- 16:39:42.906 INFO: Iteration 1 +- 18:53:54.281 INFO: Iteration 1 -- 16:39:44.995 INFO: Prefiltering database +- 18:53:56.561 INFO: Prefiltering database -- 16:39:47.103 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 18:53:58.854 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 16:39:47.113 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 18:53:58.864 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 16:39:47.113 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 18:53:58.864 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 16:39:47.113 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 18:53:58.864 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 16:39:47.202 INFO: Alternative alignment: 0 +- 18:53:58.962 INFO: Alternative alignment: 0 -- 16:39:47.320 INFO: 1 alignments done +- 18:53:59.161 INFO: 1 alignments done -- 16:39:47.320 INFO: Alternative alignment: 1 +- 18:53:59.161 INFO: Alternative alignment: 1 -- 16:39:47.434 INFO: 1 alignments done +- 18:53:59.353 INFO: 1 alignments done -- 16:39:47.434 INFO: Alternative alignment: 2 +- 18:53:59.353 INFO: Alternative alignment: 2 -- 16:39:47.434 INFO: Alternative alignment: 3 +- 18:53:59.353 INFO: Alternative alignment: 3 -- 16:39:49.666 INFO: Premerge done +- 18:54:01.836 INFO: Premerge done -- 16:39:49.666 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 18:54:01.836 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 16:39:49.763 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 18:54:01.959 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 -- 16:39:50.023 INFO: query.a3m is in A2M, A3M or FASTA format +- 18:54:02.247 INFO: query.a3m is in A2M, A3M or FASTA format -- 16:39:50.074 INFO: Searching 1 database HHMs without prefiltering +- 18:54:02.332 INFO: Searching 1 database HHMs without prefiltering -- 16:39:50.074 INFO: Iteration 1 +- 18:54:02.332 INFO: Iteration 1 -- 16:39:51.402 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 18:54:03.506 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 16:39:51.569 INFO: Alternative alignment: 0 +- 18:54:03.699 INFO: Alternative alignment: 0 -- 16:39:51.685 INFO: 1 alignments done +- 18:54:03.892 INFO: 1 alignments done -- 16:39:51.685 INFO: Alternative alignment: 1 +- 18:54:03.892 INFO: Alternative alignment: 1 -- 16:39:51.802 INFO: 1 alignments done +- 18:54:04.080 INFO: 1 alignments done -- 16:39:51.802 INFO: Alternative alignment: 2 +- 18:54:04.080 INFO: Alternative alignment: 2 -- 16:39:51.802 INFO: Alternative alignment: 3 +- 18:54:04.080 INFO: Alternative alignment: 3 -- 16:39:53.410 INFO: Premerge done +- 18:54:05.627 INFO: Premerge done -- 16:39:53.411 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 18:54:05.627 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 16:39:53.545 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 18:54:05.787 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29223 Searched_HMMs 1 -Date Thu May 4 16:39:53 2023 +Date Fri May 5 18:54:05 2023 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) -- 16:39:53.777 INFO: Thread 0 query.a3m +- 18:54:06.045 INFO: Thread 0 query.a3m -- 16:39:53.821 INFO: query.a3m is in A2M, A3M or FASTA format +- 18:54:06.095 INFO: query.a3m is in A2M, A3M or FASTA format -- 16:39:53.873 INFO: Searching 1 database HHMs without prefiltering +- 18:54:06.179 INFO: Searching 1 database HHMs without prefiltering -- 16:39:53.873 INFO: Iteration 1 +- 18:54:06.180 INFO: Iteration 1 -- 16:39:55.842 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 18:54:08.508 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 16:39:55.931 INFO: Alternative alignment: 0 +- 18:54:08.606 INFO: Alternative alignment: 0 -- 16:39:56.049 INFO: 1 alignments done +- 18:54:08.799 INFO: 1 alignments done -- 16:39:56.049 INFO: Alternative alignment: 1 +- 18:54:08.799 INFO: Alternative alignment: 1 -- 16:39:56.163 INFO: 1 alignments done +- 18:54:08.985 INFO: 1 alignments done -- 16:39:56.163 INFO: Alternative alignment: 2 +- 18:54:08.985 INFO: Alternative alignment: 2 -- 16:39:56.163 INFO: Alternative alignment: 3 +- 18:54:08.985 INFO: Alternative alignment: 3 -- 16:39:58.295 INFO: Premerge done +- 18:54:11.471 INFO: Premerge done -- 16:39:58.295 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 18:54:11.471 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 16:39:58.399 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 18:54:11.588 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp @@ -1779,7 +1822,7 @@ make[1]: Entering directory '/build/hhsuite-3.3.0+ds' mkdir -p /build/hhsuite-3.3.0+ds/debian/hhsuite/usr/libexec/hhsuite/bin dh_auto_install --builddirectory mybuild - cd mybuild && make -j3 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd mybuild && make -j4 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1851,7 +1894,7 @@ debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data - cd mybuild/data && make -j3 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd mybuild/data && make -j4 install DESTDIR=/build/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild/data' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/hhsuite-3.3.0+ds -B/build/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall @@ -1901,22 +1944,22 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhfilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhmake contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_ca3m contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/hhsuite-3.3.0+ds' @@ -1924,8 +1967,8 @@ make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb -dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-7_armhf.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-7_armhf.deb'. +dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-7_armhf.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-7_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-7_armhf.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-7_armhf.changes @@ -1934,12 +1977,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/7076/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7076/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/9287 and its subdirectories -I: Current time: Thu May 4 16:42:54 -12 2023 -I: pbuilder-time-stamp: 1683261774 +I: removing directory /srv/workspace/pbuilder/7076 and its subdirectories +I: Current time: Fri May 5 18:59:06 +14 2023 +I: pbuilder-time-stamp: 1683262746