Diff of the two buildlogs: -- --- b1/build.log 2021-08-09 11:07:45.237053584 +0000 +++ b2/build.log 2021-08-09 11:10:47.998217850 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 11 05:27:44 -12 2022 -I: pbuilder-time-stamp: 1662917264 +I: Current time: Tue Aug 10 01:07:47 +14 2021 +I: pbuilder-time-stamp: 1628507267 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Fri Feb 15 06:07:29 2019 -12 +gpgv: Signature made Sat Feb 16 08:07:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hhsuite_3.0~beta3+dfsg-3.dsc @@ -35,136 +35,170 @@ dpkg-source: info: applying disable-AVX-SSE.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/57341/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13340/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/13340/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13340/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b6a03a9362714585a6f52ae28c07179e' - 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='57341' - PS1='# ' - PS2='> ' + INVOCATION_ID=cca74cc85c234e4c8ee5006452dd0ba0 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=13340 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.UkQopsrZCQ/pbuilderrc_AQnB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UkQopsrZCQ/b1 --logfile b1/build.log hhsuite_3.0~beta3+dfsg-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.UkQopsrZCQ/pbuilderrc_FZk1 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UkQopsrZCQ/b2 --logfile b2/build.log hhsuite_3.0~beta3+dfsg-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/57341/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 10 01:08 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 7 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/13340/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -356,7 +390,7 @@ Get: 142 http://deb.debian.org/debian buster/main amd64 texlive-base all 2018.20190227-2 [19.7 MB] Get: 143 http://deb.debian.org/debian buster/main amd64 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] -Fetched 107 MB in 3s (39.6 MB/s) +Fetched 107 MB in 3s (39.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -996,7 +1030,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/hhsuite-3.0~beta3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/hhsuite-3.0~beta3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.0~beta3+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1075,98 +1109,96 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/hhsuite-3.0~beta3+dfsg' dh_auto_build -- NO_PNG=1 - cd mybuild && make -j16 "INSTALL=install --strip-program=true" NO_PNG=1 + cd mybuild && make -j15 "INSTALL=install --strip-program=true" NO_PNG=1 make[2]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/cmake -S"/build/hhsuite-3.0~beta3+dfsg" -B"/build/hhsuite-3.0~beta3+dfsg/mybuild" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles" "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles/progress.marks" make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/depend +make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/DependInfo.cmake" --color= -make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/depend +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-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake" --color= -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake" --color= -Scanning dependencies of target A3M_COMPRESS_OBJECT -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= +Scanning dependencies of target A3M_COMPRESS_OBJECT +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/depend -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/doc" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc/CMakeFiles/pdf.dir/DependInfo.cmake" --color= +make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +Scanning dependencies of target hhviterbialgorithm_and_ss Scanning dependencies of target CS_OBJECTS +Scanning dependencies of target pdf +[ 1%] Building CXX object src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_compress.cpp" make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build Scanning dependencies of target hhviterbialgorithm_with_celloff -Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +Scanning dependencies of target HH_OBJECTS +make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build +Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -[ 1%] Building CXX object src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build -Scanning dependencies of target pdf -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_compress.cpp" -Scanning dependencies of target hhviterbialgorithm_and_ss +[ 2%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/aa.cc" make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build +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-3.0~beta3+dfsg/mybuild' -make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build -[ 2%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -[ 4%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/aa.cc" +[ 4%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o +[ 5%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o +[ 7%] Generating hhblits-hhsearch.png +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /build/hhsuite-3.0~beta3+dfsg/doc/hhblits-hhsearch.png /build/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhblits-hhsearch.png cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/as.cc" -[ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc" cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" -[ 8%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" +[ 11%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o +[ 13%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/assert_helpers.cc" -[ 11%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o -Scanning dependencies of target HH_OBJECTS -[ 13%] Generating hhsuite-userguide.bib -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +[ 14%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o +[ 15%] Generating hhsuite-userguide.bib +[ 17%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /build/hhsuite-3.0~beta3+dfsg/doc/hhsuite-userguide.bib /build/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhsuite-userguide.bib -make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build -[ 14%] Generating hhblits-hhsearch.png -[ 15%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o +[ 18%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" +[ 20%] Generating hhsuite-userguide.tex cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/blosum_matrix.cc" -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /build/hhsuite-3.0~beta3+dfsg/doc/hhblits-hhsearch.png /build/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhblits-hhsearch.png -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc" -[ 17%] Generating hhsuite-userguide.tex -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /build/hhsuite-3.0~beta3+dfsg/doc/hhsuite-userguide.tex /build/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhsuite-userguide.tex -[ 18%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat 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-I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhblits.cpp" +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/application.cc" [ 23%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhdecl.cpp" [ 24%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhit.cpp" -[ 26%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhmatrices.cpp" -[ 27%] Generating hhsuite-userguide.pdf +[ 26%] Generating hhsuite-userguide.pdf cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. @@ -1342,8 +1374,19 @@ LaTeX Warning: Reference `fig:hhsearch_hhblits_bench' on page 10 undefined on i nput line 453. -[10 <./hhblits-hhsearch.png[ 28%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhsearch.cpp" +[10 <./hhblits-hhsearch.pngIn file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:22: +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void end_of_options() const throw(GetOptEx) { + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + const std::string& long_opt) throw(GetOptEx) { + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + template inline T getopt(char short_opt) throw(GetOptEx) { + ^~~~~ >] LaTeX Warning: Reference `2_vs_1+1' on page 11 undefined on input line 480. @@ -1357,19 +1400,9 @@ LaTeX Warning: Reference `aliformats' on page 11 undefined on input line 497. -[11] [12]In file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:22: -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void end_of_options() const throw(GetOptEx) { - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - const std::string& long_opt) throw(GetOptEx) { - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - template inline T getopt(char short_opt) throw(GetOptEx) { - ^~~~~ +[11] [12]/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:115:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + const _Option& opt) throw (GetOptEx) { + ^~~~~ [13] LaTeX Warning: Citation `Gonzalez:2010' on page 14 undefined on input line 612. @@ -1415,10 +1448,7 @@ Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] -[17]/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:115:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - const _Option& opt) throw (GetOptEx) { - ^~~~~ - +[17] Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] @@ -1775,38 +1805,25 @@ Output written on hhsuite-userguide.pdf (52 pages, 379486 bytes). Transcript written on hhsuite-userguide.log. cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/bibtex hhsuite-userguide -[ 30%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalign.cpp" +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +[ 27%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhmatrices.cpp" This is BibTeX, Version 0.99d (TeX Live 2019/dev/Debian) The top-level auxiliary file: hhsuite-userguide.aux The style file: unsrt.bst Database file #1: hhsuite-userguide.bib cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex -In file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.h:29, - from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.cc:21: -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void end_of_options() const throw(GetOptEx) { - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - const std::string& long_opt) throw(GetOptEx) { - ^~~~~ -/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - template inline T getopt(char short_opt) throw(GetOptEx) { - ^~~~~ +[ 27%] Built target hhviterbialgorithm_and_ss +[ 28%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhsearch.cpp" This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' entering extended mode (./hhsuite-userguide.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class -(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo[ 31%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -))cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhitlist.cpp" - +(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/cite/cite.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) @@ -1815,17 +1832,13 @@ (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) -(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def[ 31%] Built target A3M_COMPRESS_OBJECT -)))make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend - +(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake" --color= -) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v3.2a <2019/01/15> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bookmark.sty @@ -1839,22 +1852,28 @@ (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) 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-(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.styScanning dependencies of target a3m_database_filter +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.styIn file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.h:29, + from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.cc:21: +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void end_of_options() const throw(GetOptEx) { + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + const std::string& long_opt) throw(GetOptEx) { + ^~~~~ +/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + template inline T getopt(char short_opt) throw(GetOptEx) { + ^~~~~ ) -(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.defmake[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build -)make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def -(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))[ 34%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o - -(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bkm-pdftex.defcd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_database_filter.cpp" -)) +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (./hhsuite-userguide.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii @@ -1917,7 +1936,9 @@ LaTeX Warning: Citation `Sali:1993' on page 4 undefined on input line 106. -[4] +[4][ 30%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalign.cpp" + LaTeX Warning: Citation `Mariani:2011' on page 5 undefined on input line 108. @@ -1963,28 +1984,13 @@ LaTeX Warning: Citation `Higgins:2011' on page 8 undefined on input line 312. -[8] [9] [10] [11 <./hhblits-hhsearch.pngmake[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake" --color= -[ 34%] Built target hhviterbialgorithm_with_celloff -make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake" --color= -Scanning dependencies of target a3m_database_reduce -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build -Scanning dependencies of target a3m_database_extract -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build -make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -[ 36%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_database_reduce.cpp" -[ 37%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_database_extract.cpp" ->] [12] [13]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - [14] +[8] [9] [10] [11 <./hhblits-hhsearch.png[ 31%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhitlist.cpp" +[ 33%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhposteriordecoder.cpp" +[ 34%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhutil.cpp" +>] [12] [13] [14] LaTeX Warning: Citation `Gonzalez:2010' on page 15 undefined on input line 612. @@ -2041,9 +2047,7 @@ LaTeX Warning: Citation `Alva:2010' on page 19 undefined on input line 801. -[19[ 37%] Built target hhviterbialgorithm_and_ss -]make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend - +[19] LaTeX Warning: Citation `Chothia:1986' on page 20 undefined on input line 804. @@ -2056,9 +2060,7 @@ LaTeX Warning: Citation `Remmert:2010' on page 20 undefined on input line 804. -[20]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake" --color= - +[20] LaTeX Warning: Citation `Soding:2006b' on page 21 undefined on input line 835. @@ -2086,14 +2088,11 @@ LaTeX Warning: Citation `Sadreyev:2008' on page 24 undefined on input line 913. -[24]make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend - +[24] LaTeX Warning: Citation `Remmert:2011' on page 25 undefined on input line 952. -[25make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake" --color= -] +[25] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] @@ -2125,23 +2124,16 @@ Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] -[26] [27]Scanning dependencies of target a3m_reduce -make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - [28]make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build - [29]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - [30] [31Scanning dependencies of target a3m_extract -] +[26] [27] [28] [29] [30]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' + [31] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits -[32make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' -]make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build - +[32] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits -[33]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - [34] [35] +[33] [34] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] @@ -2169,8 +2161,7 @@ Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] -[36[ 39%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -] +[36] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] @@ -2206,8 +2197,7 @@ Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] -[38cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_reduce.cpp" -] +[38] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] @@ -2223,9 +2213,7 @@ Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] -[39][ 40%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_extract.cpp" - +[39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] @@ -2241,7 +2229,8 @@ Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] -[40] +[40][ 34%] Built target hhviterbialgorithm_with_celloff + Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] @@ -2269,16 +2258,17 @@ Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] -[42] [43][ 42%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhutil.cpp" - [44] +[42] [43] [44] LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2101. LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2138. -[45] +[45][ 36%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/util.cpp" +make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' + Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] @@ -2302,7 +2292,9 @@ Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] -[47] [48] +[47] [48[ 37%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o +]cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp" + Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : ] [12] [13] [14][ 53%] Linking CXX executable ../bin/a3m_database_extract -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 - [15] +make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build +make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' +[ 43%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o +cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_database_extract.cpp" +>] [12] [13] [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 648--649 -[16]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - +[16] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] @@ -2490,13 +2490,11 @@ Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] -[18]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_extract -lffindex - +[18] Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] -[19] [20][ 53%] Built target a3m_database_reduce - [21] [22] [23] [24] [25] +[19] [20] [21] [22] [23] [24] [25] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] @@ -2528,9 +2526,7 @@ Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] -[26][ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhposteriordecoderrunner.cpp" - [27] [28] [29] [30] [31] +[26] [27] [28] [29] [30] [31] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits @@ -2638,8 +2634,7 @@ Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] -[41]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - +[41] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] @@ -2663,9 +2658,7 @@ Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] -[42] [43]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' - [44] [45][ 55%] Built target a3m_database_extract - +[42] [43] [44] [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] @@ -2673,8 +2666,7 @@ Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] -[46][ 55%] Built target a3m_reduce - +[46] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] @@ -2690,28 +2682,23 @@ Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] -[47] [48][ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" - +[47] [48] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . -[49] [50] [51][ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o - +[49] [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 -[52]cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhfullalignment.cpp" - (./hhsuite-userguide.bbl[ 59%] Linking CXX executable ../bin/a3m_extract - [53] [54]) [55] (./hhsuite-userguide.auxcd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 +[52] (./hhsuite-userguide.bbl [53][ 44%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o + [54]) [55] (./hhsuite-userguide.auxcd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhmm.cpp" ) ) (see the transcript file for additional information)../hhsuite_3.0~beta3+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/13340/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13340/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/57341 and its subdirectories -I: Current time: Sun Sep 11 05:30:44 -12 2022 -I: pbuilder-time-stamp: 1662917444 +I: removing directory /srv/workspace/pbuilder/13340 and its subdirectories +I: Current time: Tue Aug 10 01:10:47 +14 2021 +I: pbuilder-time-stamp: 1628507447