Diff of the two buildlogs: -- --- b1/build.log 2021-08-07 15:35:10.666659072 +0000 +++ b2/build.log 2021-08-07 15:37:38.777070138 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 7 03:32:50 -12 2021 -I: pbuilder-time-stamp: 1628350370 +I: Current time: Sat Sep 10 11:58:16 +14 2022 +I: pbuilder-time-stamp: 1662760696 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 Mon Nov 12 03:36:34 2018 -12 +gpgv: Signature made Tue Nov 13 05:36:34 2018 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying java8_instead_of_11.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23796/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/47265/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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/47265/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/47265/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=15' - 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=16' + 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='7ce88f0380e541c1bf72ffe948e6315d' - 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='23796' - PS1='# ' - PS2='> ' + INVOCATION_ID=39be082e4a364d09bad10e4240178c90 + 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=47265 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.ZuAopwKDwc/pbuilderrc_v1nM --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZuAopwKDwc/b1 --logfile b1/build.log biojava-live_1.7.1-8.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ZuAopwKDwc/pbuilderrc_GhsN --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZuAopwKDwc/b2 --logfile b2/build.log biojava-live_1.7.1-8.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://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) 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 Aug 6 20:25 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/23796/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 Sep 10 11:58 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 10 04:46 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/47265/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -339,7 +373,7 @@ Get: 123 http://deb.debian.org/debian buster/main amd64 libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 125 http://deb.debian.org/debian buster/main amd64 libhsqldb-java all 2.4.1-2 [1633 kB] -Fetched 318 MB in 4s (76.9 MB/s) +Fetched 318 MB in 4s (76.1 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.) @@ -1048,7 +1082,7 @@ 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/biojava-live-1.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/biojava-live-1.7.1/ && 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 biojava-live dpkg-buildpackage: info: source version 1:1.7.1-8 dpkg-buildpackage: info: source distribution unstable @@ -1149,7 +1183,7 @@ [jar] Building jar: /build/biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL -Total time: 14 seconds +Total time: 13 seconds # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1427,7 +1461,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 19 seconds +Total time: 18 seconds touch build-stamp make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_auto_test @@ -1488,190 +1522,190 @@ runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Running org.biojava.bio.MergeAnnotationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.dist.DistSerTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.223 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 sec [junit] Running org.biojava.bio.dist.DistributionTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.dp.DPSerializationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.fastq.FastqTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest - [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.program.sax.BlastTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.36 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.395 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.373 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.478 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.473 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.41 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.406 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.499 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.581 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.416 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.541 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.176 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.222 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.035 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.736 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.057 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.205 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.seq.DNAToolsTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.seq.RNAToolsTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest - [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 0.477 sec + [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 0.507 sec [junit] Test org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest FAILED [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest - [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest - [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.434 sec + [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.484 sec [junit] Test org.biojava.bio.seq.io.SeqIOToolsTest FAILED [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.471 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.structure.MMcifTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.755 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.016 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.281 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest - [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.285 sec + [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.283 sec [junit] Test org.biojava.bio.structure.StructurePairAlignerTest FAILED [junit] Running org.biojava.bio.structure.StructureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Running org.biojava.bio.structure.StructureToolsTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest @@ -1679,112 +1713,112 @@ [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.543 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.58 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.GappedSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.PointLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SymbolListTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.424 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.TranslationTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec [junit] Running org.biojava.directory.OBDARegistryParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.directory.RegistryConfigurationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.directory.SystemRegistryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec [junit] Running org.biojava.naming.ObdaUriParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.ontology.OntologyTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.ontology.ParseOBOFileTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec [junit] Running org.biojava.ontology.TermImplTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.ontology.TripleImplTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.ListToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.SmallMapTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.utils.automata.NfaTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.process.ExternalProcessTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.utils.regex.RegexTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.utils.walker.WalkerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.EmptyRichAnnotationTest [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleCommentTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleCrossRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.SimpleDocRefTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.SimpleNamespaceTest - [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.004 sec [junit] Test org.biojavax.SimpleNamespaceTest FAILED [junit] Running org.biojavax.SimpleNoteTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.SimpleRankedDocRefTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.SimpleRichAnnotationTest @@ -1795,35 +1829,35 @@ [junit] Running org.biojavax.bio.seq.CompoundRichLocationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec [junit] Running org.biojavax.ga.util.GAToolsTest @@ -1835,10 +1869,10 @@ [junit] Running org.biojavax.ontology.SimpleComparableTermTest [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec BUILD SUCCESSFUL -Total time: 27 seconds +Total time: 28 seconds make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_installdocs dh_installchangelogs @@ -1869,21 +1903,23 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.7.1-8_all.deb'. +dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-8_all.deb'. dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-8_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-8_all.deb'. -dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-8_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava-live_1.7.1-8_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/47265/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/47265/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/23796 and its subdirectories -I: Current time: Sat Aug 7 03:35:10 -12 2021 -I: pbuilder-time-stamp: 1628350510 +I: removing directory /srv/workspace/pbuilder/47265 and its subdirectories +I: Current time: Sat Sep 10 12:00:41 +14 2022 +I: pbuilder-time-stamp: 1662760841