Diff of the two buildlogs: -- --- b1/build.log 2020-10-17 02:54:05.288946780 +0000 +++ b2/build.log 2020-10-17 03:06:51.251349892 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 18 20:57:58 -12 2021 -I: pbuilder-time-stamp: 1637312278 +I: Current time: Sat Oct 17 16:54:18 +14 2020 +I: pbuilder-time-stamp: 1602903259 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 '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 18 07:48:29 2019 -12 +gpgv: Signature made Sat Jan 19 09:48:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-2.dsc @@ -35,136 +35,170 @@ dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/19800/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/31190/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled10-arm64. +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/31190/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/31190/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='19800' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=31190 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.jYSS2kUrcU/pbuilderrc_3YKK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.jYSS2kUrcU/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.jYSS2kUrcU/pbuilderrc_b6Ea --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.jYSS2kUrcU/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled11-arm64 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 - -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat - -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown - -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp - -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash - -rwxr-xr-x 1 root root 97136 Feb 28 2019 date - -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93752 Feb 28 2019 df - -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir - -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 27256 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln - -rwxr-xr-x 1 root root 52544 Jul 26 2018 login - -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 38840 Jan 9 2019 more - -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm - -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 9 02:48 sh -> dash - -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty - -rwsr-xr-x 1 root root 59424 Jan 9 2019 su - -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync - -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar - -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch - -rwxr-xr-x 1 root root 27256 Feb 28 2019 true - -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount - -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34824 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/19800/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Oct 17 16:54 sh -> bash + lrwxrwxrwx 1 root root 4 Oct 7 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 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/31190/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -501,7 +535,7 @@ Get: 241 http://deb.debian.org/debian buster/main arm64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 242 http://deb.debian.org/debian buster/main arm64 libxmlunit-java all 1.6-1 [95.5 kB] Get: 243 http://deb.debian.org/debian buster/main arm64 rdfind arm64 1.4.1-1 [38.3 kB] -Fetched 335 MB in 50s (6727 kB/s) +Fetched 335 MB in 1min 11s (4697 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) @@ -1674,7 +1708,7 @@ 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/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/biojava4-live-4.2.12+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 biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1685,7 +1719,7 @@ dh clean --with javahelper jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan dh_clean rm -rf build rm -rf dist @@ -1696,13 +1730,13 @@ rm -rf doc find . -name "*.class" -delete rm -rf buildtest -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten debian/rules build dh build --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml @@ -1720,10 +1754,10 @@ sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan cd biojava-jcolorbrewer && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml @@ -1740,7 +1774,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 5 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1756,7 +1790,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 1 minute 18 seconds +Total time: 25 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1774,7 +1808,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 31 seconds +Total time: 11 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1788,7 +1822,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 11 seconds +Total time: 4 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1804,7 +1838,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 18 seconds +Total time: 6 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1822,7 +1856,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 18 seconds +Total time: 6 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1838,7 +1872,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 7 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1853,7 +1887,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 12 seconds +Total time: 4 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1871,7 +1905,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 1 minute 18 seconds +Total time: 28 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1889,7 +1923,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 45 seconds +Total time: 22 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1905,7 +1939,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 21 seconds +Total time: 13 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1923,7 +1957,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 14 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1939,7 +1973,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 17 seconds +Total time: 10 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1953,7 +1987,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 4 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1969,7 +2003,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 18 seconds +Total time: 6 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1983,7 +2017,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 27 seconds +Total time: 11 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2275,11 +2309,11 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 2 minutes 40 seconds +Total time: 1 minute 1 second # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -2308,169 +2342,169 @@ [echo] Using java version 11.0.8 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.521 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.521 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.348 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.348 sec [junit] - [junit] Testcase: testGetIndexOf took 0.25 sec + [junit] Testcase: testGetIndexOf took 0.167 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetNumGaps took 0.005 sec - [junit] Testcase: testGetStart took 0.001 sec - [junit] Testcase: testGetSequenceIndexAt took 0 sec - [junit] Testcase: testGetAccession took 0.006 sec - [junit] Testcase: testToString took 0.004 sec + [junit] Testcase: testGetNumGaps took 0.001 sec + [junit] Testcase: testGetStart took 0 sec + [junit] Testcase: testGetSequenceIndexAt took 0.001 sec + [junit] Testcase: testGetAccession took 0.001 sec + [junit] Testcase: testToString took 0.003 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec - [junit] Testcase: testCountCompounds took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAt took 0 sec + [junit] Testcase: testCountCompounds took 0.002 sec + [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.007 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.003 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.008 sec - [junit] Testcase: testGetOriginalSequence took 0.009 sec + [junit] Testcase: testGetAsList took 0.004 sec + [junit] Testcase: testGetOriginalSequence took 0.001 sec [junit] Testcase: testGetCompoundAt took 0.001 sec - [junit] Testcase: testGetLength took 0.001 sec - [junit] Testcase: testIsCircular took 0.005 sec - [junit] Testcase: testGetEnd took 0 sec - [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec - [junit] Testcase: testSimpleAlignedSequenceShort took 0.009 sec - [junit] Testcase: testGetOverlapCount took 0 sec - [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetLocationInAlignment took 0.01 sec - [junit] Testcase: testIterator took 0.003 sec + [junit] Testcase: testGetLength took 0 sec + [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetEnd took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec + [junit] Testcase: testGetOverlapCount took 0.001 sec + [junit] Testcase: testGetCompoundSet took 0.001 sec + [junit] Testcase: testGetLocationInAlignment took 0.002 sec + [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetSequenceAsString took 0.001 sec - [junit] Testcase: testGetLastIndexOf took 0 sec - [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.011 sec + [junit] Testcase: testGetLastIndexOf took 0.001 sec + [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.017 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.772 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.772 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.608 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.608 sec [junit] - [junit] Testcase: testGetIndexOf took 0.272 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.011 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.003 sec - [junit] Testcase: testToStringInt took 0.068 sec + [junit] Testcase: testGetIndexOf took 0.242 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.004 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.004 sec + [junit] Testcase: testToStringInt took 0.05 sec [junit] Testcase: testToString took 0.002 sec - [junit] Testcase: testToStringFormatted took 0.124 sec - [junit] Testcase: testSimpleProfile took 0.008 sec + [junit] Testcase: testToStringFormatted took 0.094 sec + [junit] Testcase: testSimpleProfile took 0.006 sec [junit] Testcase: testGetSize took 0.001 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec - [junit] Testcase: testGetAlignedSequences took 0.006 sec + [junit] Testcase: testGetAlignedSequences took 0 sec [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED - [junit] Testcase: testGetCompoundAtSInt took 0.001 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.01 sec - [junit] Testcase: testGetIndicesAt took 0.004 sec + [junit] Testcase: testGetCompoundAtSInt took 0 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec + [junit] Testcase: testGetIndicesAt took 0.012 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.003 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.009 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec - [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.009 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetCompoundsAt took 0.001 sec + [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec [junit] Testcase: testIterator took 0.001 sec - [junit] Testcase: testGetLastIndexOf took 0.01 sec + [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.009 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.278 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.005 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.381 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.005 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetIndexInTargetAt took 0 sec + [junit] Testcase: testGetIndexInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.005 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.011 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.005 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetNumIdenticals took 0 sec - [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec + [junit] Testcase: testGetNumIdenticals took 0.007 sec + [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.009 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.006 sec + [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumSimilars took 0.002 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.228 sec - [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testGetAlignment took 0.177 sec + [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 1.294 sec - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 1.294 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 1.028 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 1.028 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml - [junit] Nov 18, 2021 9:12:06 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Oct 17, 2020 5:01:59 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Nov 18, 2021 9:12:06 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Oct 17, 2020 5:01:59 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testConstructorWithEvalueHspFilter took 0.736 sec + [junit] Testcase: testConstructorWithEvalueHspFilter took 0.594 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2481,8 +2515,8 @@ [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] - [junit] Testcase: testConstructorWithFactoryGuess took 0.434 sec - [junit] Testcase: testConstructorWithoutFactoryGuess took 0.017 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.34 sec + [junit] Testcase: testConstructorWithoutFactoryGuess took 0.01 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2497,7 +2531,7 @@ BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed -Total time: 41 seconds +Total time: 29 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -2512,32 +2546,32 @@ [echo] Using java version 11.0.8 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.603 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.603 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 sec [junit] - [junit] Testcase: testGetQuery took 0.296 sec - [junit] Testcase: testGetScore took 0.187 sec + [junit] Testcase: testGetQuery took 0.216 sec + [junit] Testcase: testGetScore took 0.077 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.571 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.571 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.323 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.323 sec [junit] - [junit] Testcase: testGetQuery took 0.277 sec - [junit] Testcase: testGetScore took 0.113 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.006 sec - [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testGetQuery took 0.168 sec + [junit] Testcase: testGetScore took 0.048 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.377 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.377 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.054 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.054 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -2549,157 +2583,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.84 sec - [junit] Testcase: testToString took 0.036 sec - [junit] Testcase: testGetScoreMatrix took 0.024 sec - [junit] Testcase: testGetRoot took 0.298 sec - [junit] Testcase: testGetSequences took 0.017 sec - [junit] Testcase: testGetDistanceMatrix took 0.004 sec - [junit] Testcase: testGetAllPairsScores took 0.014 sec - [junit] Testcase: testIterator took 0.016 sec + [junit] Testcase: testGuideTree took 0.523 sec + [junit] Testcase: testToString took 0.019 sec + [junit] Testcase: testGetScoreMatrix took 0.028 sec + [junit] Testcase: testGetRoot took 0.3 sec + [junit] Testcase: testGetSequences took 0.009 sec + [junit] Testcase: testGetDistanceMatrix took 0.009 sec + [junit] Testcase: testGetAllPairsScores took 0.012 sec + [junit] Testcase: testIterator took 0.004 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.533 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.297 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.392 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.722 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.722 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.023 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.023 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.398 sec - [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.158 sec - [junit] Testcase: should_align_middle_anchor took 0.142 sec - [junit] Testcase: testGetQuery took 0.001 sec - [junit] Testcase: testGetScore took 0.014 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.149 sec + [junit] Testcase: testGetGapPenalty took 0.001 sec + [junit] Testcase: testGetComputationTime took 0.065 sec + [junit] Testcase: should_align_middle_anchor took 0.077 sec + [junit] Testcase: testGetQuery took 0 sec + [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.002 sec - [junit] Testcase: testGetScoreMatrix took 0.013 sec - [junit] Testcase: testGetPair took 0.003 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.007 sec [junit] Testcase: should_align_multiple_anchors took 0.002 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.022 sec - [junit] Testcase: testGetProfile took 0.023 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.01 sec + [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_ending_anchor took 0.002 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.01 sec - [junit] Testcase: testComplex took 0.053 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.081 sec - [junit] Testcase: should_align_starting_anchor took 0.012 sec + [junit] Testcase: should_align_ending_anchor took 0.001 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.003 sec + [junit] Testcase: testComplex took 0.027 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.07 sec + [junit] Testcase: should_align_starting_anchor took 0.002 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec - [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: testIntOverflowBug took 0.641 sec + [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testIntOverflowBug took 0.464 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.163 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 sec [junit] - [junit] Testcase: testOpenPenalty took 0.01 sec + [junit] Testcase: testOpenPenalty took 0.011 sec [junit] Testcase: testType took 0.001 sec - [junit] Testcase: testExtensionPenalty took 0.002 sec + [junit] Testcase: testExtensionPenalty took 0.001 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec [junit] Testcase: testSimpleGapPenalty took 0 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.535 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.535 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 sec [junit] - [junit] Testcase: testGetQuery took 0.375 sec - [junit] Testcase: testGetTarget took 0.01 sec - [junit] Testcase: testSimpleProfilePair took 0.013 sec + [junit] Testcase: testGetQuery took 0.321 sec + [junit] Testcase: testGetTarget took 0.002 sec + [junit] Testcase: testSimpleProfilePair took 0.01 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.956 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.956 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.448 sec - [junit] Testcase: testGetGapPenalty took 0.023 sec - [junit] Testcase: testGetComputationTime took 0.022 sec - [junit] Testcase: testGetQuery took 0.022 sec - [junit] Testcase: testGetScore took 0.005 sec - [junit] Testcase: testGetScoreMatrix took 0.023 sec - [junit] Testcase: testGetPair took 0.042 sec - [junit] Testcase: testGetProfile took 0.023 sec - [junit] Testcase: testGetMinScore took 0.02 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.166 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.012 sec - [junit] Testcase: testGetTarget took 0.003 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.188 sec + [junit] Testcase: testGetGapPenalty took 0.014 sec + [junit] Testcase: testGetComputationTime took 0.011 sec + [junit] Testcase: testGetQuery took 0.006 sec + [junit] Testcase: testGetScore took 0.006 sec + [junit] Testcase: testGetScoreMatrix took 0.01 sec + [junit] Testcase: testGetPair took 0.027 sec + [junit] Testcase: testGetProfile took 0.01 sec + [junit] Testcase: testGetMinScore took 0.006 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.005 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.098 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.005 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.005 sec + [junit] Testcase: testGetTarget took 0.005 sec + [junit] Testcase: testGetMaxScore took 0.003 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.397 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.397 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.011 sec - [junit] Testcase: testSetDescription took 0.044 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.012 sec + [junit] Testcase: testSetDescription took 0.057 sec [junit] Testcase: testToString took 0.097 sec [junit] Testcase: testCaseEquivalence took 0.002 sec - [junit] Testcase: test took 0.036 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.031 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.015 sec - [junit] Testcase: testSetName took 0.03 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.005 sec + [junit] Testcase: test took 0.017 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.02 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.017 sec + [junit] Testcase: testSetName took 0.019 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.01 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.778 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.778 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.233 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.244 sec [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.094 sec + [junit] Testcase: testGetComputationTime took 0.125 sec [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetScore took 0.011 sec - [junit] Testcase: testGetScoreMatrix took 0.011 sec - [junit] Testcase: testGetPair took 0.016 sec - [junit] Testcase: testSmithWaterman took 0.01 sec - [junit] Testcase: testGetProfile took 0.006 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testGetScore took 0.012 sec + [junit] Testcase: testGetScoreMatrix took 0.003 sec + [junit] Testcase: testGetPair took 0.026 sec + [junit] Testcase: testSmithWaterman took 0.005 sec + [junit] Testcase: testGetProfile took 0.003 sec + [junit] Testcase: testGetMinScore took 0.003 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.244 sec - [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.159 sec + [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.02 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.016 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.01 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.006 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec - [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec + [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0.001 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec - [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.009 sec - [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.001 sec + [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec + [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.002 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.609 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.609 sec [junit] - [junit] Testcase: testGetComputationTime took 0.336 sec - [junit] Testcase: testGuanUberbacher took 0.002 sec - [junit] Testcase: testGetScore took 0.009 sec - [junit] Testcase: testGetPair took 0.024 sec - [junit] Testcase: testGetProfile took 0.014 sec + [junit] Testcase: testGetComputationTime took 0.372 sec + [junit] Testcase: testGuanUberbacher took 0.011 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetPair took 0.013 sec + [junit] Testcase: testGetProfile took 0.012 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_shorter_target took 0.143 sec - [junit] Testcase: should_align_multiple_cuts took 0.011 sec + [junit] Testcase: should_align_shorter_target took 0.075 sec + [junit] Testcase: should_align_multiple_cuts took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: should_align_shorter_query took 0.002 sec + [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL -Total time: 51 seconds +Total time: 40 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -2722,8 +2756,8 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.686 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.686 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.141 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.141 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -2731,12 +2765,12 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 2.275 sec - [junit] Testcase: testExample1 took 0.108 sec - [junit] Testcase: testExample2 took 0.023 sec - [junit] Testcase: testExample3 took 0.018 sec - [junit] Testcase: testExample1WithCSV took 0.11 sec - [junit] Testcase: testWithCases took 0.035 sec + [junit] Testcase: testAdvancedXMLExample took 1.732 sec + [junit] Testcase: testExample1 took 0.13 sec + [junit] Testcase: testExample2 took 0.03 sec + [junit] Testcase: testExample3 took 0.038 sec + [junit] Testcase: testExample1WithCSV took 0.098 sec + [junit] Testcase: testWithCases took 0.025 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2744,14 +2778,14 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.64 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.64 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.073 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.073 sec [junit] - [junit] Testcase: shortExample1 took 0.13 sec - [junit] Testcase: shortExample2 took 1.991 sec - [junit] Testcase: shortExample3 took 0.259 sec - [junit] Testcase: shortExample4 took 0.003 sec - [junit] Testcase: shortExample5 took 0.036 sec + [junit] Testcase: shortExample1 took 0.119 sec + [junit] Testcase: shortExample2 took 1.513 sec + [junit] Testcase: shortExample3 took 0.187 sec + [junit] Testcase: shortExample4 took 0.007 sec + [junit] Testcase: shortExample5 took 0.018 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2759,19 +2793,19 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.942 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.942 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.537 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.537 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 2.489 sec - [junit] Testcase: testExample1 took 0.164 sec - [junit] Testcase: testExample2 took 0.028 sec - [junit] Testcase: testExample3 took 0.04 sec - [junit] Testcase: testExample1WithCSV took 0.066 sec - [junit] Testcase: testWithCases took 0.049 sec + [junit] Testcase: testAdvancedXMLExample took 2.154 sec + [junit] Testcase: testExample1 took 0.073 sec + [junit] Testcase: testExample2 took 0.055 sec + [junit] Testcase: testExample3 took 0.065 sec + [junit] Testcase: testExample1WithCSV took 0.052 sec + [junit] Testcase: testWithCases took 0.042 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2779,8 +2813,8 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.759 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.759 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.127 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.127 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. @@ -2995,41 +3029,41 @@ [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAbsorbance took 0.108 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 2.157 sec - [junit] Testcase: testEnrichment took 0.07 sec + [junit] Testcase: testAbsorbance took 0.074 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 1.93 sec + [junit] Testcase: testEnrichment took 0.034 sec [junit] Testcase: testApliphaticIndex took 0.002 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.039 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.019 sec [junit] Testcase: testApliphaticIndexNull took 0 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.013 sec - [junit] Testcase: testAbsorbanceNull took 0.001 sec - [junit] Testcase: testIsoelectricPointNull took 0.001 sec - [junit] Testcase: testAverageHydropathy took 0.01 sec - [junit] Testcase: testExtinctionCoefficient took 0.007 sec - [junit] Testcase: testAAComposition took 0.003 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.204 sec - [junit] Testcase: testMolecularWeight took 0.002 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.005 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.01 sec + [junit] Testcase: testAbsorbanceNull took 0 sec + [junit] Testcase: testIsoelectricPointNull took 0 sec + [junit] Testcase: testAverageHydropathy took 0.001 sec + [junit] Testcase: testExtinctionCoefficient took 0.003 sec + [junit] Testcase: testAAComposition took 0.007 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.157 sec + [junit] Testcase: testMolecularWeight took 0.007 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.011 sec [junit] Testcase: testNetChargeNull took 0.001 sec - [junit] Testcase: testExtinctionCoefficientNull took 0 sec - [junit] Testcase: testNetCharge took 0.539 sec + [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec + [junit] Testcase: testNetCharge took 0.46 sec [junit] Testcase: testEnrichmentNull took 0.001 sec - [junit] Testcase: testInstabilityIndexNull took 0.001 sec - [junit] Testcase: testAverageHydropathyNull took 0 sec - [junit] Testcase: testMolecularWeightXML took 0.353 sec - [junit] Testcase: testInstabilityIndex took 0.002 sec + [junit] Testcase: testInstabilityIndexNull took 0 sec + [junit] Testcase: testAverageHydropathyNull took 0.001 sec + [junit] Testcase: testMolecularWeightXML took 0.224 sec + [junit] Testcase: testInstabilityIndex took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.169 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec [junit] - [junit] Testcase: testFake took 0.007 sec + [junit] Testcase: testFake took 0.01 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 sec [junit] - [junit] Testcase: testFakeTest took 0.003 sec + [junit] Testcase: testFakeTest took 0.002 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] WARNING: An illegal reflective access operation has occurred @@ -3037,20 +3071,20 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.54 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.54 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.625 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.625 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: generateSchema took 1.76 sec - [junit] Testcase: readWithIDXml took 0.97 sec - [junit] Testcase: readMinXml took 0.236 sec - [junit] Testcase: readAdvancedXml took 0.108 sec - [junit] Testcase: generateXml took 0.103 sec - [junit] Testcase: readXml took 0.242 sec + [junit] Testcase: generateSchema took 1.431 sec + [junit] Testcase: readWithIDXml took 0.476 sec + [junit] Testcase: readMinXml took 0.16 sec + [junit] Testcase: readAdvancedXml took 0.133 sec + [junit] Testcase: generateXml took 0.101 sec + [junit] Testcase: readXml took 0.198 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] WARNING: An illegal reflective access operation has occurred @@ -3058,21 +3092,21 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.8 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.8 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.21 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.21 sec [junit] - [junit] Testcase: generateSchema took 1.629 sec - [junit] Testcase: generateXml took 0.409 sec - [junit] Testcase: readXml took 0.58 sec + [junit] Testcase: generateSchema took 1.242 sec + [junit] Testcase: generateXml took 0.217 sec + [junit] Testcase: readXml took 0.603 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.341 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.341 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 sec [junit] - [junit] Testcase: testFake took 0.019 sec + [junit] Testcase: testFake took 0.002 sec BUILD SUCCESSFUL -Total time: 56 seconds +Total time: 46 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -3089,7 +3123,7 @@ [echo] Using java version 11.0.8 BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 10 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -3105,253 +3139,253 @@ [echo] Using java version 11.0.8 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.48 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.542 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.542 sec [junit] - [junit] Testcase: testConvert took 0.428 sec + [junit] Testcase: testConvert took 0.468 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.013 sec - [junit] Testcase: testBuildNullDescription took 0.001 sec - [junit] Testcase: testBuildAppendQuality took 0.005 sec - [junit] Testcase: testBuild took 0.002 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec + [junit] Testcase: testBuildAppendSequence took 0.014 sec + [junit] Testcase: testBuildNullDescription took 0 sec + [junit] Testcase: testBuildAppendQuality took 0 sec + [junit] Testcase: testBuild took 0.007 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0.001 sec [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec - [junit] Testcase: testBuildNullAppendQuality took 0.001 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.001 sec + [junit] Testcase: testBuildNullAppendQuality took 0 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0.001 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0.001 sec [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec - [junit] Testcase: testBuildNullVariant took 0 sec + [junit] Testcase: testBuildNullVariant took 0.001 sec [junit] Testcase: testBuildDefault took 0 sec - [junit] Testcase: testBuildMissingSequence took 0 sec + [junit] Testcase: testBuildMissingSequence took 0.001 sec [junit] Testcase: testBuildNullQuality took 0 sec - [junit] Testcase: testBuildMultiple took 0.001 sec - [junit] Testcase: testConstructor took 0 sec + [junit] Testcase: testBuildMultiple took 0 sec + [junit] Testcase: testConstructor took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec [junit] - [junit] Testcase: testImmutable took 0.009 sec - [junit] Testcase: testBuilder took 0.01 sec - [junit] Testcase: testVariant took 0.004 sec - [junit] Testcase: testQuality took 0.013 sec + [junit] Testcase: testImmutable took 0.005 sec + [junit] Testcase: testBuilder took 0.006 sec + [junit] Testcase: testVariant took 0 sec + [junit] Testcase: testQuality took 0.01 sec [junit] Testcase: testHashCode took 0 sec - [junit] Testcase: testEquals took 0 sec + [junit] Testcase: testEquals took 0.001 sec [junit] Testcase: testDescription took 0 sec - [junit] Testcase: testConstructor took 0.001 sec - [junit] Testcase: testSequence took 0 sec + [junit] Testcase: testConstructor took 0 sec + [junit] Testcase: testSequence took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.013 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.005 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.002 sec [junit] Testcase: testConvertNullVariant took 0 sec - [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.011 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.189 sec + [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.164 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec - [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec + [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec - [junit] Testcase: testConvertNullFastq took 0 sec + [junit] Testcase: testConvertNullFastq took 0.003 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.002 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec - [junit] Testcase: testCreateDNASequenceNullFastq took 0.001 sec - [junit] Testcase: testConvertQualitiesNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec - [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec + [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec + [junit] Testcase: testConvertQualitiesNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.006 sec + [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec - [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec - [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec - [junit] Testcase: testCreateQualityScoresNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec + [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec + [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec - [junit] Testcase: testToListNotAList took 0.002 sec + [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0.001 sec + [junit] Testcase: testToListNotAList took 0.006 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec - [junit] Testcase: testQualityScores took 0.024 sec + [junit] Testcase: testQualityScores took 0.04 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec - [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0.001 sec + [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testToList took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec - [junit] Testcase: testErrorProbabilities took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0.001 sec + [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.011 sec + [junit] Testcase: testParseFastqVariant took 0.02 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec - [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec - [junit] Testcase: testIsSanger took 0.01 sec + [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec + [junit] Testcase: testIsSanger took 0.009 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec - [junit] Testcase: testIsSolexa took 0.001 sec + [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.526 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.526 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.101 sec - [junit] Testcase: testWrappingAsIllumina took 0.006 sec + [junit] Testcase: testFullRangeAsIllumina took 0.092 sec + [junit] Testcase: testWrappingAsIllumina took 0.007 sec [junit] Testcase: testValidateDescription took 0.021 sec - [junit] Testcase: testValidateRepeatDescription took 0.007 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.009 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.005 sec - [junit] Testcase: testLongReadsAsIllumina took 0.026 sec - [junit] Testcase: testParseNullReadable took 0.002 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.086 sec + [junit] Testcase: testValidateRepeatDescription took 0.006 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.005 sec + [junit] Testcase: testMiscRnaAsIllumina took 0.008 sec + [junit] Testcase: testLongReadsAsIllumina took 0.013 sec + [junit] Testcase: testParseNullReadable took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.056 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.119 sec - [junit] Testcase: testParse took 0.01 sec + [junit] Testcase: testErrorExamples took 0.14 sec + [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.003 sec - [junit] Testcase: testReadEmptyInputStream took 0.002 sec - [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testWrappedSequence took 0.009 sec + [junit] Testcase: testReadEmptyInputStream took 0.013 sec + [junit] Testcase: testParseNullParseListener took 0.001 sec [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testMultipleWrappedQuality took 0.011 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testReadURL took 0.005 sec [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.02 sec - [junit] Testcase: testWrappedQuality took 0.015 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.006 sec + [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.025 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.018 sec [junit] Testcase: testAppendVararg took 0.001 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.007 sec - [junit] Testcase: testWriteFileIterable took 0.072 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.008 sec + [junit] Testcase: testWriteFileIterable took 0.039 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.002 sec + [junit] Testcase: testAppendIterable took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testWriteFileVararg took 0.004 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.126 sec - [junit] Testcase: testFullRangeAsSanger took 0.011 sec - [junit] Testcase: testWrappingOriginal took 0.008 sec - [junit] Testcase: testLongReadsOriginal took 0.024 sec - [junit] Testcase: testMiscDnaOriginal took 0.011 sec - [junit] Testcase: testMiscRnaOriginal took 0.011 sec - [junit] Testcase: testValidateDescription took 0.036 sec - [junit] Testcase: testValidateRepeatDescription took 0.003 sec - [junit] Testcase: testFullRangeOriginal took 0.003 sec - [junit] Testcase: testWrappingAsSanger took 0.016 sec - [junit] Testcase: testLongReadsAsSanger took 0.011 sec - [junit] Testcase: testMiscDnaAsSanger took 0.007 sec - [junit] Testcase: testParseNullReadable took 0.002 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.065 sec + [junit] Testcase: testMiscRnaAsSanger took 0.097 sec + [junit] Testcase: testFullRangeAsSanger took 0.007 sec + [junit] Testcase: testWrappingOriginal took 0.006 sec + [junit] Testcase: testLongReadsOriginal took 0.013 sec + [junit] Testcase: testMiscDnaOriginal took 0.004 sec + [junit] Testcase: testMiscRnaOriginal took 0.003 sec + [junit] Testcase: testValidateDescription took 0.019 sec + [junit] Testcase: testValidateRepeatDescription took 0.016 sec + [junit] Testcase: testFullRangeOriginal took 0.009 sec + [junit] Testcase: testWrappingAsSanger took 0.003 sec + [junit] Testcase: testLongReadsAsSanger took 0.007 sec + [junit] Testcase: testMiscDnaAsSanger took 0.003 sec + [junit] Testcase: testParseNullReadable took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.064 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.1 sec - [junit] Testcase: testParse took 0.014 sec + [junit] Testcase: testErrorExamples took 0.053 sec + [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.002 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec - [junit] Testcase: testParseNullParseListener took 0.012 sec + [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.003 sec - [junit] Testcase: testCreateFastqReader took 0.011 sec + [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.023 sec - [junit] Testcase: testAppendVararg took 0 sec - [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testConvertNotSangerVariant took 0.017 sec + [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testWriteOutputStreamVararg took 0.008 sec - [junit] Testcase: testWriteFileIterable took 0.066 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.014 sec - [junit] Testcase: testAppendIterable took 0 sec + [junit] Testcase: testWriteFileIterable took 0.063 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec + [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testWriteFileVararg took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.546 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.546 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.144 sec - [junit] Testcase: testFullRangeAsSolexa took 0.01 sec - [junit] Testcase: testValidateDescription took 0.029 sec - [junit] Testcase: testValidateRepeatDescription took 0.01 sec - [junit] Testcase: testWrappingAsSolexa took 0.011 sec - [junit] Testcase: testLongReadsAsSolexa took 0.015 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.004 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.104 sec + [junit] Testcase: testFullRangeAsSolexa took 0.019 sec + [junit] Testcase: testValidateDescription took 0.045 sec + [junit] Testcase: testValidateRepeatDescription took 0.014 sec + [junit] Testcase: testWrappingAsSolexa took 0.017 sec + [junit] Testcase: testLongReadsAsSolexa took 0.017 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.013 sec [junit] Testcase: testParseNullReadable took 0.002 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.097 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.093 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.121 sec + [junit] Testcase: testErrorExamples took 0.131 sec [junit] Testcase: testParse took 0.002 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testCreateFastq took 0.013 sec + [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.002 sec - [junit] Testcase: testReadEmptyInputStream took 0.014 sec + [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.003 sec + [junit] Testcase: testMultipleWrappedQuality took 0.002 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.009 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.018 sec - [junit] Testcase: testAppendVararg took 0 sec - [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.011 sec - [junit] Testcase: testWriteFileIterable took 0.097 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.016 sec + [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testCreateFastq took 0.001 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.015 sec + [junit] Testcase: testWriteFileIterable took 0.049 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec - [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testCreateFastqWriter took 0.007 sec + [junit] Testcase: testWriteFileVararg took 0.005 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.007 sec - [junit] Testcase: testStreamNullListener took 0.006 sec - [junit] Testcase: testStreamNullReadable took 0.001 sec + [junit] Testcase: testStreamNullVariant took 0.005 sec + [junit] Testcase: testStreamNullListener took 0.005 sec + [junit] Testcase: testStreamNullReadable took 0.002 sec BUILD SUCCESSFUL Total time: 42 seconds @@ -3375,39 +3409,39 @@ [echo] Using java version 11.0.8 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest - [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: 0.055 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec [junit] [junit] Testcase: testMe took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] - [junit] Testcase: testSomeMethod took 0.002 sec + [junit] Testcase: testSomeMethod took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testGetColor took 0.008 sec [junit] Testcase: testSetStructure took 0 sec - [junit] Testcase: testClear took 0.001 sec - [junit] Testcase: testGetSelection took 0.01 sec - [junit] Testcase: testRepaint took 0 sec + [junit] Testcase: testClear took 0 sec + [junit] Testcase: testGetSelection took 0.006 sec + [junit] Testcase: testRepaint took 0.001 sec [junit] Testcase: testSetSelection took 0 sec - [junit] Testcase: testSetZoom took 0.001 sec + [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec - [junit] Testcase: testSetStyle took 0.001 sec + [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 19 seconds +Total time: 15 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -3422,8 +3456,8 @@ [echo] Using java version 11.0.8 BUILD SUCCESSFUL -Total time: 9 seconds -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +Total time: 8 seconds +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with javahelper @@ -3431,7 +3465,7 @@ dh_prep dh_install debian/rules override_jh_installjavadoc -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt binnengegaan jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ /usr/share/doc/openjdk-11-jre-headless \ @@ -3452,7 +3486,7 @@ Failed moving /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-jre-headless/api/jquery/jquery-3.3.1.js Making 20 links. -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Map '/build/biojava4-live-4.2.12+dfsg' wordt verlaten dh_installdocs dh_installchangelogs dh_lintian @@ -3470,21 +3504,23 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-2_all.deb'. -dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb'. -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-2_all.deb'. +dpkg-deb: pakket 'libbiojava4.0-java' wordt gebouwd in '../libbiojava4.0-java_4.2.12+dfsg-2_all.deb'. +dpkg-deb: pakket 'libbiojava4-java-doc' wordt gebouwd in '../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb'. +dpkg-deb: pakket 'libbiojava4-java' wordt gebouwd in '../libbiojava4-java_4.2.12+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-2_arm64.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/31190/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/31190/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/19800 and its subdirectories -I: Current time: Thu Nov 18 21:17:01 -12 2021 -I: pbuilder-time-stamp: 1637313421 +I: removing directory /srv/workspace/pbuilder/31190 and its subdirectories +I: Current time: Sat Oct 17 17:06:49 +14 2020 +I: pbuilder-time-stamp: 1602904009