Diff of the two buildlogs: -- --- b1/build.log 2023-04-27 19:41:27.241867751 +0000 +++ b2/build.log 2023-04-27 19:45:02.920309418 +0000 @@ -1,9 +1,6 @@ -W: cgroups are not available on the host, not using them. -unshare: unshare failed: Cannot allocate memory -W: pbuilder: unshare CLONE_NEWNET not available -I: pbuilder: network access is available during build! -I: Current time: Thu Apr 27 07:32:14 -12 2023 -I: pbuilder-time-stamp: 1682623934 +I: pbuilder: network access will be disabled during build +I: Current time: Thu May 30 16:04:28 +14 2024 +I: pbuilder-time-stamp: 1717034668 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -20,7 +17,7 @@ I: copying [./biojava4-live_4.2.12+dfsg.orig.tar.xz] I: copying [./biojava4-live_4.2.12+dfsg-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Dec 11 09:26:50 2022 -12 +gpgv: Signature made Mon Dec 12 11:26:50 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava4-live_4.2.12+dfsg-8.dsc: no acceptable signature found @@ -39,136 +36,169 @@ dpkg-source: info: applying fix_ambiguous_method_call.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16354/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 30 16:04 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/130957/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='16354' - PS1='# ' - PS2='> ' + INVOCATION_ID=0710eaa4956e4a3d95cc04df84e21eb6 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=130957 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.76BhPqRa/pbuilderrc_IYYk --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.76BhPqRa/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-8.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.76BhPqRa/pbuilderrc_GtAH --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.76BhPqRa/b2 --logfile b2/build.log --extrapackages usrmerge biojava4-live_4.2.12+dfsg-8.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 13860 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/16354/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 30 16:04 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -498,7 +528,7 @@ Get: 236 http://deb.debian.org/debian bookworm/main i386 libnetx-java all 0.5-4 [138 kB] Get: 237 http://deb.debian.org/debian bookworm/main i386 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 238 http://deb.debian.org/debian bookworm/main i386 libxmlunit-java all 1.6-2 [100 kB] -Fetched 455 MB in 9s (52.2 MB/s) +Fetched 455 MB in 8s (54.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19604 files and directories currently installed.) @@ -1645,8 +1675,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-8_source.changes dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -1658,8 +1699,8 @@ dh clean --with javahelper jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet dh_clean rm -rf build rm -rf dist @@ -1672,15 +1713,15 @@ rm -rf buildtest find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --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' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet 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 @@ -1698,11 +1739,11 @@ 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]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ @@ -1724,7 +1765,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 1 second cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1742,7 +1783,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 26 seconds +Total time: 9 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1760,7 +1801,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 14 seconds +Total time: 3 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1774,7 +1815,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 1 second cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1790,7 +1831,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 2 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1808,7 +1849,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 1 second cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1824,7 +1865,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 2 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1839,7 +1880,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 1 second cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1859,7 +1900,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 33 seconds +Total time: 8 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1879,7 +1920,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 16 seconds +Total time: 4 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1895,7 +1936,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 1 second cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1913,7 +1954,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 1 second cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1929,7 +1970,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 1 second cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1943,7 +1984,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 3 seconds +Total time: 1 second cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1957,7 +1998,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 1 second cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1971,7 +2012,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 2 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2153,7 +2194,7 @@ [javadoc] Loading source files for package org.jcolorbrewer... [javadoc] Loading source files for package org.jcolorbrewer.ui... [javadoc] Constructing Javadoc information... - [javadoc] warning: URL http://java.sun.com/j2se/1.6.0/docs/api/element-list was redirected to https://www.oracle.com/java/technologies/ -- Update the command-line options to suppress this warning. + [javadoc] error: Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/ (java.net.UnknownHostException: java.sun.com) [javadoc] Building index for all the packages and classes... [javadoc] Standard Doclet version 17.0.6+10-Debian-1 [javadoc] Building tree for all the packages and classes... @@ -2710,6 +2751,9 @@ [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatus.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/survival/kaplanmeier/figure/CensorStatusSelect.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeParameters.html... + [javadoc] /build/biojava4-live-4.2.12+dfsg/biojavadoc/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java:361: warning: @param argument "maxNrIterationsForOptimization" is not a parameter name. + [javadoc] * @param maxNrIterationsForOptimization + [javadoc] ^ [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeParameters.ScoringStrategy.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeSideChainMain.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/org/biojava/nbio/structure/align/ce/CeSideChainUserArgumentProcessor.html... @@ -4290,15 +4334,16 @@ [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/index-all.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/overview-summary.html... [javadoc] Generating /build/biojava4-live-4.2.12+dfsg/doc/biojava/help-doc.html... + [javadoc] 1 error [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 52 seconds +Total time: 32 seconds # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -4329,198 +4374,198 @@ [echo] Using java version 17.0.6 [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: 0.197 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.197 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 sec [junit] - [junit] Testcase: testGetIndexOf took 0.07 sec + [junit] Testcase: testGetIndexOf took 0.018 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.002 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetNumGaps took 0.001 sec + [junit] Testcase: testGetNumGaps took 0 sec [junit] Testcase: testGetStart took 0 sec - [junit] Testcase: testGetSequenceIndexAt took 0.001 sec + [junit] Testcase: testGetSequenceIndexAt took 0 sec [junit] Testcase: testGetAccession took 0.001 sec - [junit] Testcase: testToString took 0.006 sec + [junit] Testcase: testToString took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec - [junit] Testcase: testCountCompounds took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec + [junit] Testcase: testCountCompounds took 0 sec + [junit] Testcase: testGetAlignmentIndexAt took 0 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.007 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.002 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.009 sec - [junit] Testcase: testGetOriginalSequence took 0.001 sec - [junit] Testcase: testGetCompoundAt took 0.005 sec + [junit] Testcase: testGetAsList took 0.001 sec + [junit] Testcase: testGetOriginalSequence took 0 sec + [junit] Testcase: testGetCompoundAt took 0 sec [junit] Testcase: testGetLength took 0 sec - [junit] Testcase: testIsCircular took 0 sec - [junit] Testcase: testGetEnd took 0.001 sec + [junit] Testcase: testIsCircular took 0.001 sec + [junit] Testcase: testGetEnd took 0 sec [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec - [junit] Testcase: testGetOverlapCount took 0.006 sec + [junit] Testcase: testGetOverlapCount took 0 sec [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetLocationInAlignment took 0.002 sec + [junit] Testcase: testGetLocationInAlignment took 0.001 sec [junit] Testcase: testIterator took 0 sec - [junit] Testcase: testGetSequenceAsString took 0.009 sec - [junit] Testcase: testGetLastIndexOf took 0.001 sec + [junit] Testcase: testGetSequenceAsString took 0.001 sec + [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 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: 0.349 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.349 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.086 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.086 sec [junit] - [junit] Testcase: testGetIndexOf took 0.147 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.002 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.006 sec - [junit] Testcase: testToStringInt took 0.021 sec - [junit] Testcase: testToString took 0.001 sec - [junit] Testcase: testToStringFormatted took 0.05 sec + [junit] Testcase: testGetIndexOf took 0.031 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec + [junit] Testcase: testToStringInt took 0.006 sec + [junit] Testcase: testToString took 0 sec + [junit] Testcase: testToStringFormatted took 0.01 sec [junit] Testcase: testSimpleProfile took 0.001 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec - [junit] Testcase: testGetAlignedSequences took 0.002 sec + [junit] Testcase: testGetAlignedSequences took 0 sec [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED - [junit] Testcase: testGetCompoundAtSInt took 0.001 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0 sec - [junit] Testcase: testGetIndicesAt took 0.009 sec + [junit] Testcase: testGetCompoundAtSInt took 0 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec + [junit] Testcase: testGetIndicesAt took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.003 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.001 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetLength took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec + [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec - [junit] Testcase: testIsCircular took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetCompoundsAt took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundsAt took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec [junit] Testcase: testIterator took 0 sec [junit] Testcase: testGetLastIndexOf took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds took 0.004 sec + [junit] Testcase: testGetIndicesAtOutOfBounds took 0 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: 0.234 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.141 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.028 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.005 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAt took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.007 sec - [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetNumIdenticals took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.002 sec + [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec + [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.004 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryAt took 0 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.004 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundInTargetAt took 0 sec + [junit] Testcase: testGetIndexInQueryAt took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 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: 0.125 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.107 sec - [junit] Testcase: testHashCode took 0.001 sec + [junit] Testcase: testGetAlignment took 0.036 sec + [junit] Testcase: testHashCode took 0 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: 0, Errors: 0, Skipped: 2, Time elapsed: 0.387 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.387 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.085 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.085 sec [junit] ------------- Standard Error ----------------- - [junit] Apr 27, 2023 7:38:50 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 27, 2023 7:38:51 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] [junit] Testcase: testConstructorWithEvalueHspFilter took 0 sec [junit] SKIPPED: Attemps to use the network - [junit] Testcase: testConstructorWithFactoryGuess took 0.363 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.076 sec [junit] Testcase: testConstructorWithoutFactoryGuess took 0 sec [junit] SKIPPED: Attemps to use the network [junit] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastTabularParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.13 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.13 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.974 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.974 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- - [junit] Apr 27, 2023 7:38:52 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 27, 2023 7:38:52 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results - [junit] Apr 27, 2023 7:38:52 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 27, 2023 7:38:52 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] May 30, 2024 4:06:46 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testCreateObjects took 3.098 sec - [junit] Testcase: testGetFileExtensions took 0.001 sec + [junit] Testcase: testCreateObjects took 0.964 sec + [junit] Testcase: testGetFileExtensions took 0 sec [junit] Testcase: testSetFile took 0 sec [junit] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [junit] Testsuite: org.biojava.nbio.core.search.io.blast.BlastXMLParserTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.052 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.052 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.021 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.021 sec [junit] ------------- Standard Output --------------- [junit] getFileExtensions [junit] setFile @@ -4528,120 +4573,120 @@ [junit] [junit] Testcase: testCreateObjects took 0 sec [junit] SKIPPED: Attempts to use the network - [junit] Testcase: testStoreObjects took 0.004 sec + [junit] Testcase: testStoreObjects took 0.001 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED - [junit] Testcase: testGetFileExtensions took 0.026 sec + [junit] Testcase: testGetFileExtensions took 0.011 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED [junit] Testcase: testSetFile took 0 sec [junit] Running org.biojava.nbio.core.sequence.DNATest [junit] Testsuite: org.biojava.nbio.core.sequence.DNATest - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 sec - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.299 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec [junit] - [junit] Testcase: sequenceEquality took 0.077 sec - [junit] Testcase: subSequence took 0.011 sec - [junit] Testcase: singleCompoundSequence took 0.015 sec - [junit] Testcase: translateToRna took 0.076 sec - [junit] Testcase: kmerNonOverlap took 0.008 sec - [junit] Testcase: twoBit took 0.007 sec - [junit] Testcase: composition took 0.005 sec - [junit] Testcase: fourBit took 0.009 sec - [junit] Testcase: complement took 0.011 sec - [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.004 sec - [junit] Testcase: at took 0.004 sec - [junit] Testcase: gc took 0.005 sec - [junit] Testcase: basesEqual took 0.004 sec - [junit] Testcase: bogusSequence took 0.006 sec - [junit] Testcase: kmerOverlap took 0.003 sec - [junit] Testcase: reverseComplement took 0.008 sec - [junit] Testcase: reverse took 0.005 sec - [junit] Testcase: respectCase took 0.004 sec - [junit] Testcase: basesEquivalent took 0.003 sec - [junit] Testcase: badTwoBit took 0.006 sec + [junit] Testcase: sequenceEquality took 0.023 sec + [junit] Testcase: subSequence took 0.004 sec + [junit] Testcase: singleCompoundSequence took 0.003 sec + [junit] Testcase: translateToRna took 0.025 sec + [junit] Testcase: kmerNonOverlap took 0.003 sec + [junit] Testcase: twoBit took 0.003 sec + [junit] Testcase: composition took 0.002 sec + [junit] Testcase: fourBit took 0.002 sec + [junit] Testcase: complement took 0.001 sec + [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.002 sec + [junit] Testcase: at took 0.001 sec + [junit] Testcase: gc took 0.001 sec + [junit] Testcase: basesEqual took 0.002 sec + [junit] Testcase: bogusSequence took 0.001 sec + [junit] Testcase: kmerOverlap took 0.002 sec + [junit] Testcase: reverseComplement took 0.003 sec + [junit] Testcase: reverse took 0.001 sec + [junit] Testcase: respectCase took 0.001 sec + [junit] Testcase: basesEquivalent took 0.001 sec + [junit] Testcase: badTwoBit took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.EditSequenceTest [junit] Testsuite: org.biojava.nbio.core.sequence.EditSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] - [junit] Testcase: badSubstitute took 0.041 sec - [junit] Testcase: delete took 0.013 sec - [junit] Testcase: insert took 0.002 sec - [junit] Testcase: substitute took 0.001 sec + [junit] Testcase: badSubstitute took 0.019 sec + [junit] Testcase: delete took 0.002 sec + [junit] Testcase: insert took 0 sec + [junit] Testcase: substitute took 0 sec [junit] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.JoiningSequenceReaderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] - [junit] Testcase: empty took 0.071 sec + [junit] Testcase: empty took 0.019 sec [junit] Testcase: canScan took 0 sec [junit] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [junit] Testsuite: org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] - [junit] Testcase: testGetCompoundsAt took 0.078 sec + [junit] Testcase: testGetCompoundsAt took 0.019 sec [junit] Running org.biojava.nbio.core.sequence.SequenceViewTest [junit] Testsuite: org.biojava.nbio.core.sequence.SequenceViewTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] - [junit] Testcase: testLastIndexOf took 0.075 sec + [junit] Testcase: testLastIndexOf took 0.018 sec [junit] Testcase: testGetCompoundAt took 0 sec - [junit] Testcase: testInverse took 0.001 sec + [junit] Testcase: testInverse took 0 sec [junit] Running org.biojava.nbio.core.sequence.TranslationTest [junit] Testsuite: org.biojava.nbio.core.sequence.TranslationTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.98 sec - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.98 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.425 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.425 sec [junit] - [junit] Testcase: translateN took 0.059 sec - [junit] Testcase: basicTranslation took 0.002 sec - [junit] Testcase: translateBrca2 took 0.776 sec - [junit] Testcase: translateStopAtInternalStops took 0.005 sec + [junit] Testcase: translateN took 0.024 sec + [junit] Testcase: basicTranslation took 0 sec + [junit] Testcase: translateBrca2 took 0.236 sec + [junit] Testcase: translateStopAtInternalStops took 0.002 sec [junit] Testcase: getUniversal took 0 sec - [junit] Testcase: translateInternalStops took 0.014 sec - [junit] Testcase: multiFrameTranslation took 0.005 sec + [junit] Testcase: translateInternalStops took 0.001 sec + [junit] Testcase: multiFrameTranslation took 0.003 sec [junit] Testcase: waitForStartCodon took 0.001 sec - [junit] Testcase: translateInitMet took 0.005 sec - [junit] Testcase: lowerCases took 0.001 sec - [junit] Testcase: testHashCollision took 0.001 sec - [junit] Testcase: translateBrca2ExonOne took 0.001 sec + [junit] Testcase: translateInitMet took 0 sec + [junit] Testcase: lowerCases took 0 sec + [junit] Testcase: testHashCollision took 0 sec + [junit] Testcase: translateBrca2ExonOne took 0 sec [junit] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [junit] Testsuite: org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] - [junit] Testcase: testAmbiguity took 0.038 sec - [junit] Testcase: testBasicAmbiguity took 0.001 sec + [junit] Testcase: testAmbiguity took 0.014 sec + [junit] Testcase: testBasicAmbiguity took 0 sec [junit] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] - [junit] Testcase: testConstructor took 0.037 sec + [junit] Testcase: testConstructor took 0.017 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaReaderTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.FastaReaderTest - process [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testSmallFasta2 took 0.023 sec - [junit] Testcase: testProcess took 0.128 sec - [junit] Testcase: testSmallFasta took 0.001 sec + [junit] Testcase: testSmallFasta2 took 0.013 sec + [junit] Testcase: testProcess took 0.046 sec + [junit] Testcase: testSmallFasta took 0 sec [junit] Running org.biojava.nbio.core.sequence.io.FastaWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.FastaWriterTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] - [junit] Testcase: writeBasicFasta took 0.043 sec - [junit] Testcase: writeFastaEqualToLineLength took 0 sec + [junit] Testcase: writeBasicFasta took 0.021 sec + [junit] Testcase: writeFastaEqualToLineLength took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankCookbookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - DNA Sequence: AAGATGCTCCGTGGAAGGGAGCCGAGCGGTGGGCAGAGGCTGAGTCCCCGATAACGAGCGCCTCACATTTCCGTGGCATTCCCATTTGCTAGTGCGCTGCTGCGGCCGCACGCCTGATTGATATATGACTGCAATGGCACTTTTCCATTTGACATTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCCCTCTCTCTCTCCCTCTCTCTCTCTCCCTGTGTCGCTTAAACAACAGTCCTAACTTTTGTGTGTTGCAAATATAAAAGGCAAGCCATGTGACAGAGGGACAGAAGAACAAAAGCATTTGGAAGTAACAGGACCTCTTTCTAGCTCTCAGAAAAGTCTGAGAAGAAAGGAGCCCTGCGTTCCCCTAAGCTGTGCAGCAGATACTGTGATGATGGATTGCAAGTGCAAAGAGTAAGACAAAACTCCAGCACATAAAGGACAATGACAACCAGAAAGCTTCAGCCCGATCCTGCCCTTTCCTTGAACGGGACTGGATCCTAGGAGGTGAAGCCATTTCCAATTTTTTGTCCTCTGCCTCCCTCTGCTGTTCTTCTAGAGAAGTTTTTCCTTACAACAATGAGAAAACATGTACTAGCTGCATCCTTTTCTATGCTCTCCCTGCTGGTGATAATGGGAGATACAGACAGTAAAACGGACAGCTCATTCATAATGGACTCGGACCCTCGACGCTGCATGAGGCACCACTATGTGGATTCTATCAGTCACCCATTGTACAAGTGTAGCTCAAAGATGGTGCTCCTGGCCAGGTGCGAGGGGCACTGCAGCCAGGCGTCACGCTCCGAGCCTTTGGTGTCGTTCAGCACTGTCCTCAAGCAACCCTTCCGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCTGAAGGCACTGCGGCTGCGATGCTCAGGGGGCATGCGACTCACTGCCACCTACCGGTACATCCTCTCCTGTCACTGCGAGGAATGCAATTCCTGAGGCCCGCTGCTGTGTGTGGCTTCTGGATGGGACAACTGTAGAGGCAGTTCGACCAGCCAGGGAAAGACTGGCAAGAAAAGAGTTAAGGCAAAAAAGGATGCAACAATTCTCCCGGGACTCTGCATATTCTAGTAATAAAGACTCTACATGCTTGTTGACAGAGAGAGATACTCTGGGAACTTCTTTGCAGTTCCCATCTCCTTTCTCTGGTACAATTTCTTTTGGTTCATTTTCAGATTCAGGCATTTTCCCCCTTGGCTCTCAATGCTGTTTGGGTTTCCAACAATTCAGCATTAGTGGGAAAAAGTGGGCCCTCATACACAAGCGTGTCAGGCTGTCAGTGTTTGGTGCACGCTGGGGAAGAATTTACTTTGGAAAGTAGAAAAGCCCAGCTTTTCCTGGGACATCTTCTGTTATTGTTGATGTTTTTTTTTACCTTGTCATTTTGGTCTAAGGTTGCCATTGCTGCTAAAGGTTACCGATTTCAAAGTCCAGATACCAAGCATGTGGATATGTTTAGCTACGTTTACTCACAGCCAGCGAACTGACATTAAAATAACTAACAAACAGATTCTTTTATGTGATGCTGGAACTCTTGACAGCTATAATTATTATTCAGAAATGACTTTTTGAAAGTAAAAGCAGCATAAAGAATTTGTCACAGGAAGGCTGTCTCAGATAAATTATGGTAAAATTTTGTAAGGGAGCAGACTTTTAAAGACTTGCACAAATACGGATCCTGCACTGACTCTGGAAAAGGCATATATGTACTAGTGGCATGGAGAATGCACCATACTCATGCATGCAAATTAGACAACCAAGTATGAATCTATTTGTGGGTGTGCTATAGCTTTAGCCGTGTCACGGGCATCATTCTCTAATATCCACTTGTCCATGTGAAACATGTTGCCAAAATGGTGGCCTGGCTTGTCTTCTGAACGTTTGGTTCAAATGTGTTTTGGTCCTGGAGGCTCAAATTTTGAGTTATTCCCACGTTTTGAAATAAAAAGAGTATATTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS @@ -4649,11 +4694,11 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankCookbookTest - Protein Sequence: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testProcess took 0.206 sec + [junit] Testcase: testProcess took 0.059 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankReaderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process protein [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - process DNA @@ -4661,33 +4706,33 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenbankReaderTest - protein sequences: {NP_000257=MRKHVLAASFSMLSLLVIMGDTDSKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSFSTVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNS} [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testProcess took 0.219 sec - [junit] Testcase: CDStest took 0.034 sec + [junit] Testcase: testProcess took 0.044 sec + [junit] Testcase: CDStest took 0.007 sec [junit] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenbankWriterTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] - [junit] Testcase: testProcess took 0.22 sec + [junit] Testcase: testProcess took 0.079 sec [junit] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest - parseHeader [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testParseHeader took 0.019 sec + [junit] Testcase: testParseHeader took 0.008 sec [junit] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] - [junit] Testcase: testProteinSequenceFactoring[0] took 0.003 sec + [junit] Testcase: testProteinSequenceFactoring[0] took 0.002 sec [junit] Testcase: testFeatures[0] took 0 sec - [junit] Testcase: testProteinSequenceFactoring[1] took 0.001 sec + [junit] Testcase: testProteinSequenceFactoring[1] took 0 sec [junit] Testcase: testFeatures[1] took 0 sec - [junit] Testcase: testProteinSequenceFactoring[2] took 0.001 sec + [junit] Testcase: testProteinSequenceFactoring[2] took 0 sec [junit] Testcase: testFeatures[2] took 0 sec [junit] Testcase: testProteinSequenceFactoring[3] took 0 sec [junit] Testcase: testFeatures[3] took 0 sec @@ -4698,20 +4743,20 @@ [junit] Testcase: testProteinSequenceFactoring[6] took 0 sec [junit] Testcase: testFeatures[6] took 0 sec [junit] Testcase: testProteinSequenceFactoring[7] took 0 sec - [junit] Testcase: testFeatures[7] took 0.003 sec + [junit] Testcase: testFeatures[7] took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [junit] Testsuite: org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.133 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.133 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest - test wrong sequence [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testWrongSequence took 2.117 sec + [junit] Testcase: testWrongSequence took 0.278 sec [junit] Running org.biojava.nbio.core.sequence.location.InsdcParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.InsdcParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - test accession [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(CP001663.1:6463934..6465826) @@ -4719,12 +4764,12 @@ [junit] [main] INFO org.biojava.nbio.core.sequence.location.InsdcParserTest - simple location: complement(NC_000932.1:69611..69724) [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: extractAccessionTest[0] took 0.064 sec - [junit] Testcase: extractAccessionTest[1] took 0 sec + [junit] Testcase: extractAccessionTest[0] took 0.019 sec + [junit] Testcase: extractAccessionTest[1] took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.location.LocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationParserTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.077 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.077 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.019 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.019 sec [junit] [junit] Testcase: moreComplex took 0 sec [junit] SKIPPED @@ -4732,28 +4777,28 @@ [junit] SKIPPED [junit] Running org.biojava.nbio.core.sequence.location.LocationTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.LocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] - [junit] Testcase: testWithStrandSwitch took 0.052 sec + [junit] Testcase: testWithStrandSwitch took 0.02 sec [junit] Testcase: modulateCircular took 0.001 sec - [junit] Testcase: testStrandFlip took 0.001 sec - [junit] Testcase: testBasicCircularLocation took 0.002 sec - [junit] Testcase: badLocations took 0.001 sec - [junit] Testcase: completePasses took 0.001 sec - [junit] Testcase: testSubLocations took 0.002 sec + [junit] Testcase: testStrandFlip took 0 sec + [junit] Testcase: testBasicCircularLocation took 0.001 sec + [junit] Testcase: badLocations took 0 sec + [junit] Testcase: completePasses took 0 sec + [junit] Testcase: testSubLocations took 0.001 sec [junit] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [junit] Testsuite: org.biojava.nbio.core.sequence.location.TargetedLocationParserTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] - [junit] Testcase: locationTest[0] took 0.022 sec + [junit] Testcase: locationTest[0] took 0.011 sec [junit] Testcase: locationTest[1] took 0.001 sec [junit] Testcase: locationTest[2] took 0 sec [junit] Testcase: locationTest[3] took 0 sec BUILD SUCCESSFUL -Total time: 43 seconds +Total time: 15 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -4768,32 +4813,32 @@ [echo] Using java version 17.0.6 [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: 0.14 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec [junit] - [junit] Testcase: testGetQuery took 0.099 sec - [junit] Testcase: testGetScore took 0.02 sec - [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testGetQuery took 0.026 sec + [junit] Testcase: testGetScore took 0.009 sec + [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec - [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec + [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0 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: 0.182 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.182 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] - [junit] Testcase: testGetQuery took 0.116 sec - [junit] Testcase: testGetScore took 0.03 sec + [junit] Testcase: testGetQuery took 0.026 sec + [junit] Testcase: testGetScore took 0.008 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.005 sec + [junit] Testcase: testGetMaxScore took 0.001 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: 0.385 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.385 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -4805,157 +4850,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.23 sec - [junit] Testcase: testToString took 0.004 sec - [junit] Testcase: testGetScoreMatrix took 0.013 sec - [junit] Testcase: testGetRoot took 0.097 sec - [junit] Testcase: testGetSequences took 0.003 sec - [junit] Testcase: testGetDistanceMatrix took 0.003 sec - [junit] Testcase: testGetAllPairsScores took 0.003 sec - [junit] Testcase: testIterator took 0.011 sec + [junit] Testcase: testGuideTree took 0.061 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.002 sec + [junit] Testcase: testGetRoot took 0.009 sec + [junit] Testcase: testGetSequences took 0.001 sec + [junit] Testcase: testGetDistanceMatrix took 0.002 sec + [junit] Testcase: testGetAllPairsScores took 0.001 sec + [junit] Testcase: testIterator took 0.001 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: 0.179 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 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: shouldAllowZeroLengthMatches took 0.162 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.042 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: 0.697 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.697 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.096 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.025 sec [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.032 sec - [junit] Testcase: should_align_middle_anchor took 0.047 sec + [junit] Testcase: testGetComputationTime took 0.009 sec + [junit] Testcase: should_align_middle_anchor took 0.01 sec [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetScore took 0.005 sec + [junit] Testcase: testGetScore took 0 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec - [junit] Testcase: should_align_all_anchored took 0.001 sec - [junit] Testcase: testGetScoreMatrix took 0.005 sec + [junit] Testcase: should_align_all_anchored took 0 sec + [junit] Testcase: testGetScoreMatrix took 0 sec [junit] Testcase: testGetPair took 0.001 sec - [junit] Testcase: should_align_multiple_anchors took 0.001 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.012 sec + [junit] Testcase: should_align_multiple_anchors took 0 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.001 sec [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: should_align_ending_anchor took 0.001 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.011 sec - [junit] Testcase: testComplex took 0.02 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.039 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec + [junit] Testcase: testComplex took 0.005 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.009 sec [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0 sec - [junit] Testcase: testGetTarget took 0.004 sec + [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec - [junit] Testcase: testIntOverflowBug took 0.382 sec + [junit] Testcase: testIntOverflowBug took 0.127 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: 0.026 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] - [junit] Testcase: testOpenPenalty took 0.004 sec + [junit] Testcase: testOpenPenalty took 0.002 sec [junit] Testcase: testType took 0 sec - [junit] Testcase: testExtensionPenalty took 0.001 sec + [junit] Testcase: testExtensionPenalty took 0 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: 0.173 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] - [junit] Testcase: testGetQuery took 0.137 sec + [junit] Testcase: testGetQuery took 0.037 sec [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testSimpleProfilePair took 0.009 sec + [junit] Testcase: testSimpleProfilePair took 0.002 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: 0.2 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.089 sec - [junit] Testcase: testGetGapPenalty took 0.005 sec - [junit] Testcase: testGetComputationTime took 0.005 sec - [junit] Testcase: testGetQuery took 0.005 sec - [junit] Testcase: testGetScore took 0.004 sec - [junit] Testcase: testGetScoreMatrix took 0.004 sec - [junit] Testcase: testGetPair took 0.007 sec - [junit] Testcase: testGetProfile took 0.003 sec - [junit] Testcase: testGetMinScore took 0.002 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.044 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.002 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec - [junit] Testcase: testGetTarget took 0.002 sec - [junit] Testcase: testGetMaxScore took 0.003 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.035 sec + [junit] Testcase: testGetGapPenalty took 0.001 sec + [junit] Testcase: testGetComputationTime took 0.002 sec + [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetScore took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: testGetProfile took 0.002 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.015 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.001 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.001 sec + [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetMaxScore took 0 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: 0.114 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.014 sec - [junit] Testcase: testSetDescription took 0.017 sec - [junit] Testcase: testToString took 0.032 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.003 sec + [junit] Testcase: testSetDescription took 0.008 sec + [junit] Testcase: testToString took 0.014 sec [junit] Testcase: testCaseEquivalence took 0.001 sec - [junit] Testcase: test took 0.008 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.004 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.004 sec - [junit] Testcase: testSetName took 0.004 sec + [junit] Testcase: test took 0.005 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.002 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.002 sec + [junit] Testcase: testSetName took 0.002 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.002 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: 0.293 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.293 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.104 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.026 sec [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.031 sec - [junit] Testcase: testGetQuery took 0.001 sec - [junit] Testcase: testGetScore took 0.002 sec - [junit] Testcase: testGetScoreMatrix took 0.006 sec - [junit] Testcase: testGetPair took 0.009 sec + [junit] Testcase: testGetComputationTime took 0.009 sec + [junit] Testcase: testGetQuery took 0 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: testSmithWaterman took 0.001 sec [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.107 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testIsStoringScoreMatrix took 0 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.023 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec - [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetMaxScore took 0 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: 0.057 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.006 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.011 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.002 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.001 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec - [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size 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 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec - [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.001 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: 0.255 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] - [junit] Testcase: testGetComputationTime took 0.153 sec - [junit] Testcase: testGuanUberbacher took 0.001 sec + [junit] Testcase: testGetComputationTime took 0.033 sec + [junit] Testcase: testGuanUberbacher took 0 sec [junit] Testcase: testGetScore took 0.001 sec - [junit] Testcase: testGetPair took 0.004 sec + [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_shorter_target took 0.058 sec - [junit] Testcase: should_align_multiple_cuts took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.005 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: should_align_shorter_target took 0.009 sec + [junit] Testcase: should_align_multiple_cuts took 0 sec + [junit] Testcase: testGetMaxScore took 0 sec [junit] Testcase: should_align_shorter_query took 0 sec BUILD SUCCESSFUL -Total time: 21 seconds +Total time: 5 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -4973,8 +5018,8 @@ [echo] Using java version 17.0.6 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -4982,41 +5027,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 0.55 sec - [junit] Testcase: testExample1 took 0.041 sec - [junit] Testcase: testExample2 took 0.01 sec - [junit] Testcase: testExample3 took 0.011 sec - [junit] Testcase: testExample1WithCSV took 0.021 sec - [junit] Testcase: testWithCases took 0.009 sec + [junit] Testcase: testAdvancedXMLExample took 0.26 sec + [junit] Testcase: testExample1 took 0.018 sec + [junit] Testcase: testExample2 took 0.004 sec + [junit] Testcase: testExample3 took 0.005 sec + [junit] Testcase: testExample1WithCSV took 0.013 sec + [junit] Testcase: testWithCases took 0.004 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.434 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.434 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec [junit] - [junit] Testcase: shortExample1 took 0.037 sec - [junit] Testcase: shortExample2 took 0.333 sec - [junit] Testcase: shortExample3 took 0.048 sec + [junit] Testcase: shortExample1 took 0.022 sec + [junit] Testcase: shortExample2 took 0.207 sec + [junit] Testcase: shortExample3 took 0.026 sec [junit] Testcase: shortExample4 took 0.001 sec - [junit] Testcase: shortExample5 took 0.004 sec + [junit] Testcase: shortExample5 took 0.003 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.886 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.886 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 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 0.657 sec - [junit] Testcase: testExample1 took 0.032 sec - [junit] Testcase: testExample2 took 0.032 sec - [junit] Testcase: testExample3 took 0.016 sec - [junit] Testcase: testExample1WithCSV took 0.029 sec - [junit] Testcase: testWithCases took 0.013 sec + [junit] Testcase: testAdvancedXMLExample took 0.256 sec + [junit] Testcase: testExample1 took 0.01 sec + [junit] Testcase: testExample2 took 0.006 sec + [junit] Testcase: testExample3 took 0.005 sec + [junit] Testcase: testExample1WithCSV took 0.007 sec + [junit] Testcase: testWithCases took 0.004 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 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. @@ -5231,74 +5276,74 @@ [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 0.065 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 0.481 sec - [junit] Testcase: testEnrichment took 0.016 sec - [junit] Testcase: testApliphaticIndex took 0.002 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.006 sec + [junit] Testcase: testAbsorbance took 0.023 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 0.232 sec + [junit] Testcase: testEnrichment took 0.007 sec + [junit] Testcase: testApliphaticIndex took 0.001 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.004 sec [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.002 sec - [junit] Testcase: testAbsorbanceNull took 0.001 sec + [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0 sec - [junit] Testcase: testAverageHydropathy took 0 sec + [junit] Testcase: testAverageHydropathy took 0.001 sec [junit] Testcase: testExtinctionCoefficient took 0.001 sec - [junit] Testcase: testAAComposition took 0.002 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.042 sec + [junit] Testcase: testAAComposition took 0.001 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.018 sec [junit] Testcase: testMolecularWeight took 0.001 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.001 sec [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec - [junit] Testcase: testNetCharge took 0.173 sec - [junit] Testcase: testEnrichmentNull took 0.006 sec + [junit] Testcase: testNetCharge took 0.07 sec + [junit] Testcase: testEnrichmentNull took 0 sec [junit] Testcase: testInstabilityIndexNull took 0 sec - [junit] Testcase: testAverageHydropathyNull took 0.001 sec - [junit] Testcase: testMolecularWeightXML took 0.12 sec + [junit] Testcase: testAverageHydropathyNull took 0 sec + [junit] Testcase: testMolecularWeightXML took 0.034 sec [junit] Testcase: testInstabilityIndex took 0 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: 0.012 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] - [junit] Testcase: testFake took 0.002 sec + [junit] Testcase: testFake took 0.001 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: 0.04 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] - [junit] Testcase: testFakeTest took 0.021 sec + [junit] Testcase: testFakeTest took 0.009 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.827 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.827 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.334 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.334 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 0.425 sec - [junit] Testcase: readWithIDXml took 0.141 sec - [junit] Testcase: readMinXml took 0.084 sec - [junit] Testcase: readAdvancedXml took 0.042 sec - [junit] Testcase: generateXml took 0.03 sec - [junit] Testcase: readXml took 0.089 sec + [junit] Testcase: generateSchema took 0.179 sec + [junit] Testcase: readWithIDXml took 0.062 sec + [junit] Testcase: readMinXml took 0.028 sec + [junit] Testcase: readAdvancedXml took 0.015 sec + [junit] Testcase: generateXml took 0.015 sec + [junit] Testcase: readXml took 0.027 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.302 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.302 sec [junit] - [junit] Testcase: generateSchema took 0.503 sec - [junit] Testcase: generateXml took 0.143 sec - [junit] Testcase: readXml took 0.237 sec + [junit] Testcase: generateSchema took 0.191 sec + [junit] Testcase: generateXml took 0.033 sec + [junit] Testcase: readXml took 0.072 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: 0.046 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: 0.017 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] - [junit] Testcase: testFake took 0.03 sec + [junit] Testcase: testFake took 0.01 sec BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 6 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -5315,7 +5360,7 @@ [echo] Using java version 17.0.6 BUILD SUCCESSFUL -Total time: 3 seconds +Total time: 1 second # 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 @@ -5331,45 +5376,45 @@ [echo] Using java version 17.0.6 [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: 0.174 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec [junit] - [junit] Testcase: testConvert took 0.165 sec + [junit] Testcase: testConvert took 0.066 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: 0.042 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.005 sec + [junit] Testcase: testBuildAppendSequence took 0.002 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec - [junit] Testcase: testBuild took 0.002 sec + [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 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: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec - [junit] Testcase: testBuildNullSequence took 0.001 sec - [junit] Testcase: testBuildMissingDescription took 0.001 sec + [junit] Testcase: testBuildNullSequence took 0 sec + [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec - [junit] Testcase: testBuildMissingSequence took 0.001 sec + [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0 sec - [junit] Testcase: testConstructor took 0.001 sec + [junit] Testcase: testConstructor took 0 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: 0.023 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] - [junit] Testcase: testImmutable took 0.003 sec + [junit] Testcase: testImmutable took 0.001 sec [junit] Testcase: testBuilder took 0.002 sec [junit] Testcase: testVariant took 0 sec - [junit] Testcase: testQuality took 0.004 sec + [junit] Testcase: testQuality took 0.002 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec @@ -5377,56 +5422,56 @@ [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: 0.095 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.002 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0 sec [junit] Testcase: testConvertNullVariant took 0 sec - [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.048 sec + [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.026 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec - [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec + [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec - [junit] Testcase: testCreateQualityScores took 0.001 sec + [junit] Testcase: testCreateQualityScores took 0 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec - [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec + [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec - [junit] Testcase: testCreateQualityScoresNullFastq took 0.001 sec + [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec + [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0.001 sec - [junit] Testcase: testToListNotAList took 0.002 sec - [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec + [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec + [junit] Testcase: testToListNotAList took 0.001 sec + [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec - [junit] Testcase: testQualityScores took 0.006 sec - [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec + [junit] Testcase: testQualityScores took 0.003 sec + [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec - [junit] Testcase: testQualityScoresIntArray took 0.001 sec + [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 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: 0.032 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.003 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec + [junit] Testcase: testParseFastqVariant took 0.002 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec [junit] Testcase: testIsSanger took 0.003 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec @@ -5435,152 +5480,152 @@ [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: 0.155 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.043 sec - [junit] Testcase: testWrappingAsIllumina took 0.003 sec - [junit] Testcase: testValidateDescription took 0.007 sec + [junit] Testcase: testFullRangeAsIllumina took 0.022 sec + [junit] Testcase: testWrappingAsIllumina took 0.001 sec + [junit] Testcase: testValidateDescription took 0.005 sec [junit] Testcase: testValidateRepeatDescription took 0.002 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.001 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.002 sec - [junit] Testcase: testLongReadsAsIllumina took 0.005 sec - [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.039 sec + [junit] Testcase: testMiscDnaAsIllumina took 0 sec + [junit] Testcase: testMiscRnaAsIllumina took 0 sec + [junit] Testcase: testLongReadsAsIllumina took 0.002 sec + [junit] Testcase: testParseNullReadable took 0 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.022 sec [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.028 sec - [junit] Testcase: testParse took 0 sec + [junit] Testcase: testErrorExamples took 0.009 sec + [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0 sec + [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec + [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.09 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.019 sec - [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.004 sec + [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.006 sec - [junit] Testcase: testWriteFileIterable took 0.047 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec + [junit] Testcase: testWriteFileIterable took 0.021 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: testWriteFileVararg took 0.001 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: 0.26 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.056 sec - [junit] Testcase: testFullRangeAsSanger took 0.003 sec - [junit] Testcase: testWrappingOriginal took 0.003 sec - [junit] Testcase: testLongReadsOriginal took 0.011 sec - [junit] Testcase: testMiscDnaOriginal took 0.002 sec - [junit] Testcase: testMiscRnaOriginal took 0.002 sec - [junit] Testcase: testValidateDescription took 0.012 sec - [junit] Testcase: testValidateRepeatDescription took 0.002 sec - [junit] Testcase: testFullRangeOriginal took 0.002 sec + [junit] Testcase: testMiscRnaAsSanger took 0.021 sec + [junit] Testcase: testFullRangeAsSanger took 0.001 sec + [junit] Testcase: testWrappingOriginal took 0.001 sec + [junit] Testcase: testLongReadsOriginal took 0.003 sec + [junit] Testcase: testMiscDnaOriginal took 0.001 sec + [junit] Testcase: testMiscRnaOriginal took 0.001 sec + [junit] Testcase: testValidateDescription took 0.004 sec + [junit] Testcase: testValidateRepeatDescription took 0 sec + [junit] Testcase: testFullRangeOriginal took 0.001 sec [junit] Testcase: testWrappingAsSanger took 0.001 sec - [junit] Testcase: testLongReadsAsSanger took 0.004 sec - [junit] Testcase: testMiscDnaAsSanger took 0.003 sec + [junit] Testcase: testLongReadsAsSanger took 0.001 sec + [junit] Testcase: testMiscDnaAsSanger took 0 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.063 sec - [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.033 sec - [junit] Testcase: testParse took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.021 sec + [junit] Testcase: testReadEmptyFile took 0 sec + [junit] Testcase: testErrorExamples took 0.009 sec + [junit] Testcase: testParse took 0 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0.004 sec - [junit] Testcase: testMultipleWrappedQuality took 0.001 sec + [junit] Testcase: testReadFile took 0 sec + [junit] Testcase: testMultipleWrappedQuality took 0 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.008 sec - [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec + [junit] Testcase: testReadURL took 0 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0 sec [junit] Testcase: testWrappedQuality took 0.001 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: 0.077 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.008 sec - [junit] Testcase: testAppendVararg took 0 sec + [junit] Testcase: testConvertNotSangerVariant took 0.004 sec + [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.043 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec + [junit] Testcase: testWriteFileIterable took 0.02 sec + [junit] Testcase: testWriteOutputStreamIterable took 0 sec [junit] Testcase: testAppendIterable took 0 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testWriteFileVararg took 0.001 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: 0.186 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.186 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.048 sec - [junit] Testcase: testFullRangeAsSolexa took 0.004 sec - [junit] Testcase: testValidateDescription took 0.012 sec - [junit] Testcase: testValidateRepeatDescription took 0.003 sec - [junit] Testcase: testWrappingAsSolexa took 0.003 sec - [junit] Testcase: testLongReadsAsSolexa took 0.006 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec - [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.052 sec - [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.023 sec - [junit] Testcase: testParse took 0 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.021 sec + [junit] Testcase: testFullRangeAsSolexa took 0.001 sec + [junit] Testcase: testValidateDescription took 0.004 sec + [junit] Testcase: testValidateRepeatDescription took 0.001 sec + [junit] Testcase: testWrappingAsSolexa took 0.001 sec + [junit] Testcase: testLongReadsAsSolexa took 0.002 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.001 sec + [junit] Testcase: testParseNullReadable took 0 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.021 sec + [junit] Testcase: testReadEmptyFile took 0 sec + [junit] Testcase: testErrorExamples took 0.009 sec + [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec - [junit] Testcase: testReadEmptyInputStream took 0.001 sec + [junit] Testcase: testReadEmptyInputStream took 0 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0.001 sec + [junit] Testcase: testWrappedQuality took 0 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: 0.103 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.016 sec - [junit] Testcase: testAppendVararg took 0 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.005 sec + [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.056 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec + [junit] Testcase: testWriteFileIterable took 0.02 sec + [junit] Testcase: testWriteOutputStreamIterable took 0 sec + [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 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: 0.02 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.002 sec - [junit] Testcase: testStreamNullListener took 0.006 sec - [junit] Testcase: testStreamNullReadable took 0.001 sec + [junit] Testcase: testStreamNullVariant took 0.001 sec + [junit] Testcase: testStreamNullListener took 0.002 sec + [junit] Testcase: testStreamNullReadable took 0 sec BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 5 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -5601,39 +5646,39 @@ [echo] Using java version 17.0.6 [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: 0.012 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] - [junit] Testcase: testMe took 0.001 sec + [junit] Testcase: testMe took 0 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: 0.01 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] [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: 0.03 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] - [junit] Testcase: testGetColor took 0.009 sec + [junit] Testcase: testGetColor took 0.002 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec - [junit] Testcase: testGetSelection took 0.004 sec + [junit] Testcase: testGetSelection took 0.002 sec [junit] Testcase: testRepaint took 0 sec - [junit] Testcase: testSetSelection took 0.001 sec + [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 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: 0.009 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 2 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -5649,7 +5694,7 @@ BUILD SUCCESSFUL Total time: 2 seconds -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen create-stamp debian/debhelper-build-stamp dh_prep dh_install @@ -5671,21 +5716,24 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-8_all.deb'. -dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-8_all.deb'. -dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb'. +dpkg-deb: Paket »libbiojava4-java-doc« wird in »../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb« gebaut. +dpkg-deb: Paket »libbiojava4-java« wird in »../libbiojava4-java_4.2.12+dfsg-8_all.deb« gebaut. +dpkg-deb: Paket »libbiojava4.0-java« wird in »../libbiojava4.0-java_4.2.12+dfsg-8_all.deb« gebaut. dpkg-genbuildinfo --build=binary -O../biojava4-live_4.2.12+dfsg-8_i386.buildinfo dpkg-genchanges --build=binary -O../biojava4-live_4.2.12+dfsg-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload +I: copying local configuration +I: user script /srv/workspace/pbuilder/130957/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/130957/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/16354 and its subdirectories -I: Current time: Thu Apr 27 07:41:26 -12 2023 -I: pbuilder-time-stamp: 1682624486 +I: removing directory /srv/workspace/pbuilder/130957 and its subdirectories +I: Current time: Thu May 30 16:08:01 +14 2024 +I: pbuilder-time-stamp: 1717034881