Diff of the two buildlogs: -- --- b1/build.log 2023-04-29 15:16:13.826269091 +0000 +++ b2/build.log 2023-04-29 15:48:20.721680437 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 29 02:06:10 -12 2023 -I: pbuilder-time-stamp: 1682777170 +I: Current time: Sun Apr 30 05:16:56 +14 2023 +I: pbuilder-time-stamp: 1682781416 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./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 @@ -35,135 +35,167 @@ 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/32081/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21665/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 Apr 30 05:18 /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/21665/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21665/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='1a19c5d16d36423592a974438a6b86f5' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='32081' - PS1='# ' - PS2='> ' + INVOCATION_ID=a67d248a3eb64dba84a899717db2c967 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=21665 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.TImIMuD4/pbuilderrc_YUCS --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.TImIMuD4/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-8.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TImIMuD4/pbuilderrc_fVzF --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.TImIMuD4/b2 --logfile b2/build.log --extrapackages usrmerge biojava4-live_4.2.12+dfsg-8.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 5.10.0-21-armmp #1 SMP Debian 5.10.162-1 (2023-01-21) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-arm64 #1 SMP Debian 5.10.162-1 (2023-01-21) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/32081/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 06:31 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 30 05:18 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 06:31 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/21665/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -493,7 +525,7 @@ Get: 236 http://deb.debian.org/debian bookworm/main armhf libnetx-java all 0.5-4 [138 kB] Get: 237 http://deb.debian.org/debian bookworm/main armhf libvecmath-java all 1.5.2-7 [97.0 kB] Get: 238 http://deb.debian.org/debian bookworm/main armhf libxmlunit-java all 1.6-2 [100 kB] -Fetched 315 MB in 1min 11s (4417 kB/s) +Fetched 315 MB in 29s (10.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) @@ -1640,8 +1672,19 @@ 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/21665/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/21665/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 @@ -1653,8 +1696,8 @@ 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]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" dh_clean rm -rf build rm -rf dist @@ -1667,15 +1710,15 @@ 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]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» 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]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" 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 @@ -1693,11 +1736,11 @@ 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]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» 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]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" 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,' \ @@ -1719,7 +1762,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 25 seconds +Total time: 26 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1737,7 +1780,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 2 minutes 16 seconds +Total time: 2 minutes 9 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1755,7 +1798,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 1 minute 1 second +Total time: 1 minute 10 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1769,7 +1812,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 23 seconds +Total time: 22 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1785,7 +1828,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 45 seconds +Total time: 34 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1803,7 +1846,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 41 seconds +Total time: 35 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1819,7 +1862,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 1 minute 12 seconds +Total time: 38 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1834,7 +1877,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 43 seconds +Total time: 27 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1854,7 +1897,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 3 minutes 43 seconds +Total time: 2 minutes 3 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1874,7 +1917,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 1 minute 29 seconds +Total time: 57 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1890,7 +1933,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 41 seconds +Total time: 26 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1908,7 +1951,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 1 minute 29 seconds +Total time: 25 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1924,7 +1967,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 1 minute 25 seconds +Total time: 22 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1938,7 +1981,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 39 seconds +Total time: 14 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1952,7 +1995,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 57 seconds +Total time: 22 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1966,7 +2009,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 1 minute 27 seconds +Total time: 27 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -4292,12 +4335,12 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 7 minutes 43 seconds +Total time: 3 minutes 0 seconds # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» 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]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -4328,198 +4371,198 @@ [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: 1.239 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.239 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.535 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.535 sec [junit] - [junit] Testcase: testGetIndexOf took 0.52 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.008 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.003 sec + [junit] Testcase: testGetIndexOf took 0.206 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.009 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.011 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.007 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.003 sec - [junit] Testcase: testGetNumGaps took 0.009 sec - [junit] Testcase: testGetStart took 0.008 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.002 sec + [junit] Testcase: testGetNumGaps took 0.002 sec + [junit] Testcase: testGetStart took 0.004 sec [junit] Testcase: testGetSequenceIndexAt took 0.007 sec - [junit] Testcase: testGetAccession took 0.003 sec - [junit] Testcase: testToString took 0.036 sec - [junit] Testcase: testSimpleAlignedSequenceLong took 0.003 sec - [junit] Testcase: testCountCompounds took 0.022 sec - [junit] Testcase: testGetAlignmentIndexAt took 0.004 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.015 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.012 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.028 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.003 sec + [junit] Testcase: testGetAccession took 0.007 sec + [junit] Testcase: testToString took 0.005 sec + [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec + [junit] Testcase: testCountCompounds took 0.007 sec + [junit] Testcase: testGetAlignmentIndexAt took 0.007 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.006 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.011 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.007 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.037 sec - [junit] Testcase: testGetOriginalSequence took 0.002 sec - [junit] Testcase: testGetCompoundAt took 0.008 sec - [junit] Testcase: testGetLength took 0.003 sec - [junit] Testcase: testIsCircular took 0.003 sec - [junit] Testcase: testGetEnd took 0.007 sec - [junit] Testcase: testSimpleAlignedSequenceLocal took 0.006 sec - [junit] Testcase: testSimpleAlignedSequenceShort took 0.007 sec - [junit] Testcase: testGetOverlapCount took 0.002 sec - [junit] Testcase: testGetCompoundSet took 0.015 sec - [junit] Testcase: testGetLocationInAlignment took 0.016 sec - [junit] Testcase: testIterator took 0.012 sec - [junit] Testcase: testGetSequenceAsString took 0.008 sec - [junit] Testcase: testGetLastIndexOf took 0.008 sec - [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.027 sec + [junit] Testcase: testGetAsList took 0.023 sec + [junit] Testcase: testGetOriginalSequence took 0.007 sec + [junit] Testcase: testGetCompoundAt took 0.002 sec + [junit] Testcase: testGetLength took 0.006 sec + [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetEnd took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec + [junit] Testcase: testGetOverlapCount took 0.001 sec + [junit] Testcase: testGetCompoundSet took 0 sec + [junit] Testcase: testGetLocationInAlignment took 0.003 sec + [junit] Testcase: testIterator took 0.002 sec + [junit] Testcase: testGetSequenceAsString took 0.005 sec + [junit] Testcase: testGetLastIndexOf took 0.001 sec + [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.008 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: 2.782 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.782 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.955 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.955 sec [junit] - [junit] Testcase: testGetIndexOf took 0.879 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.021 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.023 sec - [junit] Testcase: testToStringInt took 0.093 sec - [junit] Testcase: testToString took 0.005 sec - [junit] Testcase: testToStringFormatted took 0.567 sec - [junit] Testcase: testSimpleProfile took 0.012 sec - [junit] Testcase: testGetSize took 0.015 sec - [junit] Testcase: testGetAlignedSequenceS took 0.017 sec - [junit] Testcase: testGetAlignedSequences took 0.012 sec - [junit] Testcase: testGetOriginalSequences took 0.022 sec + [junit] Testcase: testGetIndexOf took 0.39 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.011 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.012 sec + [junit] Testcase: testToStringInt took 0.077 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testToStringFormatted took 0.172 sec + [junit] Testcase: testSimpleProfile took 0.001 sec + [junit] Testcase: testGetSize took 0 sec + [junit] Testcase: testGetAlignedSequenceS took 0.01 sec + [junit] Testcase: testGetAlignedSequences took 0.001 sec + [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED - [junit] Testcase: testGetCompoundAtSInt took 0.012 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.018 sec - [junit] Testcase: testGetIndicesAt took 0.071 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.012 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.049 sec - [junit] Testcase: testGetCompoundAtIntInt took 0.007 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.007 sec - [junit] Testcase: testGetLength took 0.011 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.004 sec - [junit] Testcase: testIsCircular took 0.008 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.007 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.007 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.015 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.003 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.007 sec - [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.003 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.003 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.008 sec - [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.009 sec - [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.003 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.008 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.007 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.012 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.004 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.012 sec - [junit] Testcase: testGetCompoundSet took 0.011 sec - [junit] Testcase: testGetCompoundsAt took 0.007 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.011 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.012 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.003 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.011 sec - [junit] Testcase: testIterator took 0.013 sec - [junit] Testcase: testGetLastIndexOf took 0.021 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.003 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.011 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.003 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.02 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.016 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.007 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.012 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.003 sec - [junit] Testcase: testGetIndicesAtOutOfBounds took 0.007 sec + [junit] Testcase: testGetCompoundAtSInt took 0.001 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec + [junit] Testcase: testGetIndicesAt took 0.015 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.017 sec + [junit] Testcase: testGetCompoundAtIntInt took 0.006 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec + [junit] Testcase: testGetLength took 0.006 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec + [junit] Testcase: testIsCircular took 0.005 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.005 sec + [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.005 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.005 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundSet took 0.001 sec + [junit] Testcase: testGetCompoundsAt took 0.005 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.003 sec + [junit] Testcase: testIterator took 0.003 sec + [junit] Testcase: testGetLastIndexOf took 0.004 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.008 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.007 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.003 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.002 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.006 sec + [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.828 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.828 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.56 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.56 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 1.074 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.003 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.011 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.012 sec - [junit] Testcase: testGetQuery took 0.007 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.008 sec - [junit] Testcase: testGetIndexInTargetAt took 0.011 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.012 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.008 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.012 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.007 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.008 sec - [junit] Testcase: testGetCompoundInQueryAt took 0.003 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.007 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.012 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.035 sec - [junit] Testcase: testGetIndexInQueryForTargetAt took 0.008 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.011 sec - [junit] Testcase: testGetNumIdenticals took 0.008 sec - [junit] Testcase: testGetIndexInTargetForQueryAt took 0.007 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.011 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.011 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.011 sec - [junit] Testcase: testGetCompoundInTargetAt took 0.011 sec - [junit] Testcase: testGetIndexInQueryAt took 0.007 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.011 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.012 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.011 sec - [junit] Testcase: testGetTarget took 0.007 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.011 sec - [junit] Testcase: testGetNumSimilars took 0.027 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.004 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.011 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.002 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.318 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.007 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetQuery took 0.005 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetIndexInTargetAt took 0.006 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.007 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.005 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAt took 0.002 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.004 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.008 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.005 sec + [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetNumIdenticals took 0.009 sec + [junit] Testcase: testGetIndexInTargetForQueryAt took 0.004 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.003 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.007 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec + [junit] Testcase: testGetIndexInQueryAt took 0.004 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.004 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.004 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetTarget took 0.004 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.005 sec + [junit] Testcase: testGetNumSimilars took 0.004 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.011 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 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: 1.585 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.585 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.693 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.693 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 1.285 sec - [junit] Testcase: testHashCode took 0.002 sec - [junit] Testcase: testEquals took 0.011 sec + [junit] Testcase: testGetAlignment took 0.59 sec + [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testEquals took 0.004 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: 3.002 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.002 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.048 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.048 sec [junit] ------------- Standard Error ----------------- - [junit] Apr 29, 2023 2:56:17 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:19 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 29, 2023 2:56:18 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:19 AM 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 2.745 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.939 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: 33.743 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.743 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.895 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.895 sec [junit] ------------- Standard Output --------------- [junit] createObjects [junit] getFileExtensions [junit] setFile [junit] ------------- ---------------- --------------- [junit] ------------- Standard Error ----------------- - [junit] Apr 29, 2023 2:56:28 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:23 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 29, 2023 2:56:28 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:23 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 2 hits approximately in all results - [junit] Apr 29, 2023 2:56:29 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:23 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Apr 29, 2023 2:56:30 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Apr 30, 2023 5:41:24 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 117713 hits approximately in all results [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testCreateObjects took 33.515 sec - [junit] Testcase: testGetFileExtensions took 0.006 sec - [junit] Testcase: testSetFile took 0.006 sec + [junit] Testcase: testCreateObjects took 10.838 sec + [junit] Testcase: testGetFileExtensions took 0 sec + [junit] Testcase: testSetFile took 0.001 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: 0.833 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.833 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.271 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.271 sec [junit] ------------- Standard Output --------------- [junit] getFileExtensions [junit] setFile @@ -4527,83 +4570,83 @@ [junit] [junit] Testcase: testCreateObjects took 0 sec [junit] SKIPPED: Attempts to use the network - [junit] Testcase: testStoreObjects took 0.088 sec + [junit] Testcase: testStoreObjects took 0.033 sec [junit] Testcase: testSetDatabaseReferences took 0 sec [junit] SKIPPED - [junit] Testcase: testGetFileExtensions took 0.391 sec + [junit] Testcase: testGetFileExtensions took 0.132 sec [junit] Testcase: testSetQueryReferences took 0 sec [junit] SKIPPED - [junit] Testcase: testSetFile took 0.002 sec + [junit] Testcase: testSetFile took 0.009 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: 4.941 sec - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.941 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.483 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.483 sec [junit] - [junit] Testcase: sequenceEquality took 1.034 sec - [junit] Testcase: subSequence took 0.302 sec - [junit] Testcase: singleCompoundSequence took 0.206 sec - [junit] Testcase: translateToRna took 1.133 sec - [junit] Testcase: kmerNonOverlap took 0.203 sec - [junit] Testcase: twoBit took 0.121 sec - [junit] Testcase: composition took 0.101 sec - [junit] Testcase: fourBit took 0.139 sec - [junit] Testcase: complement took 0.134 sec - [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.135 sec - [junit] Testcase: at took 0.09 sec - [junit] Testcase: gc took 0.101 sec - [junit] Testcase: basesEqual took 0.11 sec - [junit] Testcase: bogusSequence took 0.064 sec - [junit] Testcase: kmerOverlap took 0.059 sec - [junit] Testcase: reverseComplement took 0.095 sec - [junit] Testcase: reverse took 0.078 sec - [junit] Testcase: respectCase took 0.102 sec - [junit] Testcase: basesEquivalent took 0.083 sec - [junit] Testcase: badTwoBit took 0.241 sec + [junit] Testcase: sequenceEquality took 0.323 sec + [junit] Testcase: subSequence took 0.093 sec + [junit] Testcase: singleCompoundSequence took 0.061 sec + [junit] Testcase: translateToRna took 0.419 sec + [junit] Testcase: kmerNonOverlap took 0.052 sec + [junit] Testcase: twoBit took 0.046 sec + [junit] Testcase: composition took 0.042 sec + [junit] Testcase: fourBit took 0.043 sec + [junit] Testcase: complement took 0.03 sec + [junit] Testcase: kmerOverlapExceedingSequenceLength took 0.038 sec + [junit] Testcase: at took 0.035 sec + [junit] Testcase: gc took 0.025 sec + [junit] Testcase: basesEqual took 0.023 sec + [junit] Testcase: bogusSequence took 0.019 sec + [junit] Testcase: kmerOverlap took 0.022 sec + [junit] Testcase: reverseComplement took 0.028 sec + [junit] Testcase: reverse took 0.022 sec + [junit] Testcase: respectCase took 0.045 sec + [junit] Testcase: basesEquivalent took 0.021 sec + [junit] Testcase: badTwoBit took 0.019 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: 0.895 sec - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 sec [junit] - [junit] Testcase: badSubstitute took 0.644 sec - [junit] Testcase: delete took 0.041 sec - [junit] Testcase: insert took 0.009 sec - [junit] Testcase: substitute took 0.005 sec + [junit] Testcase: badSubstitute took 0.218 sec + [junit] Testcase: delete took 0.029 sec + [junit] Testcase: insert took 0.003 sec + [junit] Testcase: substitute took 0.009 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: 0.845 sec - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.845 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 sec [junit] - [junit] Testcase: empty took 0.564 sec - [junit] Testcase: canScan took 0.009 sec + [junit] Testcase: empty took 0.255 sec + [junit] Testcase: canScan took 0.001 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: 0.876 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.876 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 sec [junit] - [junit] Testcase: testGetCompoundsAt took 0.684 sec + [junit] Testcase: testGetCompoundsAt took 0.225 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: 0.619 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 sec [junit] - [junit] Testcase: testLastIndexOf took 0.454 sec - [junit] Testcase: testGetCompoundAt took 0.003 sec - [junit] Testcase: testInverse took 0.007 sec + [junit] Testcase: testLastIndexOf took 0.199 sec + [junit] Testcase: testGetCompoundAt took 0.007 sec + [junit] Testcase: testInverse took 0.002 sec [junit] Running org.biojava.nbio.core.sequence.TranslationTest [junit] Testsuite: org.biojava.nbio.core.sequence.TranslationTest - [junit] Tests run: 12, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.819 sec - [junit] Tests run: 12, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 4.819 sec + [junit] Tests run: 12, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.255 sec + [junit] Tests run: 12, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.255 sec [junit] - [junit] Testcase: translateN took 1.03 sec - [junit] Testcase: basicTranslation took 0.024 sec - [junit] Testcase: translateBrca2 took 2.15 sec + [junit] Testcase: translateN took 0.457 sec + [junit] Testcase: basicTranslation took 0.016 sec + [junit] Testcase: translateBrca2 took 2.08 sec [junit] Caused an ERROR [junit] test timed out after 2000 milliseconds [junit] org.junit.runners.model.TestTimedOutException: test timed out after 2000 milliseconds [junit] at java.base@17.0.6/java.lang.StringLatin1.equals(StringLatin1.java:96) [junit] at java.base@17.0.6/java.lang.String.equals(String.java:1828) [junit] at app//org.biojava.nbio.core.sequence.transcription.Table$CaseInsensitiveTriplet.equals(Table.java:230) - [junit] at java.base@17.0.6/java.util.HashMap.getNode(HashMap.java:570) + [junit] at java.base@17.0.6/java.util.HashMap.getNode(HashMap.java:577) [junit] at java.base@17.0.6/java.util.HashMap.get(HashMap.java:556) [junit] at app//org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator.createSequences(RNAToAminoAcidTranslator.java:215) [junit] at app//org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator.createSequence(AbstractCompoundTranslator.java:178) @@ -4615,20 +4658,20 @@ [junit] at java.base@17.0.6/java.util.concurrent.FutureTask.run(FutureTask.java:264) [junit] at java.base@17.0.6/java.lang.Thread.run(Thread.java:833) [junit] - [junit] Testcase: translateStopAtInternalStops took 0.139 sec - [junit] Testcase: getUniversal took 0.002 sec - [junit] Testcase: translateInternalStops took 0.079 sec - [junit] Testcase: multiFrameTranslation took 0.053 sec - [junit] Testcase: waitForStartCodon took 0.018 sec - [junit] Testcase: translateInitMet took 0.01 sec - [junit] Testcase: lowerCases took 0.002 sec - [junit] Testcase: testHashCollision took 0.011 sec - [junit] Testcase: translateBrca2ExonOne took 0.002 sec + [junit] Testcase: translateStopAtInternalStops took 0.049 sec + [junit] Testcase: getUniversal took 0.001 sec + [junit] Testcase: translateInternalStops took 0.016 sec + [junit] Testcase: multiFrameTranslation took 0.036 sec + [junit] Testcase: waitForStartCodon took 0.005 sec + [junit] Testcase: translateInitMet took 0.015 sec + [junit] Testcase: lowerCases took 0.009 sec + [junit] Testcase: testHashCollision took 0.002 sec + [junit] Testcase: translateBrca2ExonOne took 0.013 sec BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.sequence.TranslationTest failed -Total time: 4 minutes 51 seconds +Total time: 1 minute 35 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -4643,32 +4686,32 @@ [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: 1.399 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.399 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.369 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.369 sec [junit] - [junit] Testcase: testGetQuery took 0.896 sec - [junit] Testcase: testGetScore took 0.316 sec - [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.003 sec - [junit] Testcase: testGetMinScore took 0.009 sec - [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.012 sec - [junit] Testcase: testGetTarget took 0.008 sec - [junit] Testcase: testGetMaxScore took 0.011 sec + [junit] Testcase: testGetQuery took 0.21 sec + [junit] Testcase: testGetScore took 0.092 sec + [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.006 sec + [junit] Testcase: testGetMinScore took 0.004 sec + [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.008 sec + [junit] Testcase: testGetTarget took 0.007 sec + [junit] Testcase: testGetMaxScore took 0.009 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: 1.57 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.57 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 sec [junit] - [junit] Testcase: testGetQuery took 0.94 sec - [junit] Testcase: testGetScore took 0.297 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.05 sec - [junit] Testcase: testGetMinScore took 0.004 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.008 sec - [junit] Testcase: testGetTarget took 0.004 sec - [junit] Testcase: testGetMaxScore took 0.031 sec + [junit] Testcase: testGetQuery took 0.285 sec + [junit] Testcase: testGetScore took 0.098 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.003 sec + [junit] Testcase: testGetMinScore took 0.008 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testGetTarget took 0.005 sec + [junit] Testcase: testGetMaxScore took 0.003 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: 2.909 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.909 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.918 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.918 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -4680,157 +4723,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 2.102 sec - [junit] Testcase: testToString took 0.047 sec - [junit] Testcase: testGetScoreMatrix took 0.077 sec - [junit] Testcase: testGetRoot took 0.282 sec - [junit] Testcase: testGetSequences took 0.05 sec - [junit] Testcase: testGetDistanceMatrix took 0.043 sec - [junit] Testcase: testGetAllPairsScores took 0.056 sec - [junit] Testcase: testIterator took 0.049 sec + [junit] Testcase: testGuideTree took 0.652 sec + [junit] Testcase: testToString took 0.011 sec + [junit] Testcase: testGetScoreMatrix took 0.031 sec + [junit] Testcase: testGetRoot took 0.093 sec + [junit] Testcase: testGetSequences took 0.015 sec + [junit] Testcase: testGetDistanceMatrix took 0.011 sec + [junit] Testcase: testGetAllPairsScores took 0.021 sec + [junit] Testcase: testIterator took 0.011 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: 1.868 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.868 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 1.636 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.557 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: 7.893 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.893 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.137 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.137 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.797 sec - [junit] Testcase: testGetGapPenalty took 0.004 sec - [junit] Testcase: testGetComputationTime took 0.316 sec - [junit] Testcase: should_align_middle_anchor took 0.463 sec - [junit] Testcase: testGetQuery took 0.003 sec - [junit] Testcase: testGetScore took 0.01 sec - [junit] Testcase: testNeedlemanWunsch took 0.014 sec - [junit] Testcase: should_align_all_anchored took 0.005 sec - [junit] Testcase: testGetScoreMatrix took 0.006 sec - [junit] Testcase: testGetPair took 0.013 sec - [junit] Testcase: should_align_multiple_anchors took 0.012 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.063 sec - [junit] Testcase: testGetProfile took 0.013 sec - [junit] Testcase: testGetMinScore took 0.011 sec - [junit] Testcase: should_align_ending_anchor took 0.016 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.038 sec - [junit] Testcase: testComplex took 0.263 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.383 sec - [junit] Testcase: should_align_starting_anchor took 0.014 sec - [junit] Testcase: anchors_should_not_change_score took 0.013 sec - [junit] Testcase: testGetTarget took 0.011 sec - [junit] Testcase: testGetMaxScore took 0.014 sec - [junit] Testcase: testIntOverflowBug took 5.105 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.291 sec + [junit] Testcase: testGetGapPenalty took 0.003 sec + [junit] Testcase: testGetComputationTime took 0.094 sec + [junit] Testcase: should_align_middle_anchor took 0.128 sec + [junit] Testcase: testGetQuery took 0.011 sec + [junit] Testcase: testGetScore took 0.007 sec + [junit] Testcase: testNeedlemanWunsch took 0.008 sec + [junit] Testcase: should_align_all_anchored took 0.007 sec + [junit] Testcase: testGetScoreMatrix took 0.011 sec + [junit] Testcase: testGetPair took 0.003 sec + [junit] Testcase: should_align_multiple_anchors took 0.013 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.022 sec + [junit] Testcase: testGetProfile took 0.008 sec + [junit] Testcase: testGetMinScore took 0.006 sec + [junit] Testcase: should_align_ending_anchor took 0.001 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.012 sec + [junit] Testcase: testComplex took 0.104 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.123 sec + [junit] Testcase: should_align_starting_anchor took 0.008 sec + [junit] Testcase: anchors_should_not_change_score took 0.002 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testIntOverflowBug took 1.148 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: 0.268 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec [junit] - [junit] Testcase: testOpenPenalty took 0.065 sec - [junit] Testcase: testType took 0.002 sec - [junit] Testcase: testExtensionPenalty took 0.006 sec - [junit] Testcase: testSimpleGapPenaltyShortShort took 0.006 sec - [junit] Testcase: testSimpleGapPenalty took 0.001 sec + [junit] Testcase: testOpenPenalty took 0.013 sec + [junit] Testcase: testType 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: 1.465 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.465 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 sec [junit] - [junit] Testcase: testGetQuery took 1.267 sec - [junit] Testcase: testGetTarget took 0.008 sec - [junit] Testcase: testSimpleProfilePair took 0.032 sec + [junit] Testcase: testGetQuery took 0.485 sec + [junit] Testcase: testGetTarget took 0.002 sec + [junit] Testcase: testSimpleProfilePair took 0.02 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: 2.91 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.91 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.963 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.963 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 1.127 sec - [junit] Testcase: testGetGapPenalty took 0.077 sec - [junit] Testcase: testGetComputationTime took 0.062 sec - [junit] Testcase: testGetQuery took 0.076 sec - [junit] Testcase: testGetScore took 0.072 sec - [junit] Testcase: testGetScoreMatrix took 0.104 sec - [junit] Testcase: testGetPair took 0.126 sec - [junit] Testcase: testGetProfile took 0.063 sec - [junit] Testcase: testGetMinScore took 0.05 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.059 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.584 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.058 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.066 sec - [junit] Testcase: testGetTarget took 0.045 sec - [junit] Testcase: testGetMaxScore took 0.057 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.422 sec + [junit] Testcase: testGetGapPenalty took 0.025 sec + [junit] Testcase: testGetComputationTime took 0.032 sec + [junit] Testcase: testGetQuery took 0.023 sec + [junit] Testcase: testGetScore took 0.019 sec + [junit] Testcase: testGetScoreMatrix took 0.029 sec + [junit] Testcase: testGetPair took 0.046 sec + [junit] Testcase: testGetProfile took 0.024 sec + [junit] Testcase: testGetMinScore took 0.006 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.013 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.156 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.005 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.015 sec + [junit] Testcase: testGetTarget took 0.014 sec + [junit] Testcase: testGetMaxScore took 0.009 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: 1.264 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.264 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.591 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.591 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.095 sec - [junit] Testcase: testSetDescription took 0.228 sec - [junit] Testcase: testToString took 0.354 sec - [junit] Testcase: testCaseEquivalence took 0.014 sec - [junit] Testcase: test took 0.113 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.098 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.051 sec - [junit] Testcase: testSetName took 0.078 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.02 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.054 sec + [junit] Testcase: testSetDescription took 0.146 sec + [junit] Testcase: testToString took 0.124 sec + [junit] Testcase: testCaseEquivalence took 0.002 sec + [junit] Testcase: test took 0.04 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.039 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.012 sec + [junit] Testcase: testSetName took 0.041 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.009 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: 2.435 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.435 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.798 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.798 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.872 sec - [junit] Testcase: testGetGapPenalty took 0.004 sec - [junit] Testcase: testGetComputationTime took 0.204 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.255 sec + [junit] Testcase: testGetGapPenalty took 0.001 sec + [junit] Testcase: testGetComputationTime took 0.124 sec [junit] Testcase: testGetQuery took 0.005 sec - [junit] Testcase: testGetScore took 0.028 sec - [junit] Testcase: testGetScoreMatrix took 0.024 sec - [junit] Testcase: testGetPair took 0.069 sec - [junit] Testcase: testSmithWaterman took 0.019 sec - [junit] Testcase: testGetProfile took 0.032 sec - [junit] Testcase: testGetMinScore took 0.023 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.008 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.856 sec - [junit] Testcase: testSetStoringScoreMatrix took 0.007 sec - [junit] Testcase: testGetTarget took 0.003 sec - [junit] Testcase: testGetMaxScore took 0.015 sec + [junit] Testcase: testGetScore took 0.005 sec + [junit] Testcase: testGetScoreMatrix took 0.004 sec + [junit] Testcase: testGetPair took 0.021 sec + [junit] Testcase: testSmithWaterman took 0.008 sec + [junit] Testcase: testGetProfile took 0.008 sec + [junit] Testcase: testGetMinScore took 0.006 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.005 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.253 sec + [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.009 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: 0.366 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.366 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.162 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.162 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.082 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.023 sec - [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.008 sec - [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0.002 sec - [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0.002 sec - [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.002 sec - [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.01 sec - [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.002 sec - [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0.002 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.039 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.012 sec + [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.009 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 sec + [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.001 sec + [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor 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 0.001 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: 1.576 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.576 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 sec [junit] - [junit] Testcase: testGetComputationTime took 1.018 sec + [junit] Testcase: testGetComputationTime took 0.402 sec [junit] Testcase: testGuanUberbacher took 0.006 sec [junit] Testcase: testGetScore took 0.005 sec - [junit] Testcase: testGetPair took 0.024 sec - [junit] Testcase: testGetProfile took 0.006 sec - [junit] Testcase: testGetMinScore took 0.004 sec - [junit] Testcase: should_align_shorter_target took 0.255 sec - [junit] Testcase: should_align_multiple_cuts took 0.006 sec - [junit] Testcase: testGetMaxScore took 0.013 sec - [junit] Testcase: should_align_shorter_query took 0.005 sec + [junit] Testcase: testGetPair took 0.02 sec + [junit] Testcase: testGetProfile took 0.002 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: should_align_shorter_target took 0.147 sec + [junit] Testcase: should_align_multiple_cuts took 0.008 sec + [junit] Testcase: testGetMaxScore took 0.007 sec + [junit] Testcase: should_align_shorter_query took 0.003 sec BUILD SUCCESSFUL -Total time: 3 minutes 42 seconds +Total time: 1 minute 9 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -4848,8 +4891,8 @@ [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: 11.265 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.265 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.987 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.987 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -4857,41 +4900,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 9.416 sec - [junit] Testcase: testExample1 took 0.65 sec - [junit] Testcase: testExample2 took 0.254 sec - [junit] Testcase: testExample3 took 0.091 sec - [junit] Testcase: testExample1WithCSV took 0.569 sec - [junit] Testcase: testWithCases took 0.041 sec + [junit] Testcase: testAdvancedXMLExample took 3.396 sec + [junit] Testcase: testExample1 took 0.234 sec + [junit] Testcase: testExample2 took 0.075 sec + [junit] Testcase: testExample3 took 0.034 sec + [junit] Testcase: testExample1WithCSV took 0.169 sec + [junit] Testcase: testWithCases took 0.027 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: 9.153 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.153 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.716 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.716 sec [junit] - [junit] Testcase: shortExample1 took 0.787 sec - [junit] Testcase: shortExample2 took 6.642 sec - [junit] Testcase: shortExample3 took 1.349 sec - [junit] Testcase: shortExample4 took 0.029 sec - [junit] Testcase: shortExample5 took 0.156 sec + [junit] Testcase: shortExample1 took 0.215 sec + [junit] Testcase: shortExample2 took 2.035 sec + [junit] Testcase: shortExample3 took 0.33 sec + [junit] Testcase: shortExample4 took 0.021 sec + [junit] Testcase: shortExample5 took 0.052 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: 10.634 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.634 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.457 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.457 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 8.527 sec - [junit] Testcase: testExample1 took 0.69 sec - [junit] Testcase: testExample2 took 0.373 sec - [junit] Testcase: testExample3 took 0.225 sec - [junit] Testcase: testExample1WithCSV took 0.38 sec - [junit] Testcase: testWithCases took 0.234 sec + [junit] Testcase: testAdvancedXMLExample took 1.87 sec + [junit] Testcase: testExample1 took 0.163 sec + [junit] Testcase: testExample2 took 0.113 sec + [junit] Testcase: testExample3 took 0.07 sec + [junit] Testcase: testExample1WithCSV took 0.101 sec + [junit] Testcase: testWithCases took 0.06 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: 20.376 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.376 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.338 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.338 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. @@ -5106,74 +5149,74 @@ [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 0.785 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 9.526 sec - [junit] Testcase: testEnrichment took 0.4 sec - [junit] Testcase: testApliphaticIndex took 0.023 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.166 sec - [junit] Testcase: testApliphaticIndexNull took 0.002 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.49 sec - [junit] Testcase: testAbsorbanceNull took 0.02 sec - [junit] Testcase: testIsoelectricPointNull took 0.011 sec - [junit] Testcase: testAverageHydropathy took 0.031 sec - [junit] Testcase: testExtinctionCoefficient took 0.04 sec - [junit] Testcase: testAAComposition took 0.034 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 2.041 sec - [junit] Testcase: testMolecularWeight took 0.038 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.137 sec - [junit] Testcase: testNetChargeNull took 0.019 sec - [junit] Testcase: testExtinctionCoefficientNull took 0.01 sec - [junit] Testcase: testNetCharge took 3.56 sec - [junit] Testcase: testEnrichmentNull took 0.008 sec - [junit] Testcase: testInstabilityIndexNull took 0.003 sec - [junit] Testcase: testAverageHydropathyNull took 0.006 sec - [junit] Testcase: testMolecularWeightXML took 2.665 sec - [junit] Testcase: testInstabilityIndex took 0.009 sec + [junit] Testcase: testAbsorbance took 0.198 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 2.038 sec + [junit] Testcase: testEnrichment took 0.069 sec + [junit] Testcase: testApliphaticIndex took 0.004 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.021 sec + [junit] Testcase: testApliphaticIndexNull took 0.001 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.084 sec + [junit] Testcase: testAbsorbanceNull took 0.001 sec + [junit] Testcase: testIsoelectricPointNull took 0 sec + [junit] Testcase: testAverageHydropathy took 0.002 sec + [junit] Testcase: testExtinctionCoefficient took 0.008 sec + [junit] Testcase: testAAComposition took 0.003 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.287 sec + [junit] Testcase: testMolecularWeight took 0.002 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.031 sec + [junit] Testcase: testNetChargeNull took 0.005 sec + [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec + [junit] Testcase: testNetCharge took 0.938 sec + [junit] Testcase: testEnrichmentNull took 0.001 sec + [junit] Testcase: testInstabilityIndexNull took 0.001 sec + [junit] Testcase: testAverageHydropathyNull took 0.001 sec + [junit] Testcase: testMolecularWeightXML took 0.481 sec + [junit] Testcase: testInstabilityIndex took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.246 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.246 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec [junit] - [junit] Testcase: testFake took 0.077 sec + [junit] Testcase: testFake took 0.011 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: 0.601 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.601 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 sec [junit] - [junit] Testcase: testFakeTest took 0.377 sec + [junit] Testcase: testFakeTest took 0.1 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: 15.619 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 15.619 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.197 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.197 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 8.623 sec - [junit] Testcase: readWithIDXml took 2.59 sec - [junit] Testcase: readMinXml took 0.916 sec - [junit] Testcase: readAdvancedXml took 0.538 sec - [junit] Testcase: generateXml took 0.664 sec - [junit] Testcase: readXml took 2.076 sec + [junit] Testcase: generateSchema took 1.796 sec + [junit] Testcase: readWithIDXml took 0.446 sec + [junit] Testcase: readMinXml took 0.22 sec + [junit] Testcase: readAdvancedXml took 0.18 sec + [junit] Testcase: generateXml took 0.135 sec + [junit] Testcase: readXml took 0.365 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: 10.862 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.862 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.521 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.521 sec [junit] - [junit] Testcase: generateSchema took 7.359 sec - [junit] Testcase: generateXml took 1.04 sec - [junit] Testcase: readXml took 2.277 sec + [junit] Testcase: generateSchema took 2.259 sec + [junit] Testcase: generateXml took 0.442 sec + [junit] Testcase: readXml took 0.753 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: 0.322 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.322 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 sec [junit] - [junit] Testcase: testFake took 0.14 sec + [junit] Testcase: testFake took 0.154 sec BUILD SUCCESSFUL -Total time: 3 minutes 54 seconds +Total time: 1 minute 6 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -5190,7 +5233,7 @@ [echo] Using java version 17.0.6 BUILD SUCCESSFUL -Total time: 52 seconds +Total time: 16 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -5206,256 +5249,256 @@ [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: 1.906 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.906 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.944 sec [junit] - [junit] Testcase: testConvert took 1.812 sec + [junit] Testcase: testConvert took 0.918 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: 0.313 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.074 sec - [junit] Testcase: testBuildNullDescription took 0.006 sec - [junit] Testcase: testBuildAppendQuality took 0.006 sec - [junit] Testcase: testBuild took 0.015 sec + [junit] Testcase: testBuildAppendSequence took 0.013 sec + [junit] Testcase: testBuildNullDescription took 0 sec + [junit] Testcase: testBuildAppendQuality took 0 sec + [junit] Testcase: testBuild took 0.002 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0.001 sec - [junit] Testcase: testBuildDefaultVariant took 0.001 sec + [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0.001 sec - [junit] Testcase: testBuildNullAppendQuality took 0.001 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0.001 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.002 sec - [junit] Testcase: testBuildNullAppendSequence took 0.005 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0.005 sec - [junit] Testcase: testBuildNullSequence took 0.001 sec - [junit] Testcase: testBuildMissingDescription took 0.001 sec - [junit] Testcase: testBuildNullVariant took 0.001 sec - [junit] Testcase: testBuildDefault took 0.001 sec - [junit] Testcase: testBuildMissingSequence 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 sec + [junit] Testcase: testBuildMissingDescription took 0 sec + [junit] Testcase: testBuildNullVariant took 0 sec + [junit] Testcase: testBuildDefault took 0 sec + [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0.001 sec - [junit] Testcase: testBuildMultiple took 0.002 sec + [junit] Testcase: testBuildMultiple took 0.001 sec [junit] Testcase: testConstructor took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] - [junit] Testcase: testImmutable took 0.018 sec - [junit] Testcase: testBuilder took 0.023 sec + [junit] Testcase: testImmutable took 0.014 sec + [junit] Testcase: testBuilder took 0.007 sec [junit] Testcase: testVariant took 0.001 sec - [junit] Testcase: testQuality took 0.034 sec - [junit] Testcase: testHashCode took 0.001 sec - [junit] Testcase: testEquals took 0.001 sec - [junit] Testcase: testDescription took 0.001 sec - [junit] Testcase: testConstructor took 0.002 sec + [junit] Testcase: testQuality took 0.013 sec + [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testEquals took 0 sec + [junit] Testcase: testDescription took 0 sec + [junit] Testcase: testConstructor took 0.001 sec [junit] Testcase: testSequence took 0 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: 1.015 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.015 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.403 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.026 sec - [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.011 sec - [junit] Testcase: testConvertNullVariant took 0.001 sec - [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.015 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.596 sec - [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec - [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec - [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec - [junit] Testcase: testQualityScoresNullIntArray took 0.001 sec - [junit] Testcase: testConvertNullFastq took 0.001 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.01 sec + [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.004 sec + [junit] Testcase: testConvertNullVariant took 0 sec + [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.257 sec + [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.005 sec + [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec + [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.006 sec + [junit] Testcase: testQualityScoresNullIntArray took 0 sec + [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0.001 sec - [junit] Testcase: testCreateQualityScores took 0.009 sec + [junit] Testcase: testCreateQualityScores took 0.002 sec [junit] Testcase: testCreateErrorProbabilities took 0.001 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0.001 sec - [junit] Testcase: testConvertQualitiesNullFastq took 0.009 sec - [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.002 sec - [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.006 sec - [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.006 sec - [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.002 sec - [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.009 sec - [junit] Testcase: testCreateQualityScoresNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec + [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.001 sec + [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0.001 sec + [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec + [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0.001 sec - [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.006 sec + [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0.001 sec - [junit] Testcase: testToListNotAList took 0.015 sec - [junit] Testcase: testConvertQualitiesNullVariant took 0.009 sec - [junit] Testcase: testConvertSameVariant took 0.001 sec - [junit] Testcase: testQualityScores took 0.065 sec + [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec + [junit] Testcase: testToListNotAList took 0.006 sec + [junit] Testcase: testConvertQualitiesNullVariant took 0 sec + [junit] Testcase: testConvertSameVariant took 0 sec + [junit] Testcase: testQualityScores took 0.025 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0.001 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0.001 sec - [junit] Testcase: testCreateDNASequence took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.002 sec - [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec + [junit] Testcase: testCreateDNASequence took 0 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.003 sec [junit] Testcase: testQualityScoresIntArray took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testToList took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0.001 sec - [junit] Testcase: testErrorProbabilities took 0.001 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: 0.208 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.033 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0.003 sec - [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.002 sec - [junit] Testcase: testIsSanger took 0.046 sec - [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.002 sec + [junit] Testcase: testParseFastqVariant took 0.008 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec + [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec + [junit] Testcase: testIsSanger took 0.006 sec + [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0.001 sec - [junit] Testcase: testIsIllumina took 0.001 sec - [junit] Testcase: testDescription took 0.009 sec + [junit] Testcase: testIsIllumina took 0 sec + [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.957 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.957 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.872 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.872 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.533 sec - [junit] Testcase: testWrappingAsIllumina took 0.018 sec - [junit] Testcase: testValidateDescription took 0.137 sec - [junit] Testcase: testValidateRepeatDescription took 0.039 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.035 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.043 sec - [junit] Testcase: testLongReadsAsIllumina took 0.053 sec - [junit] Testcase: testParseNullReadable took 0.011 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.567 sec - [junit] Testcase: testReadEmptyFile took 0.004 sec - [junit] Testcase: testErrorExamples took 0.263 sec - [junit] Testcase: testParse took 0.006 sec - [junit] Testcase: testCreateFastq took 0.001 sec + [junit] Testcase: testFullRangeAsIllumina took 0.15 sec + [junit] Testcase: testWrappingAsIllumina took 0.019 sec + [junit] Testcase: testValidateDescription took 0.038 sec + [junit] Testcase: testValidateRepeatDescription took 0.014 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.012 sec + [junit] Testcase: testMiscRnaAsIllumina took 0.013 sec + [junit] Testcase: testLongReadsAsIllumina took 0.019 sec + [junit] Testcase: testParseNullReadable took 0.004 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.185 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.152 sec + [junit] Testcase: testParse took 0.005 sec + [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0.001 sec - [junit] Testcase: testWrappedSequence took 0.009 sec - [junit] Testcase: testReadEmptyInputStream took 0.007 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0.002 sec - [junit] Testcase: testMultipleWrappedQuality took 0.013 sec - [junit] Testcase: testCreateFastqReader took 0.001 sec - [junit] Testcase: testReadURL took 0.003 sec - [junit] Testcase: testCreateFastqWriter took 0.009 sec - [junit] Testcase: testReadEmptyURL took 0.004 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.014 sec - [junit] Testcase: testWrappedQuality took 0.019 sec + [junit] Testcase: testWrappedSequence took 0.011 sec + [junit] Testcase: testReadEmptyInputStream took 0.006 sec + [junit] Testcase: testParseNullParseListener took 0.006 sec + [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testMultipleWrappedQuality took 0.008 sec + [junit] Testcase: testCreateFastqReader took 0 sec + [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.013 sec + [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.702 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.702 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.097 sec - [junit] Testcase: testAppendVararg took 0.003 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.036 sec - [junit] Testcase: testWriteFileIterable took 0.416 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.007 sec - [junit] Testcase: testAppendIterable took 0.002 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testWriteFileVararg took 0.028 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.019 sec + [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.014 sec + [junit] Testcase: testWriteFileIterable took 0.152 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.006 sec + [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testWriteFileVararg took 0.005 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: 1.907 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.907 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.351 sec - [junit] Testcase: testFullRangeAsSanger took 0.019 sec - [junit] Testcase: testWrappingOriginal took 0.024 sec - [junit] Testcase: testLongReadsOriginal took 0.077 sec - [junit] Testcase: testMiscDnaOriginal took 0.017 sec - [junit] Testcase: testMiscRnaOriginal took 0.018 sec - [junit] Testcase: testValidateDescription took 0.072 sec - [junit] Testcase: testValidateRepeatDescription took 0.013 sec - [junit] Testcase: testFullRangeOriginal took 0.012 sec - [junit] Testcase: testWrappingAsSanger took 0.013 sec + [junit] Testcase: testMiscRnaAsSanger took 0.164 sec + [junit] Testcase: testFullRangeAsSanger took 0.007 sec + [junit] Testcase: testWrappingOriginal took 0.02 sec + [junit] Testcase: testLongReadsOriginal took 0.023 sec + [junit] Testcase: testMiscDnaOriginal took 0.013 sec + [junit] Testcase: testMiscRnaOriginal took 0.007 sec + [junit] Testcase: testValidateDescription took 0.024 sec + [junit] Testcase: testValidateRepeatDescription took 0.004 sec + [junit] Testcase: testFullRangeOriginal took 0.008 sec + [junit] Testcase: testWrappingAsSanger took 0.004 sec [junit] Testcase: testLongReadsAsSanger took 0.03 sec - [junit] Testcase: testMiscDnaAsSanger took 0.019 sec - [junit] Testcase: testParseNullReadable took 0.013 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.571 sec - [junit] Testcase: testReadEmptyFile took 0.007 sec - [junit] Testcase: testErrorExamples took 0.328 sec - [junit] Testcase: testParse took 0.008 sec + [junit] Testcase: testMiscDnaAsSanger took 0.01 sec + [junit] Testcase: testParseNullReadable took 0.011 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.14 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.102 sec + [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testReadInputStream took 0.005 sec - [junit] Testcase: testWrappedSequence took 0.016 sec - [junit] Testcase: testReadEmptyInputStream took 0.014 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0.006 sec - [junit] Testcase: testMultipleWrappedQuality took 0.02 sec - [junit] Testcase: testCreateFastqReader took 0.001 sec - [junit] Testcase: testReadURL took 0.002 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testReadEmptyURL took 0.011 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.027 sec - [junit] Testcase: testWrappedQuality took 0.016 sec + [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testWrappedSequence took 0.007 sec + [junit] Testcase: testReadEmptyInputStream took 0.003 sec + [junit] Testcase: testParseNullParseListener took 0.007 sec + [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testMultipleWrappedQuality took 0.003 sec + [junit] Testcase: testCreateFastqReader took 0 sec + [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testReadEmptyURL took 0.006 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec + [junit] Testcase: testWrappedQuality took 0.006 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: 0.645 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.645 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.355 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.064 sec - [junit] Testcase: testAppendVararg took 0.003 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.03 sec - [junit] Testcase: testWriteFileIterable took 0.427 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.004 sec - [junit] Testcase: testAppendIterable took 0.002 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testWriteFileVararg took 0.021 sec + [junit] Testcase: testConvertNotSangerVariant took 0.041 sec + [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testCreateFastq took 0.004 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.016 sec + [junit] Testcase: testWriteFileIterable took 0.218 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec + [junit] Testcase: testAppendIterable took 0 sec + [junit] Testcase: testCreateFastqWriter took 0.004 sec + [junit] Testcase: testWriteFileVararg took 0.01 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: 1.944 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.944 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.755 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.755 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.449 sec - [junit] Testcase: testFullRangeAsSolexa took 0.016 sec - [junit] Testcase: testValidateDescription took 0.081 sec - [junit] Testcase: testValidateRepeatDescription took 0.048 sec - [junit] Testcase: testWrappingAsSolexa took 0.04 sec - [junit] Testcase: testLongReadsAsSolexa took 0.053 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.034 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.229 sec + [junit] Testcase: testFullRangeAsSolexa took 0.006 sec + [junit] Testcase: testValidateDescription took 0.021 sec + [junit] Testcase: testValidateRepeatDescription took 0.007 sec + [junit] Testcase: testWrappingAsSolexa took 0.006 sec + [junit] Testcase: testLongReadsAsSolexa took 0.011 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.011 sec [junit] Testcase: testParseNullReadable took 0.011 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.547 sec - [junit] Testcase: testReadEmptyFile took 0.004 sec - [junit] Testcase: testErrorExamples took 0.393 sec - [junit] Testcase: testParse took 0.014 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testReadInputStream took 0.001 sec - [junit] Testcase: testWrappedSequence took 0.016 sec - [junit] Testcase: testReadEmptyInputStream took 0.01 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0.003 sec - [junit] Testcase: testMultipleWrappedQuality took 0.017 sec - [junit] Testcase: testCreateFastqReader took 0.001 sec - [junit] Testcase: testReadURL took 0.007 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.226 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.101 sec + [junit] Testcase: testParse took 0.002 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testWrappedSequence took 0.004 sec + [junit] Testcase: testReadEmptyInputStream took 0.023 sec + [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testMultipleWrappedQuality took 0.009 sec + [junit] Testcase: testCreateFastqReader took 0 sec + [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0.004 sec - [junit] Testcase: testReadEmptyURL took 0.008 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.01 sec - [junit] Testcase: testWrappedQuality took 0.007 sec + [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.005 sec + [junit] Testcase: testWrappedQuality took 0.003 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: 0.979 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.979 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.115 sec - [junit] Testcase: testAppendVararg took 0.007 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.021 sec + [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.046 sec - [junit] Testcase: testWriteFileIterable took 0.598 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.008 sec - [junit] Testcase: testAppendIterable took 0.002 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testWriteFileVararg took 0.046 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.014 sec + [junit] Testcase: testWriteFileIterable took 0.201 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.01 sec + [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testWriteFileVararg took 0.018 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: 0.18 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.021 sec - [junit] Testcase: testStreamNullListener took 0.042 sec - [junit] Testcase: testStreamNullReadable took 0.006 sec + [junit] Testcase: testStreamNullVariant took 0.006 sec + [junit] Testcase: testStreamNullListener took 0.006 sec + [junit] Testcase: testStreamNullReadable took 0.002 sec BUILD SUCCESSFUL -Total time: 2 minutes 16 seconds +Total time: 52 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -5476,39 +5519,39 @@ [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: 0.132 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec [junit] - [junit] Testcase: testMe took 0.01 sec + [junit] Testcase: testMe took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 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: testSomeMethod took 0.006 sec + [junit] Testcase: testSomeMethod took 0.002 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: 0.146 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec [junit] - [junit] Testcase: testGetColor took 0.029 sec + [junit] Testcase: testGetColor took 0.024 sec [junit] Testcase: testSetStructure took 0.001 sec - [junit] Testcase: testClear took 0.001 sec - [junit] Testcase: testGetSelection took 0.02 sec - [junit] Testcase: testRepaint took 0.001 sec - [junit] Testcase: testSetSelection took 0.001 sec + [junit] Testcase: testClear took 0 sec + [junit] Testcase: testGetSelection took 0.01 sec + [junit] Testcase: testRepaint took 0 sec + [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec - [junit] Testcase: testSetColor took 0.001 sec - [junit] Testcase: testSetStyle took 0.001 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: 0.234 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: 0.201 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 sec [junit] - [junit] Testcase: testStructureLoad took 0.03 sec + [junit] Testcase: testStructureLoad took 0.002 sec BUILD SUCCESSFUL -Total time: 1 minute 8 seconds +Total time: 17 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -5523,8 +5566,8 @@ [echo] Using java version 17.0.6 BUILD SUCCESSFUL -Total time: 39 seconds -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +Total time: 10 seconds +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» create-stamp debian/debhelper-build-stamp dh_prep dh_install @@ -5546,9 +5589,9 @@ 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: generazione del pacchetto "libbiojava4-java-doc" in "../libbiojava4-java-doc_4.2.12+dfsg-8_all.deb". +dpkg-deb: generazione del pacchetto "libbiojava4.0-java" in "../libbiojava4.0-java_4.2.12+dfsg-8_all.deb". +dpkg-deb: generazione del pacchetto "libbiojava4-java" in "../libbiojava4-java_4.2.12+dfsg-8_all.deb". dpkg-genbuildinfo --build=binary -O../biojava4-live_4.2.12+dfsg-8_armhf.buildinfo dpkg-genchanges --build=binary -O../biojava4-live_4.2.12+dfsg-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5556,12 +5599,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/21665/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21665/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/32081 and its subdirectories -I: Current time: Sat Apr 29 03:16:05 -12 2023 -I: pbuilder-time-stamp: 1682781365 +I: removing directory /srv/workspace/pbuilder/21665 and its subdirectories +I: Current time: Sun Apr 30 05:48:13 +14 2023 +I: pbuilder-time-stamp: 1682783293