Diff of the two buildlogs: -- --- b1/build.log 2021-12-25 22:30:03.584929400 +0000 +++ b2/build.log 2021-12-25 22:37:28.986995427 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 27 16:47:16 -12 2023 -I: pbuilder-time-stamp: 1674881236 +I: Current time: Sun Dec 26 12:30:07 +14 2021 +I: pbuilder-time-stamp: 1640471407 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.6w0sfQPM/trustedkeys.kbx': General error -gpgv: Signature made Mon Jul 13 07:29:24 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.BCp8bAhA/trustedkeys.kbx': General error +gpgv: Signature made Tue Jul 14 09:29:24 2020 +14 gpgv: using RSA key 58B66D48736BE93B052DE6729C5C99EB05BD750A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-3.1.dsc @@ -35,135 +35,169 @@ dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/899265/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1709051/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1709051/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1709051/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fb050a0348e648feb0b5ff06ac0ac17b' - 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='899265' - PS1='# ' - PS2='> ' + INVOCATION_ID=daef9278657e44fd8b5bb37cbf8f8441 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1709051 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.UifiCnpyL2/pbuilderrc_pwJK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UifiCnpyL2/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.UifiCnpyL2/pbuilderrc_r3VG --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UifiCnpyL2/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/899265/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 26 12:30 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1709051/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -478,7 +512,7 @@ Get: 219 http://deb.debian.org/debian bullseye/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libxmlunit-java all 1.6-2 [100 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 rdfind amd64 1.4.1-1+b3 [40.7 kB] -Fetched 351 MB in 5s (72.4 MB/s) +Fetched 351 MB in 13s (26.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -1560,7 +1594,8 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-3.1_source.changes +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-3.1_source.changes dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-3.1 dpkg-buildpackage: info: source distribution unstable @@ -1573,7 +1608,7 @@ 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 '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf build rm -rf dist @@ -1594,7 +1629,7 @@ 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 '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' 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 @@ -1616,7 +1651,7 @@ 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 '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' 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,' \ @@ -1638,7 +1673,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 3 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1654,7 +1689,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 18 seconds +Total time: 17 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1672,7 +1707,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 5 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1686,7 +1721,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 2 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1702,7 +1737,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 7 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1720,7 +1755,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 4 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1736,7 +1771,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 5 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1751,7 +1786,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 5 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1769,7 +1804,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 22 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1787,7 +1822,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 8 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1803,7 +1838,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 3 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1821,7 +1856,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 4 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1837,7 +1872,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 4 seconds +Total time: 3 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1879,7 +1914,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 4 seconds +Total time: 8 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2172,12 +2207,12 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 34 seconds # rm -rf biojavadoc make[1]: Leaving 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 '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -2208,25 +2243,25 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.075 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.075 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.08 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.08 sec [junit] - [junit] Testcase: testGetIndexOf took 0.031 sec + [junit] Testcase: testGetIndexOf took 0.035 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0.001 sec - [junit] Testcase: testGetSequenceIndexAt took 0.001 sec - [junit] Testcase: testGetAccession took 0 sec + [junit] Testcase: testGetSequenceIndexAt took 0 sec + [junit] Testcase: testGetAccession took 0.001 sec [junit] Testcase: testToString took 0.002 sec - [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec + [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec [junit] Testcase: testCountCompounds took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAt took 0 sec + [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.002 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.003 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED @@ -2241,136 +2276,136 @@ [junit] Testcase: testGetOverlapCount took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec [junit] Testcase: testGetLocationInAlignment took 0.002 sec - [junit] Testcase: testIterator took 0 sec + [junit] Testcase: testIterator took 0.001 sec [junit] Testcase: testGetSequenceAsString took 0.001 sec - [junit] Testcase: testGetLastIndexOf took 0.001 sec + [junit] Testcase: testGetLastIndexOf took 0 sec [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.369 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.369 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.166 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.166 sec [junit] - [junit] Testcase: testGetIndexOf took 0.153 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.009 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.003 sec - [junit] Testcase: testToStringInt took 0.025 sec - [junit] Testcase: testToString took 0.001 sec - [junit] Testcase: testToStringFormatted took 0.064 sec - [junit] Testcase: testSimpleProfile took 0.006 sec - [junit] Testcase: testGetSize took 0 sec - [junit] Testcase: testGetAlignedSequenceS took 0 sec + [junit] Testcase: testGetIndexOf took 0.068 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.002 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.002 sec + [junit] Testcase: testToStringInt took 0.011 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testToStringFormatted took 0.031 sec + [junit] Testcase: testSimpleProfile took 0.001 sec + [junit] Testcase: testGetSize took 0.001 sec + [junit] Testcase: testGetAlignedSequenceS took 0.001 sec [junit] Testcase: testGetAlignedSequences took 0.001 sec - [junit] Testcase: testGetOriginalSequences took 0.005 sec + [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.005 sec - [junit] Testcase: testGetIndicesAt took 0.007 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec + [junit] Testcase: testGetIndicesAt took 0.003 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.016 sec - [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.003 sec + [junit] Testcase: testGetCompoundAtIntInt took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.002 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetCompoundsAt took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundsAt took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec - [junit] Testcase: testIterator took 0 sec - [junit] Testcase: testGetLastIndexOf took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec + [junit] Testcase: testIterator took 0.001 sec + [junit] Testcase: testGetLastIndexOf took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.161 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.058 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.012 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetCompoundInQueryAt took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.011 sec - [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetNumIdenticals took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.002 sec + [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec + [junit] Testcase: testGetNumIdenticals took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAt took 0.009 sec - [junit] Testcase: testGetIndexInQueryAt took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAt took 0 sec + [junit] Testcase: testGetIndexInQueryAt took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.016 sec - [junit] Testcase: testGetNumSimilars took 0.002 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetNumSimilars took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.233 sec - [junit] Testcase: testHashCode took 0 sec - [junit] Testcase: testEquals took 0.001 sec + [junit] Testcase: testGetAlignment took 0.092 sec + [junit] Testcase: testHashCode took 0.001 sec + [junit] Testcase: testEquals took 0 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.318 sec - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.318 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.348 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.348 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml - [junit] Jan 27, 2023 4:51:37 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Dec 26, 2021 12:35:50 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Jan 27, 2023 4:51:37 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Dec 26, 2021 12:35:50 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testConstructorWithEvalueHspFilter took 0.179 sec + [junit] Testcase: testConstructorWithEvalueHspFilter took 0.184 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2381,8 +2416,8 @@ [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] - [junit] Testcase: testConstructorWithFactoryGuess took 0.116 sec - [junit] Testcase: testConstructorWithoutFactoryGuess took 0.005 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.139 sec + [junit] Testcase: testConstructorWithoutFactoryGuess took 0.006 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2397,7 +2432,7 @@ BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed -Total time: 10 seconds +Total time: 8 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -2412,32 +2447,32 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec [junit] - [junit] Testcase: testGetQuery took 0.05 sec - [junit] Testcase: testGetScore took 0.023 sec + [junit] Testcase: testGetQuery took 0.056 sec + [junit] Testcase: testGetScore took 0.021 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec + [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec [junit] - [junit] Testcase: testGetQuery took 0.059 sec - [junit] Testcase: testGetScore took 0.025 sec + [junit] Testcase: testGetQuery took 0.064 sec + [junit] Testcase: testGetScore took 0.022 sec [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -2449,157 +2484,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.097 sec - [junit] Testcase: testToString took 0.003 sec + [junit] Testcase: testGuideTree took 0.122 sec + [junit] Testcase: testToString took 0.005 sec [junit] Testcase: testGetScoreMatrix took 0.005 sec - [junit] Testcase: testGetRoot took 0.023 sec + [junit] Testcase: testGetRoot took 0.03 sec [junit] Testcase: testGetSequences took 0.002 sec [junit] Testcase: testGetDistanceMatrix took 0.002 sec - [junit] Testcase: testGetAllPairsScores took 0.003 sec - [junit] Testcase: testIterator took 0.003 sec + [junit] Testcase: testGetAllPairsScores took 0.002 sec + [junit] Testcase: testIterator took 0.002 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.088 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.091 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.41 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.41 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.065 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.064 sec [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.023 sec - [junit] Testcase: should_align_middle_anchor took 0.027 sec + [junit] Testcase: testGetComputationTime took 0.022 sec + [junit] Testcase: should_align_middle_anchor took 0.028 sec [junit] Testcase: testGetQuery took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec - [junit] Testcase: should_align_all_anchored took 0.001 sec + [junit] Testcase: should_align_all_anchored took 0.002 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.003 sec - [junit] Testcase: testGetProfile took 0.001 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.004 sec + [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: should_align_ending_anchor took 0.001 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.003 sec - [junit] Testcase: testComplex took 0.01 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.019 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec + [junit] Testcase: testComplex took 0.013 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.021 sec [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: testIntOverflowBug took 0.19 sec + [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: testIntOverflowBug took 0.225 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: 0.014 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] [junit] Testcase: testOpenPenalty took 0.003 sec - [junit] Testcase: testType took 0 sec - [junit] Testcase: testExtensionPenalty took 0.001 sec - [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec + [junit] Testcase: testType took 0.001 sec + [junit] Testcase: testExtensionPenalty took 0 sec + [junit] Testcase: testSimpleGapPenaltyShortShort took 0.001 sec [junit] Testcase: testSimpleGapPenalty took 0 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec [junit] - [junit] Testcase: testGetQuery took 0.103 sec + [junit] Testcase: testGetQuery took 0.089 sec [junit] Testcase: testGetTarget took 0.002 sec - [junit] Testcase: testSimpleProfilePair took 0.005 sec + [junit] Testcase: testSimpleProfilePair took 0.007 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.134 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.094 sec [junit] Testcase: testGetGapPenalty took 0.005 sec - [junit] Testcase: testGetComputationTime took 0.008 sec - [junit] Testcase: testGetQuery took 0.005 sec - [junit] Testcase: testGetScore took 0.003 sec - [junit] Testcase: testGetScoreMatrix took 0.004 sec - [junit] Testcase: testGetPair took 0.014 sec - [junit] Testcase: testGetProfile took 0.009 sec + [junit] Testcase: testGetComputationTime took 0.003 sec + [junit] Testcase: testGetQuery took 0.002 sec + [junit] Testcase: testGetScore took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.003 sec + [junit] Testcase: testGetPair took 0.007 sec + [junit] Testcase: testGetProfile took 0.003 sec [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.074 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.023 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec - [junit] Testcase: testGetTarget took 0.009 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.032 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.001 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.001 sec + [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.021 sec - [junit] Testcase: testSetDescription took 0.046 sec - [junit] Testcase: testToString took 0.077 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.006 sec + [junit] Testcase: testSetDescription took 0.021 sec + [junit] Testcase: testToString took 0.03 sec [junit] Testcase: testCaseEquivalence took 0.001 sec - [junit] Testcase: test took 0.018 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.014 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.006 sec - [junit] Testcase: testSetName took 0.015 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.004 sec + [junit] Testcase: test took 0.009 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.007 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.003 sec + [junit] Testcase: testSetName took 0.005 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.003 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.137 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.055 sec [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.048 sec - [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetScore took 0.001 sec - [junit] Testcase: testGetScoreMatrix took 0.008 sec - [junit] Testcase: testGetPair took 0.006 sec - [junit] Testcase: testSmithWaterman took 0.003 sec - [junit] Testcase: testGetProfile took 0.002 sec - [junit] Testcase: testGetMinScore took 0.003 sec + [junit] Testcase: testGetComputationTime took 0.019 sec + [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetScore took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.005 sec + [junit] Testcase: testSmithWaterman took 0.002 sec + [junit] Testcase: testGetProfile took 0.001 sec + [junit] Testcase: testGetMinScore took 0 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.056 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.039 sec [junit] Testcase: testSetStoringScoreMatrix took 0.001 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.005 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.003 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.004 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.002 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec - [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0.001 sec + [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec - [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0.001 sec + [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 sec [junit] - [junit] Testcase: testGetComputationTime took 0.128 sec + [junit] Testcase: testGetComputationTime took 0.093 sec [junit] Testcase: testGuanUberbacher took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec [junit] Testcase: testGetPair took 0.006 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_shorter_target took 0.042 sec + [junit] Testcase: should_align_shorter_target took 0.028 sec [junit] Testcase: should_align_multiple_cuts took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL -Total time: 14 seconds +Total time: 12 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -2617,8 +2652,8 @@ [echo] Using java version 11.0.12 [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: 1.276 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.276 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.562 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.562 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -2626,41 +2661,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 1.17 sec - [junit] Testcase: testExample1 took 0.034 sec - [junit] Testcase: testExample2 took 0.008 sec - [junit] Testcase: testExample3 took 0.009 sec - [junit] Testcase: testExample1WithCSV took 0.028 sec - [junit] Testcase: testWithCases took 0.006 sec + [junit] Testcase: testAdvancedXMLExample took 0.488 sec + [junit] Testcase: testExample1 took 0.023 sec + [junit] Testcase: testExample2 took 0.006 sec + [junit] Testcase: testExample3 took 0.006 sec + [junit] Testcase: testExample1WithCSV took 0.019 sec + [junit] Testcase: testWithCases took 0.008 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.742 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.742 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.623 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.623 sec [junit] - [junit] Testcase: shortExample1 took 0.056 sec - [junit] Testcase: shortExample2 took 0.583 sec - [junit] Testcase: shortExample3 took 0.072 sec - [junit] Testcase: shortExample4 took 0.001 sec - [junit] Testcase: shortExample5 took 0.008 sec + [junit] Testcase: shortExample1 took 0.047 sec + [junit] Testcase: shortExample2 took 0.49 sec + [junit] Testcase: shortExample3 took 0.067 sec + [junit] Testcase: shortExample4 took 0.002 sec + [junit] Testcase: shortExample5 took 0.006 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.84 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.84 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.675 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.675 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 0.705 sec + [junit] Testcase: testAdvancedXMLExample took 0.592 sec [junit] Testcase: testExample1 took 0.025 sec - [junit] Testcase: testExample2 took 0.015 sec - [junit] Testcase: testExample3 took 0.023 sec - [junit] Testcase: testExample1WithCSV took 0.024 sec - [junit] Testcase: testWithCases took 0.016 sec + [junit] Testcase: testExample2 took 0.013 sec + [junit] Testcase: testExample3 took 0.01 sec + [junit] Testcase: testExample1WithCSV took 0.014 sec + [junit] Testcase: testWithCases took 0.009 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.863 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.863 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.896 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.896 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. @@ -2875,74 +2910,74 @@ [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 0.048 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 0.535 sec + [junit] Testcase: testAbsorbance took 0.053 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 0.542 sec [junit] Testcase: testEnrichment took 0.018 sec [junit] Testcase: testApliphaticIndex took 0.002 sec [junit] Testcase: testMolecularWeightXMLNull took 0.009 sec - [junit] Testcase: testApliphaticIndexNull took 0.001 sec + [junit] Testcase: testApliphaticIndexNull took 0 sec [junit] Testcase: testIsoelectricPointExpasy took 0.003 sec [junit] Testcase: testAbsorbanceNull took 0 sec [junit] Testcase: testIsoelectricPointNull took 0 sec [junit] Testcase: testAverageHydropathy took 0.001 sec - [junit] Testcase: testExtinctionCoefficient took 0.001 sec + [junit] Testcase: testExtinctionCoefficient took 0.002 sec [junit] Testcase: testAAComposition took 0.002 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.041 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.04 sec [junit] Testcase: testMolecularWeight took 0.001 sec [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec - [junit] Testcase: testNetChargeNull took 0 sec + [junit] Testcase: testNetChargeNull took 0.001 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec - [junit] Testcase: testNetCharge took 0.126 sec + [junit] Testcase: testNetCharge took 0.129 sec [junit] Testcase: testEnrichmentNull took 0.001 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0 sec - [junit] Testcase: testMolecularWeightXML took 0.054 sec + [junit] Testcase: testMolecularWeightXML took 0.068 sec [junit] Testcase: testInstabilityIndex took 0 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] - [junit] Testcase: testFake took 0.003 sec + [junit] Testcase: testFake took 0.002 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: 0.034 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] - [junit] Testcase: testFakeTest took 0.021 sec + [junit] Testcase: testFakeTest took 0.018 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.738 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.738 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: generateSchema took 0.397 sec - [junit] Testcase: readWithIDXml took 0.162 sec + [junit] Testcase: generateSchema took 0.361 sec + [junit] Testcase: readWithIDXml took 0.161 sec [junit] Testcase: readMinXml took 0.066 sec - [junit] Testcase: readAdvancedXml took 0.032 sec + [junit] Testcase: readAdvancedXml took 0.041 sec [junit] Testcase: generateXml took 0.034 sec [junit] Testcase: readXml took 0.063 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.695 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.695 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.644 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.644 sec [junit] - [junit] Testcase: generateSchema took 0.408 sec - [junit] Testcase: generateXml took 0.083 sec - [junit] Testcase: readXml took 0.19 sec + [junit] Testcase: generateSchema took 0.393 sec + [junit] Testcase: generateXml took 0.077 sec + [junit] Testcase: readXml took 0.165 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: 0.03 sec [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] - [junit] Testcase: testFake took 0.019 sec + [junit] Testcase: testFake took 0.02 sec BUILD SUCCESSFUL -Total time: 19 seconds +Total time: 12 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -2975,18 +3010,18 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec [junit] [junit] Testcase: testConvert took 0.112 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: 0.025 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.004 sec + [junit] Testcase: testBuildAppendSequence took 0.005 sec [junit] Testcase: testBuildNullDescription took 0 sec - [junit] Testcase: testBuildAppendQuality took 0.001 sec + [junit] Testcase: testBuildAppendQuality took 0 sec [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec [junit] Testcase: testBuildDefaultVariant took 0 sec @@ -2994,46 +3029,46 @@ [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.001 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 0.001 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 sec - [junit] Testcase: testBuildMultiple took 0 sec + [junit] Testcase: testBuildMultiple took 0.001 sec [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] [junit] Testcase: testImmutable took 0.002 sec [junit] Testcase: testBuilder took 0.002 sec [junit] Testcase: testVariant took 0 sec [junit] Testcase: testQuality took 0.004 sec - [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testHashCode took 0.001 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Testcase: testConstructor took 0 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: 0.091 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] [junit] Testcase: testErrorProbabilitiesNullFastq took 0.002 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec - [junit] Testcase: testConvertNullVariant took 0 sec + [junit] Testcase: testConvertNullVariant took 0.001 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.052 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.049 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec - [junit] Testcase: testConvertNullFastq took 0.001 sec + [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.001 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec @@ -3046,185 +3081,185 @@ [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec + [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.002 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec - [junit] Testcase: testConvertSameVariant took 0.001 sec - [junit] Testcase: testQualityScores took 0.004 sec + [junit] Testcase: testConvertSameVariant took 0 sec + [junit] Testcase: testQualityScores took 0.005 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0.001 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: 0.021 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.002 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec + [junit] Testcase: testParseFastqVariant took 0.003 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec - [junit] Testcase: testIsSanger took 0.003 sec + [junit] Testcase: testIsSanger took 0.004 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.033 sec - [junit] Testcase: testWrappingAsIllumina took 0.004 sec - [junit] Testcase: testValidateDescription took 0.008 sec - [junit] Testcase: testValidateRepeatDescription took 0.003 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.002 sec + [junit] Testcase: testFullRangeAsIllumina took 0.039 sec + [junit] Testcase: testWrappingAsIllumina took 0.005 sec + [junit] Testcase: testValidateDescription took 0.01 sec + [junit] Testcase: testValidateRepeatDescription took 0.004 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.003 sec [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec - [junit] Testcase: testLongReadsAsIllumina took 0.004 sec + [junit] Testcase: testLongReadsAsIllumina took 0.005 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.02 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.024 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.017 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.02 sec [junit] Testcase: testParse took 0.001 sec - [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.001 sec - [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadURL took 0 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] [junit] Testcase: testConvertNotIlluminaVariant took 0.007 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.015 sec - [junit] Testcase: testWriteOutputStreamIterable took 0 sec + [junit] Testcase: testWriteFileIterable took 0.016 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.002 sec + [junit] Testcase: testWriteFileVararg took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.04 sec - [junit] Testcase: testFullRangeAsSanger took 0.004 sec - [junit] Testcase: testWrappingOriginal took 0.003 sec + [junit] Testcase: testMiscRnaAsSanger took 0.041 sec + [junit] Testcase: testFullRangeAsSanger took 0.003 sec + [junit] Testcase: testWrappingOriginal took 0.004 sec [junit] Testcase: testLongReadsOriginal took 0.007 sec [junit] Testcase: testMiscDnaOriginal took 0.002 sec [junit] Testcase: testMiscRnaOriginal took 0.002 sec - [junit] Testcase: testValidateDescription took 0.007 sec - [junit] Testcase: testValidateRepeatDescription took 0.003 sec - [junit] Testcase: testFullRangeOriginal took 0.001 sec - [junit] Testcase: testWrappingAsSanger took 0.001 sec - [junit] Testcase: testLongReadsAsSanger took 0.003 sec + [junit] Testcase: testValidateDescription took 0.008 sec + [junit] Testcase: testValidateRepeatDescription took 0.002 sec + [junit] Testcase: testFullRangeOriginal took 0.002 sec + [junit] Testcase: testWrappingAsSanger took 0.002 sec + [junit] Testcase: testLongReadsAsSanger took 0.004 sec [junit] Testcase: testMiscDnaAsSanger took 0.001 sec - [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.022 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.021 sec + [junit] Testcase: testParseNullReadable took 0 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.019 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.02 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testReadInputStream took 0.001 sec + [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0 sec - [junit] Testcase: testMultipleWrappedQuality took 0.001 sec + [junit] Testcase: testReadFile took 0.001 sec + [junit] Testcase: testMultipleWrappedQuality took 0.002 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.007 sec + [junit] Testcase: testConvertNotSangerVariant took 0.008 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.014 sec - [junit] Testcase: testWriteOutputStreamIterable took 0 sec - [junit] Testcase: testAppendIterable took 0 sec + [junit] Testcase: testWriteFileIterable took 0.017 sec + [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec + [junit] Testcase: testAppendIterable took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.031 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.034 sec [junit] Testcase: testFullRangeAsSolexa took 0.004 sec [junit] Testcase: testValidateDescription took 0.008 sec - [junit] Testcase: testValidateRepeatDescription took 0.002 sec - [junit] Testcase: testWrappingAsSolexa took 0.002 sec - [junit] Testcase: testLongReadsAsSolexa took 0.003 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.001 sec + [junit] Testcase: testValidateRepeatDescription took 0.004 sec + [junit] Testcase: testWrappingAsSolexa took 0.003 sec + [junit] Testcase: testLongReadsAsSolexa took 0.005 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.002 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.017 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.017 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.019 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.022 sec [junit] Testcase: testParse took 0 sec - [junit] Testcase: testCreateFastq took 0.001 sec + [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec + [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0 sec - [junit] Testcase: testWrappedQuality took 0 sec + [junit] Testcase: testReadEmptyURL took 0 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec + [junit] Testcase: testWrappedQuality took 0.001 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: 0.043 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.006 sec - [junit] Testcase: testAppendVararg took 0 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.007 sec + [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.003 sec - [junit] Testcase: testWriteFileIterable took 0.016 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec + [junit] Testcase: testWriteFileIterable took 0.014 sec + [junit] Testcase: testWriteOutputStreamIterable took 0 sec + [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testWriteFileVararg took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] [junit] Testcase: testStreamNullVariant took 0.002 sec [junit] Testcase: testStreamNullListener took 0.002 sec - [junit] Testcase: testStreamNullReadable took 0.001 sec + [junit] Testcase: testStreamNullReadable took 0 sec BUILD SUCCESSFUL -Total time: 10 seconds +Total time: 11 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -3245,39 +3280,39 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] - [junit] Testcase: testMe took 0.001 sec + [junit] Testcase: testMe took 0 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] - [junit] Testcase: testSomeMethod took 0 sec + [junit] Testcase: testSomeMethod took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] - [junit] Testcase: testGetColor took 0.003 sec - [junit] Testcase: testSetStructure took 0 sec - [junit] Testcase: testClear took 0.001 sec - [junit] Testcase: testGetSelection took 0.003 sec + [junit] Testcase: testGetColor took 0.004 sec + [junit] Testcase: testSetStructure took 0.001 sec + [junit] Testcase: testClear took 0 sec + [junit] Testcase: testGetSelection took 0.004 sec [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec - [junit] Testcase: testSetZoom took 0.001 sec + [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 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: 0.013 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 3 seconds +Total time: 5 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -3303,7 +3338,7 @@ dh_install debian/rules override_jh_installjavadoc make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ $(dpkg -L $(apt-cache show default-jdk-doc | grep Depends | awk '{print $2}') | grep /usr/share/doc/ | head -n1) \ @@ -3342,9 +3377,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb'. dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb'. +dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-3.1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-3.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3352,12 +3387,14 @@ 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/1709051/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1709051/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/899265 and its subdirectories -I: Current time: Fri Jan 27 16:53:09 -12 2023 -I: pbuilder-time-stamp: 1674881589 +I: removing directory /srv/workspace/pbuilder/1709051 and its subdirectories +I: Current time: Sun Dec 26 12:37:28 +14 2021 +I: pbuilder-time-stamp: 1640471848