Diff of the two buildlogs: -- --- b1/build.log 2024-01-06 16:55:41.760445354 +0000 +++ b2/build.log 2024-01-06 17:26:05.065266436 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 04:20:44 -12 2024 -I: pbuilder-time-stamp: 1704558044 +I: Current time: Sun Jan 7 06:56:01 +14 2024 +I: pbuilder-time-stamp: 1704560161 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 [./biojava-live_1.9.5+dfsg.orig.tar.xz] I: copying [./biojava-live_1.9.5+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu May 11 21:19:05 2023 -12 +gpgv: Signature made Fri May 12 09:19:05 2023 gpgv: using RSA key B8CE4DE21080DCF903E16C40F513C419E4B9D0AC gpgv: issuer "ebourg@apache.org" gpgv: Can't check signature: No public key @@ -28,64 +28,96 @@ dpkg-source: info: applying omit_tests_with_problematic_data.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14412/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8850/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 Jan 6 16:57 /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/8850/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8850/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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/reproducible-path + 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='e40208829c364123b22f111a09388976' - 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='14412' - PS1='# ' - PS2='> ' + INVOCATION_ID=102028aeac6341f6b4a3ec0159e3e9ef + 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=8850 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.Cje8cmwq/pbuilderrc_WdsN --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.Cje8cmwq/b1 --logfile b1/build.log biojava-live_1.9.5+dfsg-3.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.Cje8cmwq/pbuilderrc_Pa5d --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.Cje8cmwq/b2 --logfile b2/build.log biojava-live_1.9.5+dfsg-3.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 jtx1a 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 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 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 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 + 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 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 @@ -96,67 +128,67 @@ -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 2023 dmesg + -rwxr-xr-x 1 root root 59128 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 2023 fusermount + -rwxr-xr-x 1 root root 55748 Mar 23 2023 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 2023 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 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 19 2022 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 2023 login + -rwxr-xr-x 1 root root 35132 Mar 23 2023 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 2023 lsblk + -rwxr-xr-x 1 root root 136808 Mar 23 2023 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 2023 more - -rwsr-xr-x 1 root root 38496 Mar 22 2023 mount - -rwxr-xr-x 1 root root 9824 Mar 22 2023 mountpoint + -rwxr-xr-x 1 root root 38504 Mar 23 2023 more + -rwsr-xr-x 1 root root 38496 Mar 23 2023 mount + -rwxr-xr-x 1 root root 9824 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 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 14152 Jul 28 11:46 run-parts + -rwxr-xr-x 1 root root 14152 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 6 16:57 sh -> /bin/bash -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 2023 su + -rwsr-xr-x 1 root root 50800 Mar 23 2023 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 2023 tar - -rwxr-xr-x 1 root root 9800 Jul 28 11:46 tempfile + -rwxr-xr-x 1 root root 9800 Jul 28 23:46 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 2023 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 2023 umount + -rwxr-xr-x 1 root root 9768 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 2023 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 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 2023 wdctl + -rwxr-xr-x 1 root root 42608 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 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/14412/tmp/hooks/D02_print_environment finished + -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/8850/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -169,7 +201,7 @@ Depends: debhelper-compat (= 13), maven-debian-helper, default-jdk, junit4, libcommons-dbcp-java, libjaxb-api-java, libjgrapht0.8-java, libjgrapht0.8-java-doc, libmaven-javadoc-plugin-java, libxerces2-java dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19288 files and directories currently installed.) +(Reading database ... 17881 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -478,10 +510,10 @@ Get: 266 http://deb.debian.org/debian bookworm/main armhf maven all 3.8.7-1 [18.9 kB] Get: 267 http://deb.debian.org/debian bookworm/main armhf maven-repo-helper all 1.11 [142 kB] Get: 268 http://deb.debian.org/debian bookworm/main armhf maven-debian-helper all 2.6.3 [108 kB] -Fetched 243 MB in 13s (18.7 MB/s) +Fetched 243 MB in 10s (25.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sgml-base. -(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 ... 19288 files and directories currently installed.) +(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 ... 17881 files and directories currently installed.) Preparing to unpack .../000-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:armhf. @@ -1753,7 +1785,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava-live-1.9.5+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 > ../biojava-live_1.9.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/8850/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/8850/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava-live-1.9.5+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 > ../biojava-live_1.9.5+dfsg-3_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.9.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -2378,8 +2414,8 @@ [INFO] Compiling 56 source files to /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: Recompile with -Xlint:deprecation for details. -[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/HSPSummaryHelper.java: Some input files use unchecked or unsafe operations. -[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/HSPSummaryHelper.java: Recompile with -Xlint:unchecked for details. +[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations. +[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ blast --- [INFO] Copying 22 resources @@ -2664,8 +2700,8 @@ [INFO] Compiling 56 source files to /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/target/classes [INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java uses or overrides a deprecated API. [INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java: Recompile with -Xlint:deprecation for details. -[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/HSPSummaryHelper.java: Some input files use unchecked or unsafe operations. -[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/HSPSummaryHelper.java: Recompile with -Xlint:unchecked for details. +[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Some input files use unchecked or unsafe operations. +[INFO] /build/reproducible-path/biojava-live-1.9.5+dfsg/blast/src/main/java/org/biojava/bio/program/sax/blastxml/StAXFeatureHandler.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [INFO] Forking sequencing 1.9.5 @@ -3024,20 +3060,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [02:31 min] -[INFO] bytecode ........................................... SUCCESS [ 22.594 s] -[INFO] core ............................................... SUCCESS [02:27 min] -[INFO] alignment .......................................... SUCCESS [ 12.679 s] -[INFO] biosql ............................................. SUCCESS [ 16.315 s] -[INFO] blast .............................................. SUCCESS [ 20.114 s] -[INFO] sequencing ......................................... SUCCESS [ 28.181 s] -[INFO] gui ................................................ SUCCESS [ 42.255 s] -[INFO] phylo .............................................. SUCCESS [ 22.887 s] +[INFO] biojava-legacy ..................................... SUCCESS [03:34 min] +[INFO] bytecode ........................................... SUCCESS [ 44.956 s] +[INFO] core ............................................... SUCCESS [03:35 min] +[INFO] alignment .......................................... SUCCESS [ 25.278 s] +[INFO] biosql ............................................. SUCCESS [ 30.825 s] +[INFO] blast .............................................. SUCCESS [ 28.520 s] +[INFO] sequencing ......................................... SUCCESS [ 36.735 s] +[INFO] gui ................................................ SUCCESS [ 47.841 s] +[INFO] phylo .............................................. SUCCESS [ 28.492 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 07:48 min -[INFO] Finished at: 2024-01-06T04:42:23-12:00 +[INFO] Total time: 11:21 min +[INFO] Finished at: 2024-01-06T17:13:35Z [INFO] ------------------------------------------------------------------------  dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava-live-1.9.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava-live-1.9.5\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava-live-1.9.5\+dfsg/debian/maven-repo --batch-mode test @@ -3100,51 +3136,490 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojavax.SimpleRankedCrossRefTest +[INFO] Running org.biojava.utils.ListToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.utils.ListToolsTest +[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest +[INFO] Running org.biojava.utils.RepeatedCharSequenceTest +JAM +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.utils.RepeatedCharSequenceTest +[INFO] Running org.biojava.utils.regex.RegexTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.239 s - in org.biojava.utils.regex.RegexTest +[INFO] Running org.biojava.utils.regex.PatternCheckerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.regex.PatternCheckerTest +[INFO] Running org.biojava.utils.walker.WalkerFactoryTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.utils.walker.WalkerFactoryTest +[INFO] Running org.biojava.utils.walker.WalkerTest +Increasing counter: Overlaps([20,50]) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) +Increasing counter: Overlaps([20,50]) +Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) +Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) +Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +OverlapsLocation: Overlaps([20,50]) +Feature: ByClass(org.biojava.bio.seq.StrandedFeature) +Feature: ByClass(org.biojava.bio.seq.ComponentFeature) +Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) +Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.utils.walker.WalkerTest +[INFO] Running org.biojava.utils.process.AllTests +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 s - in org.biojava.utils.process.AllTests +[INFO] Running org.biojava.utils.process.ExternalProcessTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s - in org.biojava.utils.process.ExternalProcessTest +[INFO] Running org.biojava.utils.SmallMapTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.utils.SmallMapTest +[INFO] Running org.biojava.utils.automata.NfaTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.utils.automata.NfaTest +[INFO] Running org.biojava.bio.AnnotationTypeTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.bio.AnnotationTypeTest +[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.362 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest +[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.bio.molbio.RestrictionEnzymeTest +[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.197 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest +[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.372 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest +[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest +idb length: 79 +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.176 s - in org.biojava.bio.seq.io.SeqIOToolsTest +[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.168 s - in org.biojava.bio.seq.io.LocationFormatterTest +[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.386 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest +[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest +[INFO] Running org.biojava.bio.seq.FeatureFilterTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.FeatureFilterTest +[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest +[INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest +template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.bio.seq.impl.ViewSequenceTest +[INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.impl.GappedSequenceTest +[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.bio.seq.impl.SubSequenceTest +[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.844 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest +[INFO] Running org.biojava.bio.seq.DNAToolsTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojava.bio.seq.DNAToolsTest +[INFO] Running org.biojava.bio.seq.CircularSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.CircularSequenceTest +[INFO] Running org.biojava.bio.seq.FilterUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.bio.seq.FilterUtilsTest +[INFO] Running org.biojava.bio.seq.SeqSerializationTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 s - in org.biojava.bio.seq.SeqSerializationTest +[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.seq.MergeFeatureHolderTest +[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest +[INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.bio.seq.db.TestHashSequenceDB +[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.seq.db.HashSequenceDBTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest +[INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest +[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest +[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest +[INFO] Running org.biojava.bio.seq.ProteinToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.seq.ProteinToolsTest +[INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.seq.FeatureHolderUtilsTest +[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.bio.seq.SimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.NewSimpleAssemblyTest +[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 s - in org.biojava.bio.seq.filter.FilterTransformerTest +[INFO] Running org.biojava.bio.seq.RNAToolsTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.bio.seq.RNAToolsTest +[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest +org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN + at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) + at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) + at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) + at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojava.bio.proteomics.aaindex.AAindexTest +[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.287 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest +[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +java.lang.NullPointerException: name is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +org.biojava.bio.seq.db.IllegalIDException: No table found with name test. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +java.lang.NullPointerException: table is null. + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) + at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at junit.framework.TestCase.runTest(TestCase.java:177) + at junit.framework.TestCase.runBare(TestCase.java:142) + at junit.framework.TestResult$1.protect(TestResult.java:122) + at junit.framework.TestResult.runProtected(TestResult.java:142) + at junit.framework.TestResult.run(TestResult.java:125) + at junit.framework.TestCase.run(TestCase.java:130) + at junit.framework.TestSuite.runTest(TestSuite.java:241) + at junit.framework.TestSuite.run(TestSuite.java:236) + at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) + at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) + at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) + at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) + at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) + at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) + at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) + at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest +[INFO] Running org.biojava.bio.proteomics.MassCalcTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.proteomics.MassCalcTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest +[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.search.MaxMismatchPatternTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest +[INFO] Running org.biojava.bio.search.SeqContentPatternTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SeqContentPatternTest +[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest +[INFO] Running org.biojava.bio.dp.EmissionStateEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.bio.dp.EmissionStateEventTest +[INFO] Running org.biojava.bio.dp.MarkovModelEventTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.bio.dp.MarkovModelEventTest +[INFO] Running org.biojava.bio.dp.DPSerializationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.327 s - in org.biojava.bio.dp.DPSerializationTest +[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.dist.TranslatedDistributionTest +[INFO] Running org.biojava.bio.dist.DistributionTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.dist.DistributionTest +[INFO] Running org.biojava.bio.dist.DistributionToolsTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.bio.dist.DistributionToolsTest +[INFO] Running org.biojava.bio.dist.DistSerTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 s - in org.biojava.bio.dist.DistSerTest +[INFO] Running org.biojava.bio.MergeAnnotationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.MergeAnnotationTest +[INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 s - in org.biojava.bio.program.indexdb.IndexToolsTest +[INFO] Running org.biojava.bio.program.phred.PhredToolsTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.biojava.bio.program.phred.PhredToolsTest +[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest +[INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 s - in org.biojava.bio.symbol.CodonPrefToolsTest +[INFO] Running org.biojava.bio.symbol.PointLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.symbol.PointLocationTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.symbol.SimpleSymbolListTest +[INFO] Running org.biojava.bio.symbol.NameTokenizationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.NameTokenizationTest +[INFO] Running org.biojava.bio.symbol.MergeLocationTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.MergeLocationTest +[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.bio.symbol.AlphabetManagerTest +[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.bio.symbol.AlphabetSerializationTest +[INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet +[INFO] Running org.biojava.bio.symbol.MotifToolsTest +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.bio.symbol.MotifToolsTest +[INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.DoubleAlphabetTest +[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest +[INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest +symbolForIndex +getAlphabet +indexForSymbol +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest +[INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.512 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest +[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.SimpleSymbolEventTest +[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.SymbolSerializationTest +[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.IntegerAlphabetTest +[INFO] Running org.biojava.bio.symbol.TranslationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.TranslationTest +[INFO] Running org.biojava.bio.symbol.RangeLocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest +[INFO] Running org.biojava.bio.symbol.CircularLocationTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.CircularLocationTest +[INFO] Running org.biojava.bio.symbol.BetweenLocationTest +[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.bio.symbol.BetweenLocationTest +[INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CrossProductTokenizationTest +[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest +[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.GappedSymbolListTest +[INFO] Running org.biojava.bio.symbol.SymbolListTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.818 s - in org.biojava.bio.symbol.SymbolListTest +[INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest +Adding symbol list taccaccagga$ +Adding symbol list taccaccagga$ +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest +[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.bio.symbol.SimpleCodonPrefTest +[INFO] Running org.biojava.bio.symbol.CompoundLocationTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.bio.symbol.CompoundLocationTest +[INFO] Running org.biojava.directory.SystemRegistryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.directory.SystemRegistryTest +[INFO] Running org.biojava.directory.RegistryConfigurationTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.RegistryConfigurationTest +[INFO] Running org.biojava.directory.OBDARegistryParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.OBDARegistryParserTest +[INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest +Reached + Attributes: No attributes +Binding: urn -> org.biojava.naming.ObdaContext@92c3b6 +Reached urn + Attributes: No attributes +Binding: open-bio.org -> org.biojava.naming.ObdaContext@f4cbe1 +Reached urn:open-bio.org + Attributes: {description=description: +This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed +by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the +module obda-specs in the cvs repository located at +pub.open-bio.org:/home/repository/obf-common. + } +Binding: type -> org.biojava.naming.ObdaContext@1aac4a7 +Reached urn:open-bio.org:type + Attributes: {description=description: +The namespace for URNs that identify data types. It is expected that the types +that are given IDs will be very general in nature, such as Sequence and +File Format. All types are of type urn:open-bio.org:type:type. Any URN in the +type namespace that is not of this type is not conforming to the OBDA +specification for this namespace. + } +Binding: type -> org.biojava.naming.ObdaContext@1ad2d17 +Reached urn:open-bio.org:type:type + Attributes: {description=description: +The OBDA URN that identifies the concept of 'type'. In a given language, this +may map to the types of data structures, or objects. Alternativel, it may +map to a particular set of keys being present in a map, or a term in an +ontology. This is not important. The important thing is that we have unique +identifiers for common types that all projects use and interact with. + } +Binding: format -> org.biojava.naming.ObdaContext@1ce4140 +Reached urn:open-bio.org:type:format + Attributes: {description=description: +A file format. Many file formats are used in bioinformatics. Entities of this +type identify a format. The format can be used to choose how to treat a file. +The format is not expected to be resolvable to a formal deffinition of the +file structure using OBDA-supplied functionality. Different applications may +chose to process a stream with the same format URN in different ways. This +type of URN is purely there to identify the format of the stream, not the +manner in which it should be processed. + } +Binding: alphabet -> org.biojava.naming.ObdaContext@1f0c5e7 +Reached urn:open-bio.org:type:alphabet + Attributes: {description=description: +A biological sequence alphabet. Biological sequences are often represented as +strings of characters. However, in differnt circumstances, the same characters +can represent different things. For example, in DNA, the 't' character +represents tyrosine. In Protein, this same character represents tryptophan. + +Associating alphabets with these sequences disambiguates their interpretation. +Alphabets do not define a mapping to or from strings, but should be used +wherever the type of the content of a sequence needs to be stated. + } +Binding: format -> org.biojava.naming.ObdaContext@82b202 +Reached urn:open-bio.org:format + Attributes: {description=description: +A namespace for OBDA URNs that define formats. All URNs within this namespace +must be of the type urn:open-bio.org:type:format. Any URN in this namespace that +is not of that type is not a valid OBDA URN. + } +Binding: enzyme -> org.biojava.naming.ObdaContext@df990 +Reached urn:open-bio.org:format:enzyme + Attributes: {description=description: +The Enzyme database entry format. The enzyme database can be downloaded from +the ebi at: + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ + +For an example of a file in this format, see: + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat + +The format is described more fully in + + ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt + } +Binding: genbank -> org.biojava.naming.ObdaContext@1506ed0 +Reached urn:open-bio.org:format:genbank + Attributes: {description=description: +The GENBANK file format associated with the GENBANK sequence database. + } +Binding: swissprot -> org.biojava.naming.ObdaContext@2c4da0 +Reached urn:open-bio.org:format:swissprot + Attributes: {description=description: +The SWISSPROT file format as used in the SWISSPROT sequence database. + } +Binding: embl -> org.biojava.naming.ObdaContext@1f3e805 +Reached urn:open-bio.org:format:embl + Attributes: {description=description: +The EMBL file format associated with entries in the EMBL sequence database. + } +Binding: alphabet -> org.biojava.naming.ObdaContext@cf5c52 +Reached urn:open-bio.org:alphabet + Attributes: {description=description: +A namespace within which to store alphabet identifiers. Alphabets should +represent URNs that represent objects of the type identified by +urn:open-bio.org:type:alphabet, and any useage outside of this is not supported. + } +Binding: rna -> org.biojava.naming.ObdaContext@618775 +Reached urn:open-bio.org:alphabet:rna + Attributes: {description=description: +The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry +or genetics introductory textbook to find out more. Commonly, the nucleotides +are reprsented by the four letters a, g, c and u. However, this is not a +formal requirement for a resource to declare this alphabet as its type. + } +Binding: protein -> org.biojava.naming.ObdaContext@ea8994 +Reached urn:open-bio.org:alphabet:protein + Attributes: {description=description: +The protein alphabet. Proteins are composed from amino-acids. To find out more, +read a biochemistry or genetics text book. It is common for protein sequences +to be represented by characters, but this is not a formal requirement for +a resource to publish an alphabet equal to this identifier. + } +Binding: dna -> org.biojava.naming.ObdaContext@a3e10c +Reached urn:open-bio.org:alphabet:dna + Attributes: {description=description: +The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry +or genetics introductory textbook to find out more. Commonly, the nucleotides +are reprsented by the four letters a, g, c and t. However, this is not a +formal requirement for a resource to declare this alphabet as its type. + } +lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@99e2cb} +My component is urn:open-bio.org:format:embl +lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@1559c74} +My component is open-bio.org:format:embl +lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@1917fe1, format=org.biojava.naming.ObdaContext@f56e2, alphabet=org.biojava.naming.ObdaContext@17349fb} +My component is format:embl +lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@66cf5d, genbank=org.biojava.naming.ObdaContext@60ce47, swissprot=org.biojava.naming.ObdaContext@50256f, embl=org.biojava.naming.ObdaContext@1918c8f} +My component is embl +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.naming.ObdaInitialContextFactoryTest +[INFO] Running org.biojava.naming.ObdaUriParserTest + +urn:obda.org:format:embl/ac +:trail +oneName +lead: +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.naming.ObdaUriParserTest +[INFO] Running org.biojava.ontology.TripleImplTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.ontology.TripleImplTest +[INFO] Running org.biojava.ontology.ParseOBOFileTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.142 s - in org.biojava.ontology.ParseOBOFileTest +[INFO] Running org.biojava.ontology.OntologyTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.ontology.OntologyTest +[INFO] Running org.biojava.ontology.TermImplTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.ontology.TermImplTest +[INFO] Running org.biojavax.SimpleDocRefTest +testGetTitle testToString -testGetCrossRef +testGetLocation +testSetCrossref +testGetCrossref testCompareTo -testGetRank +testGetAuthors +testGetAuthorList testHashCode +testSetRemark testEquals -testSetRank -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.186 s - in org.biojavax.SimpleRankedCrossRefTest -[INFO] Running org.biojavax.SimpleRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testToString -testGetNote -testSetNoteSet -testContains -testGetPropertys -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testRemoveProperty2 -testContainsProperty -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojavax.SimpleRichAnnotationTest -[INFO] Running org.biojavax.ga.impl.SimplePopulationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.879 s - in org.biojavax.ga.impl.SimplePopulationTest -[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.ga.impl.SimpleOrganismTest -[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest -[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest -[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest -[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest -[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojavax.ga.functions.ProportionalSelectionTest -[INFO] Running org.biojavax.ga.util.WeightedSetTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojavax.ga.util.WeightedSetTest -[INFO] Running org.biojavax.ga.util.GAToolsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.util.GAToolsTest +testGetCRC +testGetRemark +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.SimpleDocRefTest [INFO] Running org.biojavax.SimpleNoteTest testGetValue testToString @@ -3156,44 +3631,7 @@ testSetRank testSetTerm testSetValue -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.SimpleNoteTest -[INFO] Running org.biojavax.DummyCrossReferenceResolverTest -testGetRemoteBioEntry -testGetRemoteSymbolList -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.DummyCrossReferenceResolverTest -[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest -[INFO] Running org.biojavax.SimpleCommentTest -testSetComment -testToString -testCompareTo -testGetRank -testHashCode -testGetComment -testEquals -testSetRank -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojavax.SimpleCommentTest -[INFO] Running org.biojavax.SimpleDocRefAuthorTest -testIsConsortium -testToString -testCompareTo -testGetName -testHashCode -testEquals -testGetExtendedName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojavax.SimpleDocRefAuthorTest -[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -testGetNameClass -testToString -testCompareTo -testSetNameClass -testGetName -testHashCode -testEquals -testSetName -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest -[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.736 s - in org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojavax.SimpleNoteTest [INFO] Running org.biojavax.bio.seq.io.GenbankLocationParserTest Location 467: 467 Location 340..565: 340..565 @@ -3213,32 +3651,34 @@ Location J00194:100..202: J00194:100..202 Location (8298.8300)..10206: (8298.8300)..10206 Location join((8298.8300)..10206,1..855): join((8298.8300)..10206,1..855) -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest -[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojavax.bio.seq.io.GenbankLocationParserTest [INFO] Running org.biojavax.bio.seq.io.UniProtFormatTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojavax.bio.seq.io.UniProtFormatTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 s - in org.biojavax.bio.seq.io.UniProtFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2249_2248Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojavax.bio.seq.io.Bug2249_2248Test +[INFO] Running org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 s - in org.biojavax.bio.seq.io.INSDseqFormatTest +[INFO] Running org.biojavax.bio.seq.io.Bug2255Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in org.biojavax.bio.seq.io.Bug2255Test [INFO] Running org.biojavax.bio.seq.io.EMBLFormatTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojavax.bio.seq.io.EMBLFormatTest +[INFO] Running org.biojavax.bio.seq.io.GenbankFormatTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.815 s - in org.biojavax.bio.seq.io.GenbankFormatTest [INFO] Running org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.647 s - in org.biojavax.bio.seq.io.Bug2250_2256Test -[INFO] Running org.biojavax.bio.seq.io.Bug2255Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojavax.bio.seq.io.Bug2255Test -[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.906 s - in org.biojavax.bio.seq.io.Bug2250_2256Test [INFO] Running org.biojavax.bio.seq.SimpleRichLocationTest testEquals [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichLocationTest -[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest -testEquals -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.seq.RichLocationToolsTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.RichLocationToolsTest [INFO] Running org.biojavax.bio.seq.CompoundRichLocationTest testEquals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.CompoundRichLocationTest +[INFO] Running org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.bio.seq.SimpleRichFeatureTest +[INFO] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest +testEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest [INFO] Running org.biojavax.bio.SimpleBioEntryTest testGetNamespace testGetNoteSet @@ -3272,22 +3712,28 @@ testGetDivision testSetTaxon testAddComment -[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s - in org.biojavax.bio.SimpleBioEntryTest -[INFO] Running org.biojavax.SimpleDocRefTest -testGetTitle +[INFO] Tests run: 32, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojavax.bio.SimpleBioEntryTest +[INFO] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +testGetNameClass testToString -testGetLocation -testSetCrossref -testGetCrossref testCompareTo -testGetAuthors -testGetAuthorList +testSetNameClass +testGetName testHashCode -testSetRemark testEquals -testGetCRC -testGetRemark -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojavax.SimpleDocRefTest +testSetName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.bio.taxa.SimpleNCBITaxonNameTest +[INFO] Running org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.CrossReferenceResolutionExceptionTest +[INFO] Running org.biojavax.SimpleDocRefAuthorTest +testIsConsortium +testToString +testCompareTo +testGetName +testHashCode +testEquals +testGetExtendedName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojavax.SimpleDocRefAuthorTest [INFO] Running org.biojavax.SimpleRankedDocRefTest testGetStart testSetLocation @@ -3299,7 +3745,131 @@ testEquals testGetEnd testSetRank -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojavax.SimpleRankedDocRefTest +[INFO] Running org.biojavax.SimpleRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testToString +testGetNote +testSetNoteSet +testContains +testGetPropertys +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testRemoveProperty2 +testContainsProperty +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojavax.SimpleRichAnnotationTest +[INFO] Running org.biojavax.SimpleRankedCrossRefTest +testToString +testGetCrossRef +testCompareTo +testGetRank +testHashCode +testEquals +testSetRank +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.SimpleRankedCrossRefTest +[INFO] Running org.biojavax.SimpleNamespaceTest +testGetAuthority +testSetDescription +testToString +testGetAcronym +testCompareTo +testGetName +testSetAuthority +testGetDescription +testHashCode +testSetAcronym +testEquals +testGetURI +testSetURI +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojavax.SimpleNamespaceTest +[INFO] Running org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.functions.SimpleMutationFunctionTest +[INFO] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojavax.ga.functions.SimpleCrossOverFunctionTest +[INFO] Running org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojavax.ga.functions.ProportionalSelectionTest +[INFO] Running org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.AbstractMutationFunctionTest +[INFO] Running org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.functions.AbstractCrossOverFunctionTest +[INFO] Running org.biojavax.ga.impl.SimplePopulationTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimplePopulationTest +[INFO] Running org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.impl.SimpleOrganismTest +[INFO] Running org.biojavax.ga.util.GAToolsTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.ga.util.GAToolsTest +[INFO] Running org.biojavax.ga.util.WeightedSetTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojavax.ga.util.WeightedSetTest +[INFO] Running org.biojavax.SimpleCrossRefTest +testGetNoteSet +testGetAccession +testToString +testCompareTo +testGetAnnotation +testSetNoteSet +testGetVersion +testHashCode +testGetDbname +testEquals +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojavax.SimpleCrossRefTest +[INFO] Running org.biojavax.SimpleCommentTest +testSetComment +testToString +testCompareTo +testGetRank +testHashCode +testGetComment +testEquals +testSetRank +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojavax.SimpleCommentTest +[INFO] Running org.biojavax.EmptyRichAnnotationTest +testGetNoteSet +testAddNote +testAsMap +testClear +testKeys +testGetNote +testSetNoteSet +testContains +testSetProperty +testRemoveNote +testGetProperty +testRemoveProperty +testEquals +testContainsProperty +[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojavax.EmptyRichAnnotationTest +[INFO] Running org.biojavax.DummyCrossReferenceResolverTest +testGetRemoteBioEntry +testGetRemoteSymbolList +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojavax.DummyCrossReferenceResolverTest +[INFO] Running org.biojavax.ontology.SimpleComparableTermTest +testSetDescription +testGetRankedCrossRefs +testToString +testGetSynonyms +testCompareTo +testAddSynonym +testGetName +testGetOntology +testSetRankedCrossRefs +testGetIdentifier +testGetAnnotation +testRemoveRankedCrossRef +testGetDescription +testSetIdentifier +testHashCode +testEquals +testAddRankedCrossRef +testRemoveSynonym +testSetObsolete +testGetObsolete +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 s - in org.biojavax.ontology.SimpleComparableTermTest [INFO] Running org.biojavax.ontology.SimpleComparableTripleTest testGetSubject testSetDescriptors @@ -3319,7 +3889,7 @@ testEquals testGetObject testRemoveSynonym -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.biojavax.ontology.SimpleComparableTripleTest +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojavax.ontology.SimpleComparableTripleTest [INFO] Running org.biojavax.ontology.SimpleComparableOntologyTest testSetTripleSet testCreateTriple @@ -3345,541 +3915,7 @@ testEquals testGetOps testImportTerm -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojavax.ontology.SimpleComparableOntologyTest -[INFO] Running org.biojavax.ontology.SimpleComparableTermTest -testSetDescription -testGetRankedCrossRefs -testToString -testGetSynonyms -testCompareTo -testAddSynonym -testGetName -testGetOntology -testSetRankedCrossRefs -testGetIdentifier -testGetAnnotation -testRemoveRankedCrossRef -testGetDescription -testSetIdentifier -testHashCode -testEquals -testAddRankedCrossRef -testRemoveSynonym -testSetObsolete -testGetObsolete -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojavax.ontology.SimpleComparableTermTest -[INFO] Running org.biojavax.SimpleNamespaceTest -testGetAuthority -testSetDescription -testToString -testGetAcronym -testCompareTo -testGetName -testSetAuthority -testGetDescription -testHashCode -testSetAcronym -testEquals -testGetURI -testSetURI -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.biojavax.SimpleNamespaceTest -[INFO] Running org.biojavax.EmptyRichAnnotationTest -testGetNoteSet -testAddNote -testAsMap -testClear -testKeys -testGetNote -testSetNoteSet -testContains -testSetProperty -testRemoveNote -testGetProperty -testRemoveProperty -testEquals -testContainsProperty -[INFO] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.EmptyRichAnnotationTest -[INFO] Running org.biojavax.SimpleCrossRefTest -testGetNoteSet -testGetAccession -testToString -testCompareTo -testGetAnnotation -testSetNoteSet -testGetVersion -testHashCode -testGetDbname -testEquals -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojavax.SimpleCrossRefTest -[INFO] Running org.biojava.naming.ObdaUriParserTest - -urn:obda.org:format:embl/ac -:trail -oneName -lead: -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.naming.ObdaUriParserTest -[INFO] Running org.biojava.naming.ObdaInitialContextFactoryTest -Reached - Attributes: No attributes -Binding: urn -> org.biojava.naming.ObdaContext@1175e74 -Reached urn - Attributes: No attributes -Binding: open-bio.org -> org.biojava.naming.ObdaContext@1b58ca3 -Reached urn:open-bio.org - Attributes: {description=description: -This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed -by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the -module obda-specs in the cvs repository located at -pub.open-bio.org:/home/repository/obf-common. - } -Binding: type -> org.biojava.naming.ObdaContext@52a00 -Reached urn:open-bio.org:type - Attributes: {description=description: -The namespace for URNs that identify data types. It is expected that the types -that are given IDs will be very general in nature, such as Sequence and -File Format. All types are of type urn:open-bio.org:type:type. Any URN in the -type namespace that is not of this type is not conforming to the OBDA -specification for this namespace. - } -Binding: type -> org.biojava.naming.ObdaContext@1826d77 -Reached urn:open-bio.org:type:type - Attributes: {description=description: -The OBDA URN that identifies the concept of 'type'. In a given language, this -may map to the types of data structures, or objects. Alternativel, it may -map to a particular set of keys being present in a map, or a term in an -ontology. This is not important. The important thing is that we have unique -identifiers for common types that all projects use and interact with. - } -Binding: format -> org.biojava.naming.ObdaContext@1009542 -Reached urn:open-bio.org:type:format - Attributes: {description=description: -A file format. Many file formats are used in bioinformatics. Entities of this -type identify a format. The format can be used to choose how to treat a file. -The format is not expected to be resolvable to a formal deffinition of the -file structure using OBDA-supplied functionality. Different applications may -chose to process a stream with the same format URN in different ways. This -type of URN is purely there to identify the format of the stream, not the -manner in which it should be processed. - } -Binding: alphabet -> org.biojava.naming.ObdaContext@1e9807f -Reached urn:open-bio.org:type:alphabet - Attributes: {description=description: -A biological sequence alphabet. Biological sequences are often represented as -strings of characters. However, in differnt circumstances, the same characters -can represent different things. For example, in DNA, the 't' character -represents tyrosine. In Protein, this same character represents tryptophan. - -Associating alphabets with these sequences disambiguates their interpretation. -Alphabets do not define a mapping to or from strings, but should be used -wherever the type of the content of a sequence needs to be stated. - } -Binding: format -> org.biojava.naming.ObdaContext@8ff1a8 -Reached urn:open-bio.org:format - Attributes: {description=description: -A namespace for OBDA URNs that define formats. All URNs within this namespace -must be of the type urn:open-bio.org:type:format. Any URN in this namespace that -is not of that type is not a valid OBDA URN. - } -Binding: enzyme -> org.biojava.naming.ObdaContext@38c59b -Reached urn:open-bio.org:format:enzyme - Attributes: {description=description: -The Enzyme database entry format. The enzyme database can be downloaded from -the ebi at: - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/ - -For an example of a file in this format, see: - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat - -The format is described more fully in - - ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt - } -Binding: genbank -> org.biojava.naming.ObdaContext@177e91b -Reached urn:open-bio.org:format:genbank - Attributes: {description=description: -The GENBANK file format associated with the GENBANK sequence database. - } -Binding: swissprot -> org.biojava.naming.ObdaContext@a664f2 -Reached urn:open-bio.org:format:swissprot - Attributes: {description=description: -The SWISSPROT file format as used in the SWISSPROT sequence database. - } -Binding: embl -> org.biojava.naming.ObdaContext@19fcf7f -Reached urn:open-bio.org:format:embl - Attributes: {description=description: -The EMBL file format associated with entries in the EMBL sequence database. - } -Binding: alphabet -> org.biojava.naming.ObdaContext@157d90a -Reached urn:open-bio.org:alphabet - Attributes: {description=description: -A namespace within which to store alphabet identifiers. Alphabets should -represent URNs that represent objects of the type identified by -urn:open-bio.org:type:alphabet, and any useage outside of this is not supported. - } -Binding: rna -> org.biojava.naming.ObdaContext@128d34a -Reached urn:open-bio.org:alphabet:rna - Attributes: {description=description: -The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry -or genetics introductory textbook to find out more. Commonly, the nucleotides -are reprsented by the four letters a, g, c and u. However, this is not a -formal requirement for a resource to declare this alphabet as its type. - } -Binding: protein -> org.biojava.naming.ObdaContext@5eaa29 -Reached urn:open-bio.org:alphabet:protein - Attributes: {description=description: -The protein alphabet. Proteins are composed from amino-acids. To find out more, -read a biochemistry or genetics text book. It is common for protein sequences -to be represented by characters, but this is not a formal requirement for -a resource to publish an alphabet equal to this identifier. - } -Binding: dna -> org.biojava.naming.ObdaContext@1bb6bea -Reached urn:open-bio.org:alphabet:dna - Attributes: {description=description: -The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry -or genetics introductory textbook to find out more. Commonly, the nucleotides -are reprsented by the four letters a, g, c and t. However, this is not a -formal requirement for a resource to declare this alphabet as its type. - } -lookup: 'urn:open-bio.org:format:embl' for {urn=org.biojava.naming.ObdaContext@67a738} -My component is urn:open-bio.org:format:embl -lookup: 'open-bio.org:format:embl' for {open-bio.org=org.biojava.naming.ObdaContext@17632c9} -My component is open-bio.org:format:embl -lookup: 'format:embl' for {type=org.biojava.naming.ObdaContext@e12bac, format=org.biojava.naming.ObdaContext@1040f2f, alphabet=org.biojava.naming.ObdaContext@c87930} -My component is format:embl -lookup: 'embl' for {enzyme=org.biojava.naming.ObdaContext@cff1a, genbank=org.biojava.naming.ObdaContext@15710fc, swissprot=org.biojava.naming.ObdaContext@5f1e4e, embl=org.biojava.naming.ObdaContext@1f9eccc} -My component is embl -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.182 s - in org.biojava.naming.ObdaInitialContextFactoryTest -[INFO] Running org.biojava.bio.proteomics.MassCalcTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.proteomics.MassCalcTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.867 s - in org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest -[INFO] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -java.lang.NullPointerException: name is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:172) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:126) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -org.biojava.bio.seq.db.IllegalIDException: No table found with name test. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.table(SimpleSymbolPropertyTableDB.java:175) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testTable(SimpleSymbolPropertyTableDBTest.java:134) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -java.lang.NullPointerException: table is null. - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB.addTable(SimpleSymbolPropertyTableDB.java:145) - at org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest.testAddTable(SimpleSymbolPropertyTableDBTest.java:113) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest -[INFO] Running org.biojava.bio.proteomics.aaindex.AAindexTest -org.biojava.bio.symbol.IllegalSymbolException: Symbol adenine not found in alphabet PROTEIN - at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:327) - at org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper.validate(AlphabetManager.java:1601) - at org.biojava.bio.symbol.SimpleSymbolPropertyTable.getDoubleValue(SimpleSymbolPropertyTable.java:67) - at org.biojava.bio.proteomics.aaindex.AAindexTest.testDoubleValue(AAindexTest.java:189) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at junit.framework.TestCase.runTest(TestCase.java:177) - at junit.framework.TestCase.runBare(TestCase.java:142) - at junit.framework.TestResult$1.protect(TestResult.java:122) - at junit.framework.TestResult.runProtected(TestResult.java:142) - at junit.framework.TestResult.run(TestResult.java:125) - at junit.framework.TestCase.run(TestCase.java:130) - at junit.framework.TestSuite.runTest(TestSuite.java:241) - at junit.framework.TestSuite.run(TestSuite.java:236) - at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90) - at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:365) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:273) - at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238) - at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:159) - at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:384) - at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:345) - at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:126) - at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:418) -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.bio.proteomics.aaindex.AAindexTest -[INFO] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.proteomics.IsoelectricPointCalcTest -[INFO] Running org.biojava.bio.dp.MarkovModelEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in org.biojava.bio.dp.MarkovModelEventTest -[INFO] Running org.biojava.bio.dp.DPSerializationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojava.bio.dp.DPSerializationTest -[INFO] Running org.biojava.bio.dp.EmissionStateEventTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dp.EmissionStateEventTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojava.bio.molbio.RestrictionEnzymeTest -[INFO] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.bio.molbio.RestrictionEnzymeManagerTest -[INFO] Running org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.dist.TranslatedDistributionTest -[INFO] Running org.biojava.bio.dist.DistributionToolsTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.243 s - in org.biojava.bio.dist.DistributionToolsTest -[INFO] Running org.biojava.bio.dist.DistributionTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.dist.DistributionTest -[INFO] Running org.biojava.bio.dist.DistSerTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 s - in org.biojava.bio.dist.DistSerTest -[INFO] Running org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.bio.program.indexdb.IndexToolsTest -[INFO] Running org.biojava.bio.program.phred.PhredToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.bio.program.phred.PhredToolsTest -[INFO] Running org.biojava.bio.AnnotationTypeTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.AnnotationTypeTest -[INFO] Running org.biojava.bio.symbol.SymbolListTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.98 s - in org.biojava.bio.symbol.SymbolListTest -[INFO] Running org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 s - in org.biojava.bio.symbol.AlphabetSerializationTest -[INFO] Running org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.AlphabetManagerTest -[INFO] Running org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.symbol.SymbolSerializationTest -[INFO] Running org.biojava.bio.symbol.MotifToolsTest -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.biojava.bio.symbol.MotifToolsTest -[INFO] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.339 s - in org.biojava.bio.symbol.SimpleWobbleDistributionTest -[INFO] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.bio.symbol.SimpleAtomicSymbolEventTest -[INFO] Running org.biojava.bio.symbol.SimpleSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleSymbolEventTest -[INFO] Running org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.symbol.TestSoftMaskedAlphabet -[INFO] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.symbol.SimpleBasisSymbolEventTest -[INFO] Running org.biojava.bio.symbol.TranslationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.TranslationTest -[INFO] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.199 s - in org.biojava.bio.symbol.CrossProductAlphabetIndexTest -[INFO] Running org.biojava.bio.symbol.CircularLocationTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.CircularLocationTest -[INFO] Running org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IntegerAlphabetTest -[INFO] Running org.biojava.bio.symbol.SimpleSymbolListTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.SimpleSymbolListTest -[INFO] Running org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.IndexedNoAmbPackTest -[INFO] Running org.biojava.bio.symbol.LinearAlphabetIndexTest -symbolForIndex -getAlphabet -indexForSymbol -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.LinearAlphabetIndexTest -[INFO] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest -[INFO] Running org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.symbol.GappedSymbolListTest -[INFO] Running org.biojava.bio.symbol.BetweenLocationTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.symbol.BetweenLocationTest -[INFO] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest -Adding symbol list taccaccagga$ -Adding symbol list taccaccagga$ -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 s - in org.biojava.bio.symbol.UkkonenSuffixTreeTest -[INFO] Running org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.SimpleCodonPrefTest -[INFO] Running org.biojava.bio.symbol.PointLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.biojava.bio.symbol.PointLocationTest -[INFO] Running org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.DoubleAlphabetTest -[INFO] Running org.biojava.bio.symbol.RangeLocationTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.RangeLocationTest -[INFO] Running org.biojava.bio.symbol.CrossProductTokenizationTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.CrossProductTokenizationTest -[INFO] Running org.biojava.bio.symbol.NameTokenizationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.symbol.NameTokenizationTest -[INFO] Running org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.CodonPrefToolsTest -[INFO] Running org.biojava.bio.symbol.CompoundLocationTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.082 s - in org.biojava.bio.symbol.CompoundLocationTest -[INFO] Running org.biojava.bio.symbol.MergeLocationTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.symbol.MergeLocationTest -[INFO] Running org.biojava.bio.MergeAnnotationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.MergeAnnotationTest -[INFO] Running org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.bio.seq.impl.GappedSequenceTest -[INFO] Running org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.bio.seq.impl.SubSequenceTest -[INFO] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.bio.seq.impl.ViewSeqSerializationTest -[INFO] Running org.biojava.bio.seq.impl.ViewSequenceTest -template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -template: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -orignal: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -copy: class org.biojava.bio.seq.Feature$Template: location=[1,2] type=synth source=my head typeTerm=any sourceTerm=any annotation={geneID=braca1} -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.bio.seq.impl.ViewSequenceTest -[INFO] Running org.biojava.bio.seq.FeatureFilterTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.bio.seq.FeatureFilterTest -[INFO] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.972 s - in org.biojava.bio.seq.io.SmartSequenceBuilderTest -[INFO] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.biojava.bio.seq.io.SymbolListCharSequenceTest -[INFO] Running org.biojava.bio.seq.io.SeqIOToolsTest -idb length: 79 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.168 s - in org.biojava.bio.seq.io.SeqIOToolsTest -[INFO] Running org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.seq.io.LocationFormatterTest -[INFO] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.247 s - in org.biojava.bio.seq.io.filterxml.FilterXMLTest -[INFO] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.331 s - in org.biojava.bio.seq.io.MSFAlignmentFormatTest -[INFO] Running org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojava.bio.seq.FeatureHolderUtilsTest -[INFO] Running org.biojava.bio.seq.DNAToolsTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.seq.DNAToolsTest -[INFO] Running org.biojava.bio.seq.SeqSerializationTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.bio.seq.SeqSerializationTest -[INFO] Running org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.32 s - in org.biojava.bio.seq.MergeFeatureHolderTest -[INFO] Running org.biojava.bio.seq.ProteinToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.ProteinToolsTest -[INFO] Running org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.bio.seq.db.TestHashSequenceDB -[INFO] Running org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.db.HashSequenceDBTest -[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest -[INFO] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 s - in org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest -[INFO] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest -[INFO] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.384 s - in org.biojava.bio.seq.db.EmblCDROMIndexStoreTest -[INFO] Running org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.seq.SimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.seq.NewSimpleAssemblyTest -[INFO] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.125 s - in org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest -[INFO] Running org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.265 s - in org.biojava.bio.seq.filter.FilterTransformerTest -[INFO] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.bio.seq.project.ProjectedFeatureHolderTest -[INFO] Running org.biojava.bio.seq.RNAToolsTest -[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.454 s - in org.biojava.bio.seq.RNAToolsTest -[INFO] Running org.biojava.bio.seq.FilterUtilsTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.bio.seq.FilterUtilsTest -[INFO] Running org.biojava.bio.seq.CircularSequenceTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.bio.seq.CircularSequenceTest -[INFO] Running org.biojava.bio.search.SeqContentPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.biojava.bio.search.SeqContentPatternTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest -[INFO] Running org.biojava.bio.search.MaxMismatchPatternTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.MaxMismatchPatternTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest -[INFO] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest -[INFO] Running org.biojava.directory.SystemRegistryTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.496 s - in org.biojava.directory.SystemRegistryTest -[INFO] Running org.biojava.directory.RegistryConfigurationTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.directory.RegistryConfigurationTest -[INFO] Running org.biojava.directory.OBDARegistryParserTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.biojava.directory.OBDARegistryParserTest -[INFO] Running org.biojava.ontology.TermImplTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TermImplTest -[INFO] Running org.biojava.ontology.TripleImplTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.ontology.TripleImplTest -[INFO] Running org.biojava.ontology.ParseOBOFileTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.64 s - in org.biojava.ontology.ParseOBOFileTest -[INFO] Running org.biojava.ontology.OntologyTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.biojava.ontology.OntologyTest -[INFO] Running org.biojava.utils.automata.NfaTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.automata.NfaTest -[INFO] Running org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.lsid.LifeScienceIdentifierTest -[INFO] Running org.biojava.utils.regex.RegexTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.regex.RegexTest -[INFO] Running org.biojava.utils.regex.PatternCheckerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.regex.PatternCheckerTest -[INFO] Running org.biojava.utils.SmallMapTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.utils.SmallMapTest -[INFO] Running org.biojava.utils.walker.WalkerFactoryTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.047 s - in org.biojava.utils.walker.WalkerFactoryTest -[INFO] Running org.biojava.utils.walker.WalkerTest -Increasing counter: Overlaps([20,50]) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: And(Overlaps([20,50]) , ByClass(org.biojava.bio.seq.StrandedFeature)) -Increasing counter: Overlaps([20,50]) -Increasing counter: ByClass(org.biojava.bio.seq.StrandedFeature) -Increasing counter: ByClass(org.biojava.bio.seq.ComponentFeature) -Increasing counter: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Increasing counter: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -OverlapsLocation: Overlaps([20,50]) -Feature: ByClass(org.biojava.bio.seq.StrandedFeature) -Feature: ByClass(org.biojava.bio.seq.ComponentFeature) -Feature: Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature)) -Feature: And(Overlaps([20,50]) , Or(ByClass(org.biojava.bio.seq.StrandedFeature) , ByClass(org.biojava.bio.seq.ComponentFeature))) -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.897 s - in org.biojava.utils.walker.WalkerTest -[INFO] Running org.biojava.utils.RepeatedCharSequenceTest -JAM -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.utils.RepeatedCharSequenceTest -[INFO] Running org.biojava.utils.process.ExternalProcessTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.utils.process.ExternalProcessTest -[INFO] Running org.biojava.utils.process.AllTests -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.utils.process.AllTests -[INFO] Running org.biojava.utils.ListToolsTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.utils.ListToolsTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.biojavax.ontology.SimpleComparableOntologyTest [INFO] [INFO] Results: [INFO] @@ -3907,12 +3943,12 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- +[INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest +[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.24 s - in org.biojava.bio.alignment.SubstitutionMatrixTest [INFO] Running org.biojava.bio.alignment.AlignmentPairTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.17 s - in org.biojava.bio.alignment.AlignmentPairTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.bio.alignment.AlignmentPairTest [INFO] Running org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.bio.alignment.FlexibleAlignmentTest -[INFO] Running org.biojava.bio.alignment.SubstitutionMatrixTest -[INFO] Tests run: 96, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.669 s - in org.biojava.bio.alignment.SubstitutionMatrixTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.bio.alignment.FlexibleAlignmentTest [INFO] [INFO] Results: [INFO] @@ -3942,7 +3978,7 @@ [INFO] ------------------------------------------------------- [INFO] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest No hsqldb driver found. -[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest +[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest [INFO] [INFO] Results: [INFO] @@ -3970,42 +4006,42 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.248 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.535 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.97 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.188 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest +[INFO] Running org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.064 s - in org.biojava.bio.program.sax.BlastTest [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.813 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.741 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.151 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.228 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.961 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.488 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.984 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 s - in org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.44 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.651 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.316 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.387 s - in org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 s - in org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.172 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.932 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.185 s - in org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.607 s - in org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test [INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.212 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test -[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.937 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test -[INFO] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.375 s - in org.biojava.bio.program.sax.blastxml.BlastXMLTest -[INFO] Running org.biojava.bio.program.sax.BlastTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.153 s - in org.biojava.bio.program.sax.BlastTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.46 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.26 s - in org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test +[INFO] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.292 s - in org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test [INFO] [INFO] Results: [INFO] @@ -4033,32 +4069,32 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.444 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.bio.program.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.biojava.bio.program.fastq.FastqTest -[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.932 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest -[INFO] Running org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.493 s - in org.biojava.bio.program.fastq.FastqToolsTest -[INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.252 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.952 s - in org.biojava.bio.program.scf.SCFTest [INFO] Running org.biojava.bio.program.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojava.bio.program.fastq.FastqVariantTest +[INFO] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.905 s - in org.biojava.bio.program.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest -[INFO] Running org.biojava.bio.program.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.bio.program.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.SangerFastqReaderTest -[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 s - in org.biojava.bio.program.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.bio.program.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.biojava.bio.program.fastq.FastqTest +[INFO] Running org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.biojava.bio.program.fastq.StreamingFastqParserTest +[INFO] Running org.biojava.bio.program.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.345 s - in org.biojava.bio.program.fastq.ConvertTest +[INFO] Running org.biojava.bio.program.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 s - in org.biojava.bio.program.fastq.SangerFastqWriterTest [INFO] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.bio.program.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.bio.program.fastq.FastqToolsTest +[INFO] Tests run: 38, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.428 s - in org.biojava.bio.program.fastq.FastqToolsTest [INFO] Running org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.bio.program.fastq.FastqBuilderTest -[INFO] Running org.biojava.bio.program.scf.SCFTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 s - in org.biojava.bio.program.scf.SCFTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.bio.program.fastq.FastqBuilderTest +[INFO] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 s - in org.biojava.bio.program.fastq.SolexaFastqReaderTest [INFO] [INFO] Results: [INFO] @@ -4106,7 +4142,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojavax.bio.phylo.io.nexus.TreesBlockTest -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.936 s - in org.biojavax.bio.phylo.io.nexus.TreesBlockTest [INFO] [INFO] Results: [INFO] @@ -4115,20 +4151,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 0.010 s] -[INFO] bytecode ........................................... SUCCESS [ 3.788 s] -[INFO] core ............................................... SUCCESS [01:12 min] -[INFO] alignment .......................................... SUCCESS [ 11.011 s] -[INFO] biosql ............................................. SUCCESS [ 11.583 s] -[INFO] blast .............................................. SUCCESS [ 30.346 s] -[INFO] sequencing ......................................... SUCCESS [ 12.359 s] -[INFO] gui ................................................ SUCCESS [ 0.305 s] -[INFO] phylo .............................................. SUCCESS [ 10.301 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 0.009 s] +[INFO] bytecode ........................................... SUCCESS [ 4.912 s] +[INFO] core ............................................... SUCCESS [ 53.187 s] +[INFO] alignment .......................................... SUCCESS [ 10.858 s] +[INFO] biosql ............................................. SUCCESS [ 10.624 s] +[INFO] blast .............................................. SUCCESS [01:00 min] +[INFO] sequencing ......................................... SUCCESS [ 10.720 s] +[INFO] gui ................................................ SUCCESS [ 0.356 s] +[INFO] phylo .............................................. SUCCESS [ 10.551 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:32 min -[INFO] Finished at: 2024-01-06T04:45:02-12:00 +[INFO] Total time: 02:42 min +[INFO] Finished at: 2024-01-06T17:16:28Z [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -4259,20 +4295,20 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava-legacy 1.9.5: [INFO] -[INFO] biojava-legacy ..................................... SUCCESS [ 1.443 s] -[INFO] bytecode ........................................... SUCCESS [ 0.155 s] -[INFO] core ............................................... SUCCESS [ 0.291 s] -[INFO] alignment .......................................... SUCCESS [ 0.126 s] -[INFO] biosql ............................................. SUCCESS [ 0.090 s] -[INFO] blast .............................................. SUCCESS [ 0.097 s] -[INFO] sequencing ......................................... SUCCESS [ 0.084 s] -[INFO] gui ................................................ SUCCESS [ 0.081 s] -[INFO] phylo .............................................. SUCCESS [ 0.076 s] +[INFO] biojava-legacy ..................................... SUCCESS [ 2.935 s] +[INFO] bytecode ........................................... SUCCESS [ 0.192 s] +[INFO] core ............................................... SUCCESS [ 0.196 s] +[INFO] alignment .......................................... SUCCESS [ 0.216 s] +[INFO] biosql ............................................. SUCCESS [ 0.124 s] +[INFO] blast .............................................. SUCCESS [ 0.162 s] +[INFO] sequencing ......................................... SUCCESS [ 0.209 s] +[INFO] gui ................................................ SUCCESS [ 0.181 s] +[INFO] phylo .............................................. SUCCESS [ 0.248 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 9.011 s -[INFO] Finished at: 2024-01-06T04:45:18-12:00 +[INFO] Total time: 6.227 s +[INFO] Finished at: 2024-01-06T17:16:46Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava1.9-java --javadoc --base-directory=/build/reproducible-path/biojava-live-1.9.5\+dfsg --non-explore Analysing pom.xml... @@ -4356,9 +4392,9 @@ dpkg-gencontrol: warning: package libbiojava-java-doc: substitution variable ${maven:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.5+dfsg-3_all.deb'. -dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.5+dfsg-3_all.deb'. dpkg-deb: building package 'libbiojava1.9-java' in '../libbiojava1.9-java_1.9.5+dfsg-3_all.deb'. +dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.9.5+dfsg-3_all.deb'. +dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.9.5+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../biojava-live_1.9.5+dfsg-3_armhf.buildinfo dpkg-genchanges --build=binary -O../biojava-live_1.9.5+dfsg-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4366,12 +4402,14 @@ 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/8850/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8850/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/14412 and its subdirectories -I: Current time: Sat Jan 6 04:55:37 -12 2024 -I: pbuilder-time-stamp: 1704560137 +I: removing directory /srv/workspace/pbuilder/8850 and its subdirectories +I: Current time: Sun Jan 7 07:25:57 +14 2024 +I: pbuilder-time-stamp: 1704561957