Diff of the two buildlogs: -- --- b1/build.log 2024-01-23 22:36:35.789604108 +0000 +++ b2/build.log 2024-01-23 23:23:41.063581606 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 24 16:15:08 -12 2025 -I: pbuilder-time-stamp: 1740456908 +I: Current time: Wed Jan 24 12:36:39 +14 2024 +I: pbuilder-time-stamp: 1706049399 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -41,51 +41,83 @@ dpkg-source: info: applying remove_tests_needing_junitx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/25528/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 23 22:36 /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/3141/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3141/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='acd136b92a65462499bcd7dae4c23fb4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='25528' - PS1='# ' - PS2='> ' + INVOCATION_ID=d01c76a4006f4bbab47b71844d560762 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3141 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.ilWGygNb/pbuilderrc_YPTv --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.ilWGygNb/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/pbuilderrc_diog --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.ilWGygNb/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash @@ -143,15 +175,15 @@ -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts + -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 23 22:36 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile + -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server @@ -171,7 +203,7 @@ -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/25528/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -664,7 +696,7 @@ Get: 395 http://deb.debian.org/debian bookworm/main i386 maven all 3.8.7-1 [18.9 kB] Get: 396 http://deb.debian.org/debian bookworm/main i386 maven-repo-helper all 1.11 [142 kB] Get: 397 http://deb.debian.org/debian bookworm/main i386 maven-debian-helper all 2.6.3 [108 kB] -Fetched 348 MB in 6s (56.5 MB/s) +Fetched 348 MB in 22s (15.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18156 files and directories currently installed.) @@ -2457,7 +2489,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/3141/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/3141/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -2472,8 +2508,8 @@ mh_unpatchpoms -plibbiojava6-java jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet dh_clean rm -rf target rm -rf biojava-*/target @@ -2481,15 +2517,15 @@ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print rm -rf biojava-forester rm -rf biojava-jcolorbrewer -make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet # Creating the directories for forester and jcolorbrewer, with symlinks. mkdir -p biojava-forester/src/main/java/ cp -a forester/org biojava-forester/src/main/java/ @@ -2500,11 +2536,11 @@ sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml dh_auto_configure mh_patchpoms -plibbiojava6-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo -make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet # Insert the correct JSON_SIMPLE_PACKAGE in the code. find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ @@ -2607,30 +2643,30 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. +[WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices... +[WARNING] Loading source files for package org.biojava.nbio.core.alignment... +[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... +[WARNING] Loading source files for package org.biojava.nbio.core.exceptions... +[WARNING] Loading source files for package org.biojava.nbio.core.search.io... +[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast... [WARNING] Loading source files for package org.biojava.nbio.core.util... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features... [WARNING] Loading source files for package org.biojava.nbio.core.sequence... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription... -[WARNING] Loading source files for package org.biojava.nbio.core.alignment... -[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices... -[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... -[WARNING] Loading source files for package org.biojava.nbio.core.exceptions... -[WARNING] Loading source files for package org.biojava.nbio.core.search.io... -[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast... -[WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -3196,220 +3232,220 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/serialized-form.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html... +[WARNING] Generating 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Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OneOfLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.GroupLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OrderLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.BondLocation.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html... -[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/ABITracerCompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-use.html... @@ -3484,50 +3520,50 @@ [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. 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[WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -4117,409 +4153,409 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/datastructures/class-use/IntMatrix.html... 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.Type.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html... +[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/DeleteableMsa.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/Chart.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/GapContribution.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/BasicSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/TestGSDI.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDII.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDI.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDIR.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIR.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/FastaParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/package-use.html... @@ -4612,12 +4648,12 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. +[WARNING] Loading source files for package demo... [WARNING] Loading source files for package org.biojava.nbio.phylo... [WARNING] Loading source files for package org.biojava.nbio.alignment... +[WARNING] Loading source files for package org.biojava.nbio.alignment.template... [WARNING] Loading source files for package org.biojava.nbio.alignment.io... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html... -[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html... +[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile +[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and +[WARNING] ^ +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning. [WARNING] ^ [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile [WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s. [WARNING] ^ -[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile -[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and -[WARNING] ^ -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/BasePairParameters.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.ObsoleteBehavior.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BcifFileReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureFiletype.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaAFPChainConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumerImpl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifBean.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConsumer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileSupplier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureConsumerImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/ChemCompConsumer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html... -[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcMain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcParameters.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleSuperimposer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html... -[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPChainer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.FatCatStartupParams.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCat.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html... -[WARNING] Generating 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.ScoringStrategy.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/package-use.html... @@ -6434,11 +6470,11 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/serialized-form.html... 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[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util... [WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color... -[WARNING] Loading source files for package org.biojava.nbio.structure.gui.events... -[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.gui... -[WARNING] Loading source files for package org.biojava.nbio.structure.align.webstart... -[WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.autosuggest... -[WARNING] Loading source files for package org.biojava.nbio.structure.align.gui... -[WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.jmol... -[WARNING] Loading source files for package org.biojava.nbio.structure.align.gui.aligpanel... -[WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -6705,137 +6741,137 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&' [WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges [WARNING] ^ -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html... @@ -6905,17 +6941,17 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. -[WARNING] Loading source files for package org.biojava.nbio.genome.homology... +[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff... +[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband... [WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid... -[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... -[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff... [WARNING] Loading source files for package org.biojava.nbio.genome... +[WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... +[WARNING] Loading source files for package org.biojava.nbio.genome.homology... +[WARNING] Loading source files for package org.biojava.nbio.genome.query... [WARNING] Loading source files for package org.biojava.nbio.genome.util... [WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq... -[WARNING] Loading source files for package org.biojava.nbio.genome.query... -[WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7008,52 +7044,52 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... 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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html... @@ -7113,10 +7149,10 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. -[WARNING] Loading source files for package org.biojava.nbio.phosphosite... [WARNING] Loading source files for package org.biojava.nbio.protmod... -[WARNING] Loading source files for package org.biojava.nbio.protmod.io... [WARNING] Loading source files for package org.biojava.nbio.protmod.structure... +[WARNING] Loading source files for package org.biojava.nbio.protmod.io... +[WARNING] Loading source files for package org.biojava.nbio.phosphosite... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7200,30 +7236,30 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html... @@ -7273,10 +7309,10 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. -[WARNING] Loading source files for package org.biojava.nbio.ws.hmmer... +[WARNING] Loading source files for package demo... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment... [WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast... -[WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.ws.hmmer... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7323,26 +7359,26 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... @@ -7392,9 +7428,9 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. -[WARNING] Loading source files for package org.biojava.nbio.ronn... -[WARNING] Loading source files for package org.biojava.nbio.data.sequence... [WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.data.sequence... +[WARNING] Loading source files for package org.biojava.nbio.ronn... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7421,20 +7457,20 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html... @@ -7485,11 +7521,11 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. +[WARNING] Loading source files for package demo... [WARNING] Loading source files for package org.biojava.nbio.aaproperties... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... -[WARNING] Loading source files for package demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7624,25 +7660,26 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html... [WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' @@ -7722,15 +7759,14 @@ [WARNING] ^ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... @@ -7804,13 +7840,13 @@ [WARNING] Javadoc Warnings [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. -[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... +[WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure... +[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... +[WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats... [WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix... -[WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators... -[WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7887,57 +7923,57 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... @@ -7997,11 +8033,11 @@ [WARNING] warning: The -footer option is no longer supported and will be ignored. [WARNING] It may be removed in a future release. [WARNING] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java... +[WARNING] Loading source files for package demo... [WARNING] Loading source files for package org.biojava.nbio.ontology... -[WARNING] Loading source files for package org.biojava.nbio.ontology.io... [WARNING] Loading source files for package org.biojava.nbio.ontology.utils... [WARNING] Loading source files for package org.biojava.nbio.ontology.obo... -[WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.ontology.io... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -8098,47 +8134,47 @@ [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/DefaultOps.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html... 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/build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/RestUtil.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/WabiTools.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_RANK.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_NAME_CLASS.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/wabi/class-use/TxSearch.RANKS.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/ws/hmmer/class-use/Test.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIO.REROOTING.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/TestRIO.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/rio/class-use/RIOException.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html... +[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html... -[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/package-use.html... @@ -12370,28 +12406,28 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 25.759 s] -[INFO] biojava-core ....................................... SUCCESS [ 9.438 s] -[INFO] biojava-forester ................................... SUCCESS [ 12.138 s] -[INFO] biojava-alignment .................................. SUCCESS [ 3.147 s] -[INFO] biojava-structure .................................. SUCCESS [ 12.404 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.583 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 4.893 s] -[INFO] biojava-genome ..................................... SUCCESS [ 3.002 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 2.163 s] -[INFO] biojava-ws ......................................... SUCCESS [ 1.854 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 1.850 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 2.382 s] -[INFO] biojava-survival ................................... SUCCESS [ 2.513 s] -[INFO] biojava-ontology ................................... SUCCESS [ 2.239 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.120 s] +[INFO] biojava ............................................ SUCCESS [ 46.534 s] +[INFO] biojava-core ....................................... SUCCESS [ 18.783 s] +[INFO] biojava-forester ................................... SUCCESS [ 21.499 s] +[INFO] biojava-alignment .................................. SUCCESS [ 6.010 s] +[INFO] biojava-structure .................................. SUCCESS [ 23.303 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 3.427 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 8.806 s] +[INFO] biojava-genome ..................................... SUCCESS [ 5.437 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 3.872 s] +[INFO] biojava-ws ......................................... SUCCESS [ 3.100 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 2.770 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 4.168 s] +[INFO] biojava-survival ................................... SUCCESS [ 4.321 s] +[INFO] biojava-ontology ................................... SUCCESS [ 3.803 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.933 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:27 min -[INFO] Finished at: 2025-02-25T04:17:45Z +[INFO] Total time: 02:39 min +[INFO] Finished at: 2024-01-23T22:41:13Z [INFO] ------------------------------------------------------------------------ -make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen 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/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test OpenJDK Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. @@ -12451,295 +12487,295 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader +[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.fasta.TestFASTAReader -[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet +[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.218 s - in org.biojava.nbio.core.util.SequenceToolsTest -[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream +[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.util.TestUncompressInputStream -[INFO] Running org.biojava.nbio.core.util.EqualsTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.core.util.EqualsTest -[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.92 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.util.StringManipulationHelperTest -[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.804 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.259 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest -[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest +[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.core.util.SoftHashMapTest -[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.986 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest +[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.util.FlatFileCacheTest -[INFO] Running org.biojava.nbio.core.util.HashcoderTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.util.HashcoderTest -[INFO] Running org.biojava.nbio.core.util.XMLHelperTest +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.core.util.XMLHelperTest -[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest - - 22 - 43.22 - some text -
2021-08-15
- - +[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.404 s - in org.biojava.nbio.core.alignment.SimpleProfileTest +[INFO] Running org.biojava.nbio.core.search.io.HspTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest -[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.core.util.CRC64ChecksumTest -[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest +getAlignment +hashCode +equals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.core.search.io.HspTest +[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest -[INFO] Running org.biojava.nbio.core.sequence.DNATest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.34 s - in org.biojava.nbio.core.search.io.SearchIOTest +[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +createObjects SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.core.sequence.DNATest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest +getFileExtensions +setFile +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.561 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +getFileExtensions SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.location.LocationTest +setFile +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.1 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.803 s - in org.biojava.nbio.core.util.StringManipulationHelperTest +[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.core.sequence.location.LocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest +[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.3 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest +[INFO] Running org.biojava.nbio.core.util.XMLHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.core.sequence.ExonComparatorTest -[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.582 s - in org.biojava.nbio.core.util.XMLHelperTest +[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest + + 22 + 43.22 + some text +
2021-08-15
+ + SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.core.sequence.RNASequenceTest -[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.421 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest +[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.4 s - in org.biojava.nbio.core.util.SoftHashMapTest +[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.578 s - in org.biojava.nbio.core.util.FlatFileCacheTest +[INFO] Running org.biojava.nbio.core.util.EqualsTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.469 s - in org.biojava.nbio.core.util.EqualsTest +[INFO] Running org.biojava.nbio.core.util.HashcoderTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.128 s - in org.biojava.nbio.core.util.HashcoderTest +[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.TestSequenceEquals -[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest +[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.551 s - in org.biojava.nbio.core.util.SequenceToolsTest +[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.EditSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest +[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 s - in org.biojava.nbio.core.util.CRC64ChecksumTest +[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.SequenceViewTest -[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.views.WindowViewTests -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.8 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.nbio.core.sequence.io.ABITracerTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 s - in org.biojava.nbio.core.sequence.ExonComparatorTest +[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 s - in org.biojava.nbio.core.sequence.RNASequenceTest +[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.339 s - in org.biojava.nbio.core.sequence.GeneSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 s - in org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest -[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest -[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.728 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.location.LocationParserTest +[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest -[INFO] Running org.biojava.nbio.core.sequence.StrandTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.StrandTest -[INFO] Running org.biojava.nbio.core.sequence.TranslationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 s - in org.biojava.nbio.core.sequence.TranslationTest -[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.TranslationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.699 s - in org.biojava.nbio.core.sequence.TranslationTest +[INFO] Running org.biojava.nbio.core.sequence.StrandTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.StrandTest [INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest -[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.sequence.ExonSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.sequence.ExonSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest -[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.GeneSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest +[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest +[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.186 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest -[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.304 s - in org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.core.alignment.SimpleProfileTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest -[INFO] Running org.biojava.nbio.core.search.io.HspTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -getAlignment -hashCode -equals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.search.io.HspTest -[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.038 s - in org.biojava.nbio.core.search.io.SearchIOTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -createObjects +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -getFileExtensions -setFile -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.79 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -getFileExtensions +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -setFile -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.115 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest +[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.fasta.TestFASTAReader [INFO] [INFO] Results: [INFO] @@ -12790,86 +12826,86 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [INFO] Running org.biojava.nbio.phylo.TestForesterWrapper SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.phylo.TestForesterWrapper -[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 s - in org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.alignment.SmithWatermanTest -[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 s - in org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.SimpleProfilePairTest -[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading -[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.io.TestStockholmParser -[INFO] Running org.biojava.nbio.alignment.GuideTreeTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.GuideTreeTest -[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.323 s - in org.biojava.nbio.alignment.TestDNAAlignment [INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.TestSubOptimalMSA -[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.164 s - in org.biojava.nbio.alignment.TestSubOptimalMSA +[INFO] Running org.biojava.nbio.alignment.GuideTreeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.934 s - in org.biojava.nbio.alignment.TestDNAAlignment -[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 s - in org.biojava.nbio.alignment.GuideTreeTest +[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest -[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest -[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 s - in org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.LocalAlignmentTest -[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 s - in org.biojava.nbio.alignment.NeedlemanWunschTest -[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest -[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 s - in org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] [INFO] Results: [INFO] @@ -12900,353 +12936,353 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestExperimentalTechniques -[INFO] Running org.biojava.nbio.structure.HetatomImplTest +[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency +[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.HetatomImplTest -[INFO] Running org.biojava.nbio.structure.TestURLIdentifier +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.153 s - in org.biojava.nbio.structure.align.client.TestStructureName +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.973 s - in org.biojava.nbio.structure.TestURLIdentifier -[INFO] Running org.biojava.nbio.structure.TestKeywords +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.297 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.727 s - in org.biojava.nbio.structure.TestKeywords -[INFO] Running org.biojava.nbio.structure.TestAtomCache +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.369 s - in org.biojava.nbio.structure.TestAtomCache -[INFO] Running org.biojava.nbio.structure.TestStructureImpl +[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.259 s - in org.biojava.nbio.structure.align.util.AtomCacheTest +[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestStructureImpl -[INFO] Running org.biojava.nbio.structure.TestCalc +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.structure.align.util.RotationAxisTest +[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment +[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.TestCalc -[INFO] Running org.biojava.nbio.structure.ChemCompTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.192 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest +[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.241 s - in org.biojava.nbio.structure.ChemCompTest -[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.271 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster +[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor +[INFO] Running org.biojava.nbio.structure.TestStructureImpl SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.105 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor -[INFO] Running org.biojava.nbio.structure.TestPdbId -[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] -[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] -[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestPdbId -[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser -[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.AtomPositionMapTest -[INFO] Running org.biojava.nbio.structure.SiteTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.structure.TestStructureImpl +[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.SiteTest -[INFO] Running org.biojava.nbio.structure.PDBStatusTest -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest -[INFO] Running org.biojava.nbio.structure.TestParsingCalcium -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Running org.biojava.nbio.structure.TestKeywords SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.128 s - in org.biojava.nbio.structure.TestKeywords +[INFO] Running org.biojava.nbio.structure.Test2JA5 +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.Test2JA5 +[INFO] Running org.biojava.nbio.structure.ResidueRangeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools -[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.084 s - in org.biojava.nbio.structure.ResidueRangeTest +[INFO] Running org.biojava.nbio.structure.Test4hhb SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.74 s - in org.biojava.nbio.structure.TestEntityHeuristics -[INFO] Running org.biojava.nbio.structure.TestAltLocs +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.821 s - in org.biojava.nbio.structure.Test4hhb +[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.341 s - in org.biojava.nbio.structure.TestAltLocs -[INFO] Running org.biojava.nbio.structure.SourceCompoundTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.65 s - in org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Running org.biojava.nbio.structure.ResidueNumberTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.structure.ResidueNumberTest +[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.011 s - in org.biojava.nbio.structure.contact.TestContactCalc +[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.184 s - in org.biojava.nbio.structure.SourceCompoundTest -[INFO] Running org.biojava.nbio.structure.io.TestShortLines +Interface + - 4.0 +Interface + - 5.477225575051661 +Interface + - 5.477225575051661 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder +[INFO] Running org.biojava.nbio.structure.TestNucleotides +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestNucleotides +[INFO] Running org.biojava.nbio.structure.TestAtomIterator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestAtomIterator +[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.249 s - in org.biojava.nbio.structure.io.TestShortLines -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.05 s - in org.biojava.nbio.structure.TestEntityHeuristics +[INFO] Running org.biojava.nbio.structure.ChemCompTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.065 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.466 s - in org.biojava.nbio.structure.ChemCompTest +[INFO] Running org.biojava.nbio.structure.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.ElementTest +[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.816 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 5.35 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering +[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.918 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader -[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.707 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.014 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo +[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.876 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles -[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestSiftsParsing -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands -[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.044 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[INFO] Running org.biojava.nbio.structure.PDBStatusTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.013 s - in org.biojava.nbio.structure.PDBStatusTest +[INFO] Running org.biojava.nbio.structure.TestDNAAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestDNAAlignment +[INFO] Running org.biojava.nbio.structure.TestStructureSerialization SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.476 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles -[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing -[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.087 s - in org.biojava.nbio.structure.TestStructureSerialization +[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.553 s - in org.biojava.nbio.structure.io.TestHeaderOnly -[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.357 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider +[INFO] Running org.biojava.nbio.structure.SiteTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest -[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.SiteTest +[INFO] Running org.biojava.nbio.structure.TestCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.io.TestDBRefParsing -[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseOnAsymId -[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestHardBioUnits -[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.structure.TestCalc +[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.3 s - in org.biojava.nbio.structure.io.TestMMCIFWriting -[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestTitleParsing -[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.855 s - in org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -Using PDB_DIR=/tmp as temporary file directory -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.56 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.544 s - in org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.766 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.037 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions +[INFO] Running org.biojava.nbio.structure.HetatomImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.616 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader -[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.structure.HetatomImplTest +[INFO] Running org.biojava.nbio.structure.TestAtomCache SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.896 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest -[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestStructureCrossReferences -[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.801 s - in org.biojava.nbio.structure.TestAtomCache +[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters +[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest -[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.088 s - in org.biojava.nbio.structure.align.util.AtomCacheTest -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.004 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser +[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[INFO] Running org.biojava.nbio.structure.TestBond +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestBond +[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestLoadStructureFromURL +[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[INFO] Running org.biojava.nbio.structure.TestAltLocs SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer -[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.578 s - in org.biojava.nbio.structure.TestAltLocs +[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.011 s - in org.biojava.nbio.structure.AtomPositionMapTest +[INFO] Running org.biojava.nbio.structure.TestParsingCalcium +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestParsingCalcium +[INFO] Running org.biojava.nbio.structure.TestPdbId +[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] +[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] +[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.structure.TestPdbId +[INFO] Running org.biojava.nbio.structure.SourceCompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion -[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.039 s - in org.biojava.nbio.structure.SourceCompoundTest +[INFO] Running org.biojava.nbio.structure.TestChargeAdder +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestChargeAdder +[INFO] Running org.biojava.nbio.structure.TestURLIdentifier SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 s - in org.biojava.nbio.structure.align.client.TestStructureName -[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency -[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment -[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.743 s - in org.biojava.nbio.structure.TestURLIdentifier +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands +[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest -[INFO] Running org.biojava.nbio.structure.ElementTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest -[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestLoadStructureFromURL -[INFO] Running org.biojava.nbio.structure.TestDNAAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.TestDNAAlignment -[INFO] Running org.biojava.nbio.structure.Test2JA5 -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.Test2JA5 -[INFO] Running org.biojava.nbio.structure.ResidueRangeTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.34 s - in org.biojava.nbio.structure.io.TestHeaderOnly +[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestHardBioUnits +[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.051 s - in org.biojava.nbio.structure.ResidueRangeTest -[INFO] Running org.biojava.nbio.structure.TestAtomIterator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestAtomIterator -[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[INFO] Running org.biojava.nbio.structure.TestStructureSerialization +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.79 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.054 s - in org.biojava.nbio.structure.TestStructureSerialization -[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.024 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions -[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.401 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.3 s - in org.biojava.nbio.structure.geometry.TestSuperPosition -[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.117 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding +[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestTitleParsing +[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP -[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.819 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestVeryLongFileName -[INFO] Running org.biojava.nbio.structure.ResidueNumberTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ResidueNumberTest -[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.423 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup -[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.278 s - in org.biojava.nbio.structure.io.TestMMCIFWriting +[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.02 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.82 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering -[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.025 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo -[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.669 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestSiftsParsing +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 s - in org.biojava.nbio.structure.io.TestParseOnAsymId +[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.446 s - in org.biojava.nbio.structure.TestEntityResIndexMapping -[INFO] Running org.biojava.nbio.structure.TestChargeAdder -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestChargeAdder -[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test +Using PDB_DIR=/tmp as temporary file directory +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.842 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.934 s - in org.biojava.nbio.structure.PdbFileFormat30Test -[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.419 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -Interface - - 4.0 -Interface - - 5.477225575051661 -Interface - - 5.477225575051661 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder -[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.008 s - in org.biojava.nbio.structure.contact.TestContactCalc -[INFO] Running org.biojava.nbio.structure.TestCloning -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestCloning -[INFO] Running org.biojava.nbio.structure.TestBond -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBond -[INFO] Running org.biojava.nbio.structure.TestNucleotides -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestNucleotides -[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.633 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[INFO] Running org.biojava.nbio.structure.io.TestShortLines SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.03 s - in org.biojava.nbio.structure.asa.TestAsaCalc -[INFO] Running org.biojava.nbio.structure.Test4hhb +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 s - in org.biojava.nbio.structure.io.TestShortLines +[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 s - in org.biojava.nbio.structure.Test4hhb -[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.534 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles +[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.225 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider -[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Running org.biojava.nbio.structure.TestCloning +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestCloning +[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] [INFO] Results: [INFO] @@ -13294,20 +13330,20 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Running org.biojava.nbio.structure.gui.ViewerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Running org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.078 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [INFO] [INFO] Results: [INFO] @@ -13335,51 +13371,51 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest -[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.TestGenomeMapping -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.043 s - in org.biojava.nbio.genome.TestGenomeMapping +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.883 s - in org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Running org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.genome.FeatureListTest [INFO] Running org.biojava.nbio.genome.TestIssue355 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestIssue355 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.genome.TestIssue355 +[INFO] Running org.biojava.nbio.genome.TestLocation +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.genome.TestLocation [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestChromosomeMappingTools -[INFO] Running org.biojava.nbio.genome.TestLocation -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestLocation -[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.genome.TestChromosomeMappingTools +[INFO] Running org.biojava.nbio.genome.TestGenomeMapping +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 s - in org.biojava.nbio.genome.TestGenomeMapping +[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.413 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.473 s - in org.biojava.nbio.genome.GeneFeatureHelperTest -[INFO] Running org.biojava.nbio.genome.FeatureListTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] [INFO] Results: [INFO] @@ -13407,20 +13443,20 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest +[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.563 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.079 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.283 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest -[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.442 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] [INFO] Results: [INFO] @@ -13449,7 +13485,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.057 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.122 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] @@ -13481,9 +13517,9 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.563 s - in org.biojava.nbio.ronn.JronnTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.513 s - in org.biojava.nbio.ronn.JronnTest [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.046 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.091 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] [INFO] Results: [INFO] @@ -13511,32 +13547,6 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.454 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest -[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.371 s - in org.biojava.nbio.aaproperties.xml.ElementTest -[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest -[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest -SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". -SLF4J: Defaulting to no-operation (NOP) logger implementation -SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint -NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 -SequenceName,A,N,MolecularWeight -NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 -SequenceName,A,N,MolecularWeight -NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -13553,22 +13563,48 @@ SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.369 s - in org.biojava.nbio.aaproperties.CommandPromptTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.766 s - in org.biojava.nbio.aaproperties.CommandPromptTest +[INFO] Running org.biojava.nbio.aaproperties.CookBookTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.535 s - in org.biojava.nbio.aaproperties.CookBookTest +[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.62 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest +[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". +SLF4J: Defaulting to no-operation (NOP) logger implementation +SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest -[INFO] Running org.biojava.nbio.aaproperties.CookBookTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 s - in org.biojava.nbio.aaproperties.CookBookTest +SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint +NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 +SequenceName,A,N,MolecularWeight +NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 +SequenceName,A,N,MolecularWeight +NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.697 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] [INFO] Results: [INFO] @@ -13615,21 +13651,21 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.ontology.TestParseOBO +[INFO] Running org.biojava.nbio.ontology.TestParseSBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.ontology.TestParseOBO -[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.ontology.TestParseSBO +[INFO] Running org.biojava.nbio.ontology.TestParseOBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.ontology.TestOboFileParsing -[INFO] Running org.biojava.nbio.ontology.TestParseSBO +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.nbio.ontology.TestParseOBO +[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.ontology.TestParseSBO +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 s - in org.biojava.nbio.ontology.TestOboFileParsing [INFO] [INFO] Results: [INFO] @@ -13658,25 +13694,25 @@ [INFO] Reactor Summary for biojava 6.1.0: [INFO] [INFO] biojava ............................................ SUCCESS [ 0.002 s] -[INFO] biojava-core ....................................... SUCCESS [09:50 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.038 s] +[INFO] biojava-core ....................................... SUCCESS [09:51 min] +[INFO] biojava-forester ................................... SUCCESS [ 0.575 s] [INFO] biojava-alignment .................................. SUCCESS [03:00 min] -[INFO] biojava-structure .................................. SUCCESS [16:21 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.451 s] +[INFO] biojava-structure .................................. SUCCESS [16:20 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.025 s] [INFO] biojava-structure-gui .............................. SUCCESS [01:00 min] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] -[INFO] biojava-modfinder .................................. SUCCESS [ 40.088 s] -[INFO] biojava-ws ......................................... SUCCESS [ 10.046 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.034 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 40.112 s] +[INFO] biojava-ws ......................................... SUCCESS [ 10.088 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.082 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:20 min] -[INFO] biojava-survival ................................... SUCCESS [ 0.036 s] -[INFO] biojava-ontology ................................... SUCCESS [ 30.029 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.111 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.057 s] +[INFO] biojava-ontology ................................... SUCCESS [ 30.061 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.137 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 36:13 min -[INFO] Finished at: 2025-02-25T04:53:59Z +[INFO] Total time: 36:14 min +[INFO] Finished at: 2024-01-23T23:17:30Z [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -13893,26 +13929,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.384 s] -[INFO] biojava-core ....................................... SUCCESS [ 0.043 s] -[INFO] biojava-forester ................................... SUCCESS [ 0.040 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.028 s] -[INFO] biojava-structure .................................. SUCCESS [ 0.032 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.023 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 0.028 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.028 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.023 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.024 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.030 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.024 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.029 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.023 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.033 s] +[INFO] biojava ............................................ SUCCESS [ 1.167 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.152 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.116 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.077 s] +[INFO] biojava-structure .................................. SUCCESS [ 0.526 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.087 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.138 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.070 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.061 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.069 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.051 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.061 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.084 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.066 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.059 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.978 s -[INFO] Finished at: 2025-02-25T04:54:02Z +[INFO] Total time: 3.371 s +[INFO] Finished at: 2024-01-23T23:17:37Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore Analysing pom.xml... @@ -14118,14 +14154,14 @@ dh_install jh_installjavadoc debian/rules override_dh_installdocs -make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten +dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ sed -i 's/^$//' $F; \ done -make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg' +make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen dh_installchangelogs dh_lintian dh_perl @@ -14148,8 +14184,8 @@ dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb'. -dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'. +dpkg-deb: Paket »libbiojava6-java-doc« wird in »../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb« gebaut. +dpkg-deb: Paket »libbiojava6-java« wird in »../libbiojava6-java_6.1.0+dfsg-4_all.deb« gebaut. dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -14157,12 +14193,14 @@ 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/3141/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3141/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/25528 and its subdirectories -I: Current time: Mon Feb 24 16:59:34 -12 2025 -I: pbuilder-time-stamp: 1740459574 +I: removing directory /srv/workspace/pbuilder/3141 and its subdirectories +I: Current time: Wed Jan 24 13:23:39 +14 2024 +I: pbuilder-time-stamp: 1706052219