Diff of the two buildlogs: -- --- b1/build.log 2024-01-13 17:17:01.924034930 +0000 +++ b2/build.log 2024-01-13 18:33:34.291322630 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 13 04:21:40 -12 2024 -I: pbuilder-time-stamp: 1705162900 +I: Current time: Sun Jan 14 07:17:23 +14 2024 +I: pbuilder-time-stamp: 1705166243 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -45,49 +45,81 @@ dpkg-source: info: applying fix_ambiguous_method_call.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6600/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2546/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 13 17:17 /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/2546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2546/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7142199c25bc499f935f7c99c3d42291' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='6600' - PS1='# ' - PS2='> ' + INVOCATION_ID=012fe963f08f46438f2580613a2d3b1e + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2546 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.rwiwpdri/pbuilderrc_ImMi --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.rwiwpdri/b1 --logfile b1/build.log biojava5-live_5.4.0+dfsg-5.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rwiwpdri/pbuilderrc_pv6v --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.rwiwpdri/b2 --logfile b2/build.log biojava5-live_5.4.0+dfsg-5.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash @@ -147,7 +179,7 @@ -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 14152 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 13 17:17 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 2023 su @@ -173,7 +205,7 @@ -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/6600/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -662,7 +694,7 @@ Get: 393 http://deb.debian.org/debian bookworm/main armhf maven all 3.8.7-1 [18.9 kB] Get: 394 http://deb.debian.org/debian bookworm/main armhf maven-repo-helper all 1.11 [142 kB] Get: 395 http://deb.debian.org/debian bookworm/main armhf maven-debian-helper all 2.6.3 [108 kB] -Fetched 322 MB in 59s (5448 kB/s) +Fetched 322 MB in 28s (11.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17881 files and directories currently installed.) @@ -2447,7 +2479,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/biojava5-live-5.4.0+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 > ../biojava5-live_5.4.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2546/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2546/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/biojava5-live-5.4.0+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 > ../biojava5-live_5.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package biojava5-live dpkg-buildpackage: info: source version 5.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -2462,8 +2498,8 @@ mh_unpatchpoms -plibbiojava5-java jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" dh_clean rm -rf target rm -rf biojava-*/target @@ -2471,15 +2507,15 @@ -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/biojava5-live-5.4.0+dfsg' +make[1]: uscita dalla directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' dh binary --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" # 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/ @@ -2490,11 +2526,11 @@ sed 's/\(VERSION_PACKAGE\)/\15.4.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml dh_auto_configure mh_patchpoms -plibbiojava5-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava5-live-5.4.0\+dfsg/debian/maven-repo -make[1]: Leaving directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' +make[1]: uscita dalla directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" # 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 \ @@ -2585,30 +2621,30 @@ [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 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.alignment.matrices... -[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... -[WARNING] Loading source files for package org.biojava.nbio.core.alignment... +[WARNING] Loading source files for package demo... [WARNING] Loading source files for package org.biojava.nbio.core.sequence... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference... [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.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.template... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl... -[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] 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.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.transcription... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... -[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage... [WARNING] Loading source files for package org.biojava.nbio.core.sequence.features... +[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits... [WARNING] Loading source files for package org.biojava.nbio.core.util... -[WARNING] Loading source files for package demo... +[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.alignment... +[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template... +[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -3173,219 +3209,219 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html... -[WARNING] Generating 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-[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/ABITracerCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityRNACompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/RNACompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html... -[WARNING] Generating 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.IUPACTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceHeaderParserInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/GenbankHeaderFormatInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceCreatorInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReference.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblRecord.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/class-use/EmblId.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OneOfLocation.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.GroupLocation.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OrderLocation.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.BondLocation.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html... 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ProteinDomainParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/FastaParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXtags.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/SupportCount.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/MappingResults.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengths.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinableDomains.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/application/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/package-use.html... @@ -4583,12 +4619,12 @@ [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.routines... [WARNING] Loading source files for package org.biojava.nbio.alignment... +[WARNING] Loading source files for package org.biojava.nbio.alignment.routines... [WARNING] Loading source files for package org.biojava.nbio.alignment.template... [WARNING] Loading source files for package org.biojava.nbio.alignment.io... -[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 @@ -4791,22 +4827,28 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/constant-values.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html... @@ -4814,30 +4856,23 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html... -[WARNING] /build/reproducible-path/biojava5-live-5.4.0+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/biojava5-live-5.4.0+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/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Subproblem.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.QueryIndexComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Cut.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Last.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html... [WARNING] /build/reproducible-path/biojava5-live-5.4.0+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. @@ -4848,8 +4883,7 @@ [WARNING] /build/reproducible-path/biojava5-live-5.4.0+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/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html... [WARNING] /build/reproducible-path/biojava5-live-5.4.0+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. @@ -4860,25 +4894,27 @@ [WARNING] /build/reproducible-path/biojava5-live-5.4.0+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/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html... +[WARNING] /build/reproducible-path/biojava5-live-5.4.0+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/biojava5-live-5.4.0+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/biojava5-live-5.4.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html... 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.ObsoleteBehavior.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SandboxStyleStructureProvider.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BcifFileReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifFileConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsSegment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsMappingProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainEntry.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsEntity.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ChemCompGroupFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ChemCompConsumer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ChemicalComponentDictionary.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/MMcifConsumer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/MetalBondConsumer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ReducedChemCompProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ZipChemCompProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/MMcifParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/ChemCompProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/AllChemCompProvider.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/class-use/SimpleMMcifParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/PolymerType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/MetalBondDistance.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/ChemCompTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/ResidueType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructConn.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyXMLContainer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxDatabaseStatus.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxPolySeqScheme.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyGen.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Exptl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRef.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AbstractBean.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRefSeq.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxAuditRevisionHistory.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructOperListXMLContainer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxEntityNonPoly.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntityPolySeq.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Refine.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssembly.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntitySrcSyn.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructSite.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxPolySeqScheme.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructNcsOper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructConn.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructKeywords.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructAsym.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntitySrcNat.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/DatabasePdbrevRecord.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssembly.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/DatabasePDBremark.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Symmetry.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemCompDescriptor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AtomSite.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Struct.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AtomSites.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Cell.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructSiteGen.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Entity.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/DatabasePDBrev.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AuditAuthor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntitySrcSyn.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/DatabasePdbrevRecord.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemComp.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/DatabasePDBremark.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/CIFLabel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/IgnoreField.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyGenXMLContainer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Entity.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructAsym.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Cell.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxChemCompIdentifier.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxAuditRevisionHistory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AtomSites.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AtomSite.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntitySrcGen.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemCompBond.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxNonPolyScheme.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxChemCompDescriptor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructOperList.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemCompAtom.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemCompBond.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AuditAuthor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxDatabaseStatus.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyXMLContainer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/ChemCompDescriptor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyGen.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRefSeqDif.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxEntityNonPoly.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Exptl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/AbstractBean.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructOperListXMLContainer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntityPoly.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructOperList.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRef.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructRefSeq.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructSiteGen.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntityPolySeq.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/EntitySrcGen.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/Symmetry.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/StructNcsOper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/AssignmentXMLSerializer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/PDBDomainProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/PDPProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/RemoteDomainProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/PDPDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/RemotePDPProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProviderFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/BasePairParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseSquareMatrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SparseVector.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/math/class-use/SymbolTable.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/Programs.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/AngleOutlier.html... 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/ModelledSubgroup.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/SymmClash.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/WwPDBValidationInformation.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/BondOutlier.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/validation/class-use/Program.html... -[WARNING] Generating 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-[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/UnitCellBoundingBox.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/class-use/SymoplibParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapElements.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/SpaceGroupMapRoot.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html... -[WARNING] Generating 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxStructAssemblyGenXMLContainer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/PdbxChemCompDescriptor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/model/class-use/IgnoreField.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/ChemCompTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/PolymerType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/MetalBondDistance.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmcif/chem/class-use/ResidueType.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html... +[WARNING] Generating 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/MultiThreadedDBSearch.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/MultipleStructureAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/ClusterAltAligs.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignmentFactory.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/FarmJob.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/BioJavaStructureAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StrucAligParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AbstractStructureAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AFPTwister.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/CallableStructureAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/MultiThreadedDBSearch.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/ClusterAltAligs.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignment.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructurePairAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IdxComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/GapArray.html... -[WARNING] Generating 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AFPTwister.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/StructureAlignmentFactory.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/AbstractStructureAlignment.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/class-use/FarmJob.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/RotationAxis.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/UserConfiguration.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPChainScorer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.IdentityMap.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.DuplicationHint.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/MatrixListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.CPRange.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/UserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPMain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/StartupParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/ConfigStrucAligParams.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.ScoringStrategy.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/HasResultXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsRelation.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlign.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignParameters.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignResult.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/RepresentativeXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/HasResultXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PositionInQueueXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/RepresentativeXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/JFatCatClient.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/FarmJobRunnable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/CountProgressListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/JobKillException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/FarmJobParameters.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.FatCatStartupParams.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCat.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatFlexible.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPChainer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/events/class-use/AlignmentProgressListener.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcMain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcParameters.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleSuperimposer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html... -[WARNING] Generating 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[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -6877,145 +6913,145 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/constant-values.html... 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[WARNING] /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: 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/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DBResultTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/GUIFarmJobRunnable.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/GUIAlignmentProgressListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalcDB.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DBResultTable.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/GUIAlignmentProgressListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DBSearchGUI.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalcDB.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartDBSearchResults.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartDBSearch.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoNWALignment.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCE.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowValidationResults.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/WebStartClientDemo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowCATHDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AFPFromFasta.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowLargeAssembly.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartDBSearch.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html... [WARNING] /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:44: warning: invalid input: '&' @@ -7086,17 +7122,17 @@ [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.parsers.geneid... -[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... +[WARNING] Loading source files for package org.biojava.nbio.genome.util... +[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.gff... -[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit... -[WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq... +[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename... +[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... +[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.homology... -[WARNING] Loading source files for package org.biojava.nbio.genome.uniprot... -[WARNING] Loading source files for package org.biojava.nbio.genome.util... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7190,53 +7226,53 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/SimpleTwoBitFileProvider.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/SimpleTwoBitFileProvider.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html... @@ -7294,8 +7330,8 @@ [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] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7379,30 +7415,30 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html... @@ -7450,10 +7486,10 @@ [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 demo... +[WARNING] Loading source files for package org.biojava.nbio.ws.hmmer... [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 org.biojava.nbio.ws.hmmer... -[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 @@ -7500,26 +7536,26 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/serialized-form.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html... @@ -7567,9 +7603,9 @@ [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.data.sequence... -[WARNING] Loading source files for package org.biojava.nbio.ronn... [WARNING] Loading source files for package demo... +[WARNING] Loading source files for package org.biojava.nbio.ronn... +[WARNING] Loading source files for package org.biojava.nbio.data.sequence... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -7596,20 +7632,20 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html... @@ -7687,11 +7723,11 @@ [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.profeat... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml... -[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 @@ -7826,17 +7862,17 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html... [WARNING] /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&' @@ -7914,25 +7950,25 @@ [WARNING] /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java:123: warning: invalid input: '&' [WARNING] * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
[WARNING] ^ +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... @@ -8009,8 +8045,8 @@ [WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... [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.cox.matrix... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -8087,57 +8123,57 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html... @@ -8193,11 +8229,11 @@ [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/biojava5-live-5.4.0+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.obo... [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 demo... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1 @@ -8294,47 +8330,47 @@ [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileEventListener.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileHandler.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/obo/class-use/OboFileParser.SOPair.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AlreadyExistsException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntoTools.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.html... -[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Triple.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Variable.Impl.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html... 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[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat... [WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor... @@ -8665,59 +8701,59 @@ [WARNING] Loading source files for package org.biojava.nbio.survival.data... [WARNING] Loading source files for package org.biojava.nbio.survival.cox... [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.cox.matrix... [WARNING] Loading source files for package org.biojava.nbio.ontology.obo... [WARNING] Loading source files for package org.biojava.nbio.ontology... [WARNING] Loading source files for package org.biojava.nbio.ontology.io... 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/build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/MappingResults.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/TestGSDI.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIException.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/SDIR.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/forester/sdi/class-use/GSDII.html... +[WARNING] 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[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html... +[WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/jcolorbrewer/class-use/ColorBrewer.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/demo/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/package-use.html... [WARNING] Generating /build/reproducible-path/biojava5-live-5.4.0+dfsg/target/site/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html... @@ -12704,27 +12740,27 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [01:50 min] -[INFO] biojava-core ....................................... SUCCESS [ 48.338 s] -[INFO] biojava-forester ................................... SUCCESS [ 50.916 s] -[INFO] biojava-alignment .................................. SUCCESS [ 17.681 s] -[INFO] biojava-structure .................................. SUCCESS [ 58.089 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 8.156 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 25.257 s] -[INFO] biojava-genome ..................................... SUCCESS [ 14.697 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 11.781 s] -[INFO] biojava-ws ......................................... SUCCESS [ 9.527 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 8.788 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 29.047 s] -[INFO] biojava-survival ................................... SUCCESS [ 13.749 s] -[INFO] biojava-ontology ................................... SUCCESS [ 11.850 s] +[INFO] biojava ............................................ SUCCESS [04:49 min] +[INFO] biojava-core ....................................... SUCCESS [02:38 min] +[INFO] biojava-forester ................................... SUCCESS [02:55 min] +[INFO] biojava-alignment .................................. SUCCESS [01:00 min] +[INFO] biojava-structure .................................. SUCCESS [03:29 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 29.385 s] +[INFO] biojava-structure-gui .............................. SUCCESS [01:18 min] +[INFO] biojava-genome ..................................... SUCCESS [ 45.061 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 33.125 s] +[INFO] biojava-ws ......................................... SUCCESS [ 25.203 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 25.875 s] +[INFO] biojava-aa-prop .................................... SUCCESS [01:15 min] +[INFO] biojava-survival ................................... SUCCESS [ 38.990 s] +[INFO] biojava-ontology ................................... SUCCESS [ 31.714 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 07:02 min -[INFO] Finished at: 2024-01-13T16:36:14Z +[INFO] Total time: 21:25 min +[INFO] Finished at: 2024-01-13T17:49:10Z [INFO] ------------------------------------------------------------------------ -make[1]: Leaving directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' +make[1]: uscita dalla directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» 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/biojava5-live-5.4.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava5-live-5.4.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava5-live-5.4.0\+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. @@ -12780,178 +12816,178 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.427 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet -[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.419 s - in org.biojava.nbio.core.search.io.SearchIOTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -createObjects +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.74 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[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. -getFileExtensions -setFile -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.582 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest -[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -getFileExtensions +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.764 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[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. -setFile -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.311 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest -[INFO] Running org.biojava.nbio.core.search.io.HspTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.712 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest 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: 0.374 s - in org.biojava.nbio.core.search.io.HspTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.3 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[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. -[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.586 s - in org.biojava.nbio.core.alignment.SimpleProfileTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.724 s - in org.biojava.nbio.core.sequence.SequenceViewTest +[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: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.429 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest -[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.016 s - in org.biojava.nbio.core.sequence.DNATest +[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. -[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.413 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.696 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.292 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest -[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.932 s - in org.biojava.nbio.core.sequence.io.ABITracerTest +[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: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.18 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.TranslationTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.644 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.652 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[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. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.258 s - in org.biojava.nbio.core.sequence.TranslationTest -[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest +[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. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.293 s - in org.biojava.nbio.core.sequence.EditSequenceTest -[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.284 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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 s - in org.biojava.nbio.core.sequence.TestSequenceEquals -[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.088 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. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.638 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.652 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[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: 1.366 s - in org.biojava.nbio.core.sequence.io.ABITracerTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.828 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.656 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest -[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.249 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.569 s - in org.biojava.nbio.core.sequence.TranslationTest +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.281 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest -[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 s - in org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.536 s - in org.biojava.nbio.core.sequence.location.LocationParserTest +[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest 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: 0.289 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.856 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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.795 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.8 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.304 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest -[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest -[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.596 s - in org.biojava.nbio.core.sequence.TestSequenceEquals +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.214 s - in org.biojava.nbio.core.sequence.location.LocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.601 s - in org.biojava.nbio.core.util.TestUncompressInputStream +[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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.812 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest -[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest +setFile +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.644 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.306 s - in org.biojava.nbio.core.sequence.location.LocationTest -[INFO] Running org.biojava.nbio.core.sequence.DNATest +getFileExtensions +setFile +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.984 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +[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: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 s - in org.biojava.nbio.core.sequence.DNATest -[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests +getAlignment +hashCode +equals +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.056 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 s - in org.biojava.nbio.core.sequence.views.WindowViewTests -[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.8 s - in org.biojava.nbio.core.search.io.SearchIOTest +[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.nbio.core.sequence.SequenceViewTest -[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 s - in org.biojava.nbio.core.fasta.TestFASTAReader +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.285 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest -[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.876 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.nbio.core.util.TestUncompressInputStream -[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader +[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.784 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 s - in org.biojava.nbio.core.fasta.TestFASTAReader +[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.008 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [INFO] [INFO] Results: [INFO] @@ -12998,90 +13034,90 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running 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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator -[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 s - in org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator 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: 0.332 s - in org.biojava.nbio.phylo.TestForesterWrapper -[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator +[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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.464 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest -[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.923 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[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. -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.534 s - in org.biojava.nbio.alignment.TestSubOptimalMSA -[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.86 s - in org.biojava.nbio.alignment.SmithWatermanTest +[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.382 s - in org.biojava.nbio.alignment.SimpleProfilePairTest -[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.48 s - in org.biojava.nbio.alignment.NeedlemanWunschTest +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.423 s - in org.biojava.nbio.alignment.io.TestStockholmParser -[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.024 s - in org.biojava.nbio.alignment.TestSubOptimalMSA +[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: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.005 s - in org.biojava.nbio.alignment.NeedlemanWunschTest -[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.077 s - in org.biojava.nbio.alignment.SimpleProfilePairTest +[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: 0.574 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest -[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.218 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.202 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: 0.388 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest +[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.388 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest -[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.716 s - in org.biojava.nbio.alignment.LocalAlignmentTest +[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest -[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.652 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.751 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading -[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.alignment.GuideTreeTest +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.414 s - in org.biojava.nbio.alignment.LocalAlignmentTest -[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.952 s - in org.biojava.nbio.alignment.io.TestStockholmParser +[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: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.548 s - in org.biojava.nbio.alignment.SmithWatermanTest -[INFO] Running org.biojava.nbio.alignment.GuideTreeTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.36 s - in org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest +[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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.526 s - in org.biojava.nbio.alignment.GuideTreeTest -[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.564 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.473 s - in org.biojava.nbio.alignment.TestDNAAlignment -[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.56 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest +[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: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [INFO] [INFO] Results: [INFO] @@ -13114,373 +13150,373 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.structure.TestChargeAdder -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.249 s - in org.biojava.nbio.structure.TestChargeAdder -[INFO] Running org.biojava.nbio.structure.TestCloning -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.273 s - in org.biojava.nbio.structure.TestCloning -[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.264 s - in org.biojava.nbio.structure.AtomPositionMapTest -[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.265 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. -Interface - - 4.0 -Interface - - 5.477225575051661 -Interface - - 5.477225575051661 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.556 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder -[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.288 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters +[INFO] Running org.biojava.nbio.structure.Test2JA5 +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.408 s - in org.biojava.nbio.structure.Test2JA5 +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.302 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.255 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.769 s - in org.biojava.nbio.structure.ChemCompTest +[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.344 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: 0.306 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.252 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[INFO] Running org.biojava.nbio.structure.Test4hhb +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.628 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: 0.526 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor +[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.412 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.495 s - in org.biojava.nbio.structure.Test4hhb -[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.254 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[INFO] Running org.biojava.nbio.structure.TestURLIdentifier +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.14 s - in org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.652 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.536 s - in org.biojava.nbio.structure.TestURLIdentifier -[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.676 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Running org.biojava.nbio.structure.TestBond +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.532 s - in org.biojava.nbio.structure.TestBond +[INFO] Running org.biojava.nbio.structure.TestAtomIterator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.618 s - in org.biojava.nbio.structure.TestAtomIterator +[INFO] Running org.biojava.nbio.structure.ResidueNumberTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.596 s - in org.biojava.nbio.structure.ResidueNumberTest +[INFO] Running org.biojava.nbio.structure.TestParsingCalcium +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.568 s - in org.biojava.nbio.structure.TestParsingCalcium +[INFO] Running org.biojava.nbio.structure.TestChargeAdder +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.792 s - in org.biojava.nbio.structure.TestChargeAdder +[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP -[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.748 s - in org.biojava.nbio.structure.HetatomImplTest +[INFO] Running org.biojava.nbio.structure.TestNucleotides +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.823 s - in org.biojava.nbio.structure.TestNucleotides +[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.808 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.274 s - in org.biojava.nbio.structure.geometry.TestSuperPosition -[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.301 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions -[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.273 s - in org.biojava.nbio.structure.TestStructureCrossReferences -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.27 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor -[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.284 s - in org.biojava.nbio.structure.TestStructureImpl +[INFO] Running org.biojava.nbio.structure.PDBStatusTest 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: 0.87 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster -[INFO] Running org.biojava.nbio.structure.Test2JA5 -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.274 s - in org.biojava.nbio.structure.Test2JA5 -[INFO] Running org.biojava.nbio.structure.SiteTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.916 s - in org.biojava.nbio.structure.PDBStatusTest +[INFO] Running org.biojava.nbio.structure.TestCloning +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.696 s - in org.biojava.nbio.structure.TestCloning +[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.382 s - in org.biojava.nbio.structure.SiteTest -[INFO] Running org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 35.356 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: 0.492 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo +[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. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 s - in org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest -[INFO] Running org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.428 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: 0.708 s - in org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.488 s - in org.biojava.nbio.structure.TestLoadStructureFromURL +[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.66 s - in org.biojava.nbio.structure.TestStructureCrossReferences +[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. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.482 s - in org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest -[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.66 s - in org.biojava.nbio.structure.TestCalc +[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.646 s - in org.biojava.nbio.structure.PdbFileFormat30Test -[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.336 s - in org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Running org.biojava.nbio.structure.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.636 s - in org.biojava.nbio.structure.ElementTest +[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.837 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.266 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.484 s - in org.biojava.nbio.structure.SourceCompoundTest +[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: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 5.692 s - in org.biojava.nbio.structure.io.TestHeaderOnly -[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 6.7 s - in org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Running org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest 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: 13, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 9.093 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles -[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.264 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.282 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[INFO] Running org.biojava.nbio.structure.io.TestMmCIFSpecialCases +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 1.102 s - in org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest +[INFO] Running org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest 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: 0.325 s - in org.biojava.nbio.structure.io.TestMmCIFSpecialCases -[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.264 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.255 s - in org.biojava.nbio.structure.io.TestTitleParsing -[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.266 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.404 s - in org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest +[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: 0.407 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest -[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.932 s - in org.biojava.nbio.structure.SiteTest +[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: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.583 s - in org.biojava.nbio.structure.io.TestMMCIFWriting -[INFO] Running org.biojava.nbio.structure.io.TestShortLines +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.82 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.719 s - in org.biojava.nbio.structure.io.TestShortLines -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.262 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.258 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[WARNING] Tests run: 13, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 19.855 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles +[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.388 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.38 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.385 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.85 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: 0.271 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.056 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.632 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[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. -[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.587 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils -[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.612 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 5.625 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader -[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 7.744 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.331 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[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. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 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: 0.282 s - in org.biojava.nbio.structure.io.TestParseOnAsymId -[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.263 s - in org.biojava.nbio.structure.io.TestHardBioUnits -[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.259 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.255 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +Using PDB_DIR=/tmp as temporary file directory +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.979 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.491 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 7.296 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[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. -Using PDB_DIR=/tmp as temporary file directory -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.14 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider -[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.65 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.329 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: 0.258 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding +[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 5.337 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: 0.251 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.452 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: 0.268 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.385 s - in org.biojava.nbio.structure.io.TestSiftsParsing -[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.25 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.62 s - in org.biojava.nbio.structure.io.TestMMCIFWriting +[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: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 4.504 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: 0.254 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing -[INFO] Running org.biojava.nbio.structure.TestAltLocs +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.795 s - in org.biojava.nbio.structure.io.TestShortLines +[INFO] Running org.biojava.nbio.structure.io.TestMmCIFSpecialCases 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: 1.346 s - in org.biojava.nbio.structure.TestAltLocs -[INFO] Running org.biojava.nbio.structure.SourceCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.401 s - in org.biojava.nbio.structure.io.TestMmCIFSpecialCases +[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.23 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: 0.3 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.275 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.055 s - in org.biojava.nbio.structure.SourceCompoundTest -[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.26 s - in org.biojava.nbio.structure.TestLoadStructureFromURL -[INFO] Running org.biojava.nbio.structure.HetatomImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.468 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.27 s - in org.biojava.nbio.structure.io.TestTitleParsing +[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. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.586 s - in org.biojava.nbio.structure.HetatomImplTest -[INFO] Running org.biojava.nbio.structure.TestCalc +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.513 s - in org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.3 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[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. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.537 s - in org.biojava.nbio.structure.TestCalc -[INFO] Running org.biojava.nbio.structure.TestStructureSerialization +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 5.788 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.245 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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.025 s - in org.biojava.nbio.structure.TestStructureSerialization -[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.253 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters -[INFO] Running org.biojava.nbio.structure.TestStructureImpl +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 6.356 s - in org.biojava.nbio.structure.io.TestHeaderOnly +[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.239 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.285 s - in org.biojava.nbio.structure.io.TestHardBioUnits +[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing 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: 0.492 s - in org.biojava.nbio.structure.TestStructureImpl -[INFO] Running org.biojava.nbio.structure.TestNucleotides -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.262 s - in org.biojava.nbio.structure.TestNucleotides -[INFO] Running org.biojava.nbio.structure.ElementTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s - in org.biojava.nbio.structure.ElementTest -[INFO] Running org.biojava.nbio.structure.TestDownloadChemCompProvider +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.798 s - in org.biojava.nbio.structure.io.TestSiftsParsing +[INFO] Running org.biojava.nbio.structure.TestDNAAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.229 s - in org.biojava.nbio.structure.TestDNAAlignment +[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.519 s - in org.biojava.nbio.structure.TestDownloadChemCompProvider -[INFO] Running org.biojava.nbio.structure.TestAtomCache +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.131 s - in org.biojava.nbio.structure.TestEntityHeuristics +[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: 3, Time elapsed: 0.665 s - in org.biojava.nbio.structure.TestAtomCache -[INFO] Running org.biojava.nbio.structure.TestParsingCalcium -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.257 s - in org.biojava.nbio.structure.TestParsingCalcium -[INFO] Running org.biojava.nbio.structure.ChemCompTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.045 s - in org.biojava.nbio.structure.TestURLIdentifier +[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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.589 s - in org.biojava.nbio.structure.ChemCompTest -[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.268 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier -[INFO] Running org.biojava.nbio.structure.PDBStatusTest +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.35 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. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.33 s - in org.biojava.nbio.structure.PDBStatusTest -[INFO] Running org.biojava.nbio.structure.validation.TestValidationReportParsing -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.099 s - in org.biojava.nbio.structure.validation.TestValidationReportParsing -[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.183 s - in org.biojava.nbio.structure.Test4hhb +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.362 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: 0.305 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: 0.259 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo -[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.628 s - in org.biojava.nbio.structure.TestStructureSerialization +[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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 13.506 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering -[INFO] Running org.biojava.nbio.structure.ResidueNumberTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 s - in org.biojava.nbio.structure.ResidueNumberTest -[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 s - in org.biojava.nbio.structure.align.util.RotationAxisTest +[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. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.457 s - in org.biojava.nbio.structure.TestVeryLongFileName +[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.373 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.251 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.226 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. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.359 s - in org.biojava.nbio.structure.align.client.TestStructureName -[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.377 s - in org.biojava.nbio.structure.align.client.TestStructureName +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.272 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.256 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[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. -[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.39 s - in org.biojava.nbio.structure.align.util.AtomCacheTest -[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.468 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: 0.276 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[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: 0.327 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: 0.259 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.608 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[INFO] Running org.biojava.nbio.structure.align.TestAlignDBSearchPairs +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.237 s - in org.biojava.nbio.structure.align.TestAlignDBSearchPairs [INFO] Running org.biojava.nbio.structure.align.ce.TestWebStartClient 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: 0.344 s - in org.biojava.nbio.structure.align.ce.TestWebStartClient +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.652 s - in org.biojava.nbio.structure.align.ce.TestWebStartClient [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. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.468 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest -[INFO] Running org.biojava.nbio.structure.align.TestAlignDBSearchPairs -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 s - in org.biojava.nbio.structure.align.TestAlignDBSearchPairs -[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.4 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest +[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.52 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.4 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.266 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.298 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 3.2 s - in org.biojava.nbio.structure.TestAltLocs +[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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.532 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer -[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.269 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.26 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: 0.259 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.32 s - in org.biojava.nbio.structure.TestAtomCache +[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.476 s - in org.biojava.nbio.structure.AtomPositionMapTest +[INFO] Running org.biojava.nbio.structure.validation.TestValidationReportParsing +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.594 s - in org.biojava.nbio.structure.validation.TestValidationReportParsing +[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: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.394 s - in org.biojava.nbio.structure.asa.TestAsaCalc -[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.298 s - in org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.252 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. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 2.052 s - in org.biojava.nbio.structure.TestEntityResIndexMapping -[INFO] Running org.biojava.nbio.structure.TestBond -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.292 s - in org.biojava.nbio.structure.TestBond -[INFO] Running org.biojava.nbio.structure.TestAtomIterator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.261 s - in org.biojava.nbio.structure.TestAtomIterator -[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.259 s - in org.biojava.nbio.structure.TestExperimentalTechniques -[INFO] Running org.biojava.nbio.structure.TestDNAAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.264 s - in org.biojava.nbio.structure.TestDNAAlignment -[INFO] Running org.biojava.nbio.structure.ResidueRangeTest +Interface + - 4.0 +Interface + - 5.477225575051661 +Interface + - 5.477225575051661 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.481 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder +[INFO] Running org.biojava.nbio.structure.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: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.364 s - in org.biojava.nbio.structure.ResidueRangeTest -[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.441 s - in org.biojava.nbio.structure.TestDownloadChemCompProvider +[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.227 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.216 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser +[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.22 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[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. +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 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: 0.211 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: 0.274 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.592 s - in org.biojava.nbio.structure.TestEntityHeuristics +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.279 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.211 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign [INFO] [INFO] Results: [INFO] @@ -13527,19 +13563,19 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.structure.gui.ViewerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.nbio.structure.gui.ViewerTest -[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.218 s - in org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.182 s - in org.biojava.nbio.structure.gui.RenderStyleTest [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: 0.24 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Running org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 s - in org.biojava.nbio.structure.gui.ViewerTest +[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] [INFO] Results: [INFO] @@ -13567,51 +13603,51 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.genome.TestIssue355 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 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: 0.208 s - in org.biojava.nbio.genome.TestLocation -[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: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.423 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest -[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.581 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 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: 0.336 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.495 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: 0.333 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 s - in org.biojava.nbio.genome.TestLocation +[INFO] Running org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.188 s - in org.biojava.nbio.genome.FeatureListTest [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: 0.247 s - in org.biojava.nbio.genome.TestChromosomeMappingTools +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 s - in org.biojava.nbio.genome.TestChromosomeMappingTools [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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.3 s - in org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.261 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.TestGenomeMapping -[WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 9, Time elapsed: 0.224 s - in org.biojava.nbio.genome.TestGenomeMapping -[INFO] Running org.biojava.nbio.genome.FeatureListTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.21 s - in org.biojava.nbio.genome.FeatureListTest +[WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 9, Time elapsed: 0.189 s - in org.biojava.nbio.genome.TestGenomeMapping +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.238 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.242 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: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.413 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: 0.494 s - in org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.601 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.368 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: 0.663 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.537 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: 0.306 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Running org.biojava.nbio.genome.TestIssue355 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 s - in org.biojava.nbio.genome.TestIssue355 [INFO] [INFO] Results: [INFO] @@ -13640,19 +13676,19 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.198 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.191 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.198 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. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.394 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest -[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.207 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.35 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [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. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.324 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.409 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] [INFO] Results: [INFO] @@ -13681,7 +13717,7 @@ [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: 0.222 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.191 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] @@ -13713,9 +13749,9 @@ 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: 17.212 s - in org.biojava.nbio.ronn.JronnTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.022 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: 6.222 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.197 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] [INFO] Results: [INFO] @@ -13743,66 +13779,66 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest +[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 -SAOV_0114,53660.5723,41370.0,41370.0,4.986 -SAOV_0094,45884.0164,57760.0,57760.0,8.5193 -SAA6008_00126,95002.026,55240.0,55740.0,5.7263 +NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 SequenceName,A,N,MolecularWeight -SAOV_0114,0.101,0.0525,53660.5723 -SAOV_0094,0.0537,0.0767,45884.0164 -SAA6008_00126,0.0955,0.0414,95002.026 +NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 SequenceName,A,N,MolecularWeight -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: 1.845 s - in org.biojava.nbio.aaproperties.CommandPromptTest +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: 2.159 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s - in org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest -[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 s - in org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest +[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: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.896 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest -[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.612 s - in org.biojava.nbio.aaproperties.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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest -[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.985 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[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: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.13 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest -[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.304 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest +[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: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.876 s - in org.biojava.nbio.aaproperties.xml.ElementTest -[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +[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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest -[INFO] Running org.biojava.nbio.aaproperties.CookBookTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.278 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: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.793 s - in org.biojava.nbio.aaproperties.CookBookTest -[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.094 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest 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 +SAOV_0114,53660.5723,41370.0,41370.0,4.986 +SAOV_0094,45884.0164,57760.0,57760.0,8.5193 +SAA6008_00126,95002.026,55240.0,55740.0,5.7263 SequenceName,A,N,MolecularWeight -NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 +SAOV_0114,0.101,0.0525,53660.5723 +SAOV_0094,0.0537,0.0767,45884.0164 +SAA6008_00126,0.0955,0.0414,95002.026 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: 1.87 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest +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: 1.928 s - in org.biojava.nbio.aaproperties.CommandPromptTest [INFO] [INFO] Results: [INFO] @@ -13849,21 +13885,21 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.biojava.nbio.ontology.TestParseSBO +[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: 0.776 s - in org.biojava.nbio.ontology.TestParseSBO -[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.479 s - in org.biojava.nbio.ontology.TestOboFileParsing +[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: 1.068 s - in org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.732 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: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 s - in org.biojava.nbio.ontology.TestParseOBO +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.452 s - in org.biojava.nbio.ontology.TestParseOBO [INFO] [INFO] Results: [INFO] @@ -13872,25 +13908,25 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.006 s] -[INFO] biojava-core ....................................... SUCCESS [05:42 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.222 s] -[INFO] biojava-alignment .................................. SUCCESS [03:00 min] -[INFO] biojava-structure .................................. SUCCESS [17:20 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.070 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 50.322 s] +[INFO] biojava ............................................ SUCCESS [ 0.023 s] +[INFO] biojava-core ....................................... SUCCESS [05:57 min] +[INFO] biojava-forester ................................... SUCCESS [ 0.513 s] +[INFO] biojava-alignment .................................. SUCCESS [03:20 min] +[INFO] biojava-structure .................................. SUCCESS [19:31 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.054 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 50.281 s] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] -[INFO] biojava-modfinder .................................. SUCCESS [ 40.251 s] -[INFO] biojava-ws ......................................... SUCCESS [ 10.116 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 30.136 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 40.250 s] +[INFO] biojava-ws ......................................... SUCCESS [ 10.114 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 30.115 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:30 min] -[INFO] biojava-survival ................................... SUCCESS [ 0.082 s] -[INFO] biojava-ontology ................................... SUCCESS [ 30.108 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.089 s] +[INFO] biojava-ontology ................................... SUCCESS [ 30.153 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 33:16 min -[INFO] Finished at: 2024-01-13T17:09:35Z +[INFO] Total time: 36:04 min +[INFO] Finished at: 2024-01-13T18:25:31Z [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -14094,25 +14130,25 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 1.389 s] -[INFO] biojava-core ....................................... SUCCESS [ 0.169 s] -[INFO] biojava-forester ................................... SUCCESS [ 0.118 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.121 s] -[INFO] biojava-structure .................................. SUCCESS [ 0.142 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.088 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 0.102 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.092 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.082 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.078 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.081 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.110 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.081 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.074 s] +[INFO] biojava ............................................ SUCCESS [ 1.592 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.161 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.147 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.150 s] +[INFO] biojava-structure .................................. SUCCESS [ 0.273 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.151 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.124 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.099 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.116 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.112 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.097 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.114 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.098 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.081 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 3.579 s -[INFO] Finished at: 2024-01-13T17:09:43Z +[INFO] Total time: 4.396 s +[INFO] Finished at: 2024-01-13T18:25:41Z [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava5-java --javadoc --base-directory=/build/reproducible-path/biojava5-live-5.4.0\+dfsg --non-explore Analysing pom.xml... @@ -14330,14 +14366,14 @@ dh_install jh_installjavadoc debian/rules override_dh_installdocs -make[1]: Entering directory '/build/reproducible-path/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" 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/biojava5-live-5.4.0+dfsg' +make[1]: uscita dalla directory «/build/reproducible-path/biojava5-live-5.4.0+dfsg» dh_installchangelogs dh_lintian dh_perl @@ -14360,8 +14396,8 @@ dpkg-gencontrol: warning: package libbiojava5-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava5-java' in '../libbiojava5-java_5.4.0+dfsg-5_all.deb'. -dpkg-deb: building package 'libbiojava5-java-doc' in '../libbiojava5-java-doc_5.4.0+dfsg-5_all.deb'. +dpkg-deb: generazione del pacchetto "libbiojava5-java-doc" in "../libbiojava5-java-doc_5.4.0+dfsg-5_all.deb". +dpkg-deb: generazione del pacchetto "libbiojava5-java" in "../libbiojava5-java_5.4.0+dfsg-5_all.deb". dpkg-genbuildinfo --build=binary -O../biojava5-live_5.4.0+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../biojava5-live_5.4.0+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -14369,12 +14405,14 @@ 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/2546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2546/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/6600 and its subdirectories -I: Current time: Sat Jan 13 05:16:55 -12 2024 -I: pbuilder-time-stamp: 1705166215 +I: removing directory /srv/workspace/pbuilder/2546 and its subdirectories +I: Current time: Sun Jan 14 08:33:27 +14 2024 +I: pbuilder-time-stamp: 1705170807