Diff of the two buildlogs:
--
--- b1/build.log 2024-01-23 22:36:35.789604108 +0000
+++ b2/build.log 2024-01-23 23:23:41.063581606 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Mon Feb 24 16:15:08 -12 2025
-I: pbuilder-time-stamp: 1740456908
+I: Current time: Wed Jan 24 12:36:39 +14 2024
+I: pbuilder-time-stamp: 1706049399
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
@@ -41,51 +41,83 @@
dpkg-source: info: applying remove_tests_needing_junitx.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/25528/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos2-i386.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Jan 23 22:36 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='i386'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
- DISTRIBUTION='bookworm'
- HOME='/root'
- HOST_ARCH='i386'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+ BASH_VERSION='5.2.15(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=i386
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 '
+ DIRSTACK=()
+ DISTRIBUTION=bookworm
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=i686
+ HOST_ARCH=i386
IFS='
'
- INVOCATION_ID='acd136b92a65462499bcd7dae4c23fb4'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- LD_LIBRARY_PATH='/usr/lib/libeatmydata'
- LD_PRELOAD='libeatmydata.so'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='25528'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=d01c76a4006f4bbab47b71844d560762
+ LANG=C
+ LANGUAGE=de_CH:de
+ LC_ALL=C
+ LD_LIBRARY_PATH=/usr/lib/libeatmydata
+ LD_PRELOAD=libeatmydata.so
+ MACHTYPE=i686-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=3141
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/pbuilderrc_YPTv --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.dsc'
- SUDO_GID='112'
- SUDO_UID='107'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://85.184.249.68:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/pbuilderrc_diog --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ilWGygNb/b2 --logfile b2/build.log biojava6-live_6.1.0+dfsg-4.dsc'
+ SUDO_GID=112
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://78.137.99.97:3128
I: uname -a
- Linux ionos6-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
@@ -143,15 +175,15 @@
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
- -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts
+ -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
- lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
+ lrwxrwxrwx 1 root root 9 Jan 23 22:36 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 23 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
- -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile
+ -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
@@ -171,7 +203,7 @@
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
-I: user script /srv/workspace/pbuilder/25528/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -664,7 +696,7 @@
Get: 395 http://deb.debian.org/debian bookworm/main i386 maven all 3.8.7-1 [18.9 kB]
Get: 396 http://deb.debian.org/debian bookworm/main i386 maven-repo-helper all 1.11 [142 kB]
Get: 397 http://deb.debian.org/debian bookworm/main i386 maven-debian-helper all 2.6.3 [108 kB]
-Fetched 348 MB in 6s (56.5 MB/s)
+Fetched 348 MB in 22s (15.8 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:i386.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 18156 files and directories currently installed.)
@@ -2457,7 +2489,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-4_source.changes
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for bookworm
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/biojava6-live-6.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava6-live_6.1.0+dfsg-4_source.changes
dpkg-buildpackage: info: source package biojava6-live
dpkg-buildpackage: info: source version 6.1.0+dfsg-4
dpkg-buildpackage: info: source distribution unstable
@@ -2472,8 +2508,8 @@
mh_unpatchpoms -plibbiojava6-java
jh_clean
debian/rules override_dh_clean
-make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
-dpkg: warning: --compare-versions used with obsolete relation operator '>'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten
+dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet
dh_clean
rm -rf target
rm -rf biojava-*/target
@@ -2481,15 +2517,15 @@
-exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print
rm -rf biojava-forester
rm -rf biojava-jcolorbrewer
-make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen
debian/rules binary
dpkg: warning: --compare-versions used with obsolete relation operator '>'
dh binary --with javahelper
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
-make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
-dpkg: warning: --compare-versions used with obsolete relation operator '>'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten
+dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet
# Creating the directories for forester and jcolorbrewer, with symlinks.
mkdir -p biojava-forester/src/main/java/
cp -a forester/org biojava-forester/src/main/java/
@@ -2500,11 +2536,11 @@
sed 's/\(VERSION_PACKAGE\)/\16.1.0+dfsg/; s/VERSION_PACKAGE\(.*\)+dfsg[0-9]*/\1/' debian/poms/pomJcolorbrewer.xml > biojava-jcolorbrewer/pom.xml
dh_auto_configure
mh_patchpoms -plibbiojava6-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo
-make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen
jh_linkjars
debian/rules override_dh_auto_build
-make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
-dpkg: warning: --compare-versions used with obsolete relation operator '>'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten
+dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet
# Insert the correct JSON_SIMPLE_PACKAGE in the code.
find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \
-exec sed -i.json-simple \
@@ -2607,30 +2643,30 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
+[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.exceptions...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
+[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
[WARNING] Loading source files for package org.biojava.nbio.core.util...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.views...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence.location.template...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.views...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template...
[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.storage...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.compound...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.edits...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader...
-[WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
-[WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
-[WARNING] Loading source files for package org.biojava.nbio.core.exceptions...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io...
-[WARNING] Loading source files for package org.biojava.nbio.core.search.io.blast...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template...
+[WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -3196,220 +3232,220 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/serialized-form.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/UncompressFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/DemoSixFrameTranslation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/demo/class-use/ParseFastaFileDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/ScaledSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SimpleSubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/SubstitutionMatrixHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/DefaultAAIndexProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAindexFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/class-use/AAIndexFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/class-use/SimpleProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SubstitutionMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfileView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/SequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/ProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/AlignedSequence.Step.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableSequencePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/Profile.StringFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableAlignedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/class-use/MutableProfilePair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/CompoundNotFoundException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/TranslationException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/ParserException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Hsp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/SearchIO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/ResultFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/class-use/Result.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHitBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastHspBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastResultBuilder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastTabularParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/class-use/BlastXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/CRC64Checksum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FileDownloadUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/ConcurrencyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SoftHashMap.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Equals.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/UncompressInputStream.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/Hashcoder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/FlatFileCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/PrettyXMLWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/XMLHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/StringManipulationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TranscriptSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/TaxonomyID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ProteinSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/AccessionID.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/ArrayListProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/SequenceFileProxyLoader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/UniprotProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/StringProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/class-use/GenbankProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Substitute.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Insert.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.Delete.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/class-use/Edit.AbstractEdit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ReversedSequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DBReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/Qualifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/DatabaseReferenceInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureRetriever.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QualityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeaturesKeyWordInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/FeatureDbReferenceInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/TextFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/QuantityFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/class-use/AbstractFeature.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Frame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/RNAToAminoAcidTranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.Codon.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/TranscriptionEngine.Builder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OneOfLocation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.GroupLocation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.OrderLocation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcLocations.BondLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimplePoint.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/InsdcParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/LocationHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SequenceLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/SimpleLocation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/class-use/FuzzyPoint.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Point.Resolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AccesionedLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/Location.Tools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/class-use/AbstractLocation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/AbstractReference.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/ReferenceInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/class-use/GenbankReference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ComplementSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/WindowedSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/RnaSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/class-use/ReversedSequenceView.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceMixin.SequenceIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundTranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/CompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractSequence.AnnotationType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceProxyView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompoundTranslator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Compound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ComplementCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/SequenceView.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Sequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/AbstractNucleotideCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/ProxySequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/LightweightProfile.StringFormat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/class-use/Accessioned.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/DNACompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNARNAHybridCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityDNACompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AminoAcidCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/AmbiguityRNACompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/RNACompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/NucleotideCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/ABITracerCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/class-use/CodonCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/BitSequenceReader.BitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/JoiningSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/TwoBitSequenceReader.TwoBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/FourBitSequenceReader.FourBitArrayWorker.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/ArrayListSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SequenceAsStringHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/class-use/SingleCompoundSequenceReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericInsdcHeaderFormat.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/CasePreservingProteinSequenceCreator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/IUPACParser.IUPACTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyRNASequenceCreator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyProteinSequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericFastaHeaderFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReaderHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/BufferedReaderBytesRead.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaGeneWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/RNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriterHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/PlainFastaHeaderParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriterHelper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenericGenbankHeaderParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReaderHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FileProxyDNASequenceCreator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/GenbankSequenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/DNASequenceCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/FastaSequenceParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ABITrace.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/class-use/ProteinSequenceCreator.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/SequenceParserInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/class-use/FastaHeaderFormatInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/IOUtils.ReaderProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/class-use/ClasspathResource.html...
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@@ -3484,50 +3520,50 @@
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] Loading source files for package org.forester.datastructures...
-[WARNING] Loading source files for package org.forester.application...
-[WARNING] Loading source files for package org.forester.go...
-[WARNING] Loading source files for package org.forester.go.etc...
+[WARNING] Loading source files for package org.forester.test...
+[WARNING] Loading source files for package org.forester.test.examples...
+[WARNING] Loading source files for package org.forester.rio...
+[WARNING] Loading source files for package org.forester.phylogeny.iterators...
+[WARNING] Loading source files for package org.forester.phylogeny.data...
+[WARNING] Loading source files for package org.forester.phylogeny...
+[WARNING] Loading source files for package org.forester.phylogeny.factories...
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[WARNING] Loading source files for package org.forester.archaeopteryx.phylogeny.data...
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[WARNING] Loading source files for package org.forester.archaeopteryx.tools...
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+[WARNING] Loading source files for package org.forester.evoinference.parsimony...
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+[WARNING] Loading source files for package org.forester.applications...
+[WARNING] Loading source files for package org.forester.ws.hmmer...
+[WARNING] Loading source files for package org.forester.ws.seqdb...
+[WARNING] Loading source files for package org.forester.ws.wabi...
+[WARNING] Loading source files for package org.forester.application...
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[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -4117,409 +4153,409 @@
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.PHYLOGENY_GRAPHICS_TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.NODE_LABEL_DIRECTION.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.CLADOGRAM_TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeColorSet.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxA.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.PHYLOGENY_GRAPHICS_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.NODE_LABEL_DIRECTION.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.CLADOGRAM_TYPE.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/BasicPhylogeniesWebserviceClient.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.WsPhylogenyFormat.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/BasicPhylogeniesWebserviceClient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhyloInferenceDialog.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferenceOptions.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/SequenceDataRetriver.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.MSA_PRG.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/Blast.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/MappingResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/SupportCount.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/BasicSpecies.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/Species.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_shared_chars.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/reinv_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aaa.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2graphics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/map_lengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/core_chars.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/wiki_examples.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/set_comparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_distances.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_shared_chars.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/wiki_examples.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/inverted_dcs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aaa.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/shared_chars_in_ext_nodes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_distances.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/tax_code_cleaner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/aa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2graphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/simple_node_processor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2coloredgraphics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/get_subtree_specific_chars.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/simple_node_processor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/AsciiHistogram.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/EasyWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/DescriptiveStatistics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/CommandLineArguments.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyColors.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTableParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.DescendingIntComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/GeneralTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/CommandProcessBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicDescriptiveStatistics.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/WindowsUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ExternalProgram.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.PhylogeneticTreeFormats.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/BasicSpecies.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/species/class-use/Species.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/applications/class-use/map_lengths.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/hmmer/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_RANK.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_NAME_CLASS.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.RANKS.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/RestUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/phyloxml_converter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/decoratorX.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/rio.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/support_transfer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/goac.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/support_statistics.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gsdi.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/count_support.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/phylostrip.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/fasta_split.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/mcc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam_go.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pccx.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/confadd.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/dom_dup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/annotator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/surfacing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/nj.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2go.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/table2fasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/msa_compactor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/decorator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/check_fasta.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/meta_ontologizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/RandomThing.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/AbstractRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/ResidueRenderer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Time.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/HmmerRest.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.DoublePointer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Test.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/DevelopmentTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/MsaRenderer.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/ProteinId.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Protein.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicDomain.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/Domain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/protein/class-use/ProteinId.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/TestPccx.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/TestPccx.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ScoringMethodForExternalNode.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BasicExternalNodeBasedCoverageExtender.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ModelingUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverageMethodOptions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/Coverage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/LogBranchLengthBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculationMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/Mapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoParser.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaFormatException.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/BasicMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/ClustalOmega.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/Chart.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/BasicSequence.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/TestGSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDII.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/GSDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.TaxonomyComparisonBase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIutil.ALGORITHM.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDIException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/sdi/class-use/SDI.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusCharactersParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusPhylogeniesParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/PaupLogParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusConstants.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/class-use/NexusBinaryStatesMatrixParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/FastaParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.ReturnType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmPfamOutputParser.FilterType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/GeneralMsaParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/SymmetricalDistanceMatrixParser.InputMatrixType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/IteratingPhylogenyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.ReturnType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/HmmscanPerDomainTableParser.FilterType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/class-use/PhylogenyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/IdentifierParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DomainArchitectureParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ReferenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AccessionParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceRelationParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DateParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BinaryCharactersParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/DistributionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ColorParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ConfidenceParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/UriParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PolygonParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PointParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/ProteinDomainParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/EventParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PhylogenyDataPhyloXmlParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/SequenceParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/PropertyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/TaxonomyParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/BranchWidthParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/XmlElement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlDataFormatException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/class-use/PhyloXmlParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/class-use/AnnotationParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXParser.TAXONOMY_EXTRACTION.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXtags.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/class-use/NHXFormatException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/ParserUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/util/class-use/PhylogenyParserException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlMapping.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/parsers/tol/class-use/TolXmlHandler.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/SequenceWriter.SEQ_FORMAT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhylogenyWriter.FORMAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/io/writers/class-use/PhyloXmlNodeWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Hello3d.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Time.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/MsaRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/Test.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/neTest.DoublePointer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/DevelopmentTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/HmmerRest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/AbstractRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/ResidueRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/development/class-use/RandomThing.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
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@@ -4612,12 +4648,12 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
[WARNING] Loading source files for package org.biojava.nbio.phylo...
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-[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
@@ -4820,75 +4856,71 @@
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:31: warning: Tag @link: reference not found: Profile
[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
[WARNING] ^
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:31: warning: Tag @link: reference not found: Profile
[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
[WARNING] ^
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html...
+[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:32: warning: Tag @link: reference not found: Profile
+[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
+[WARNING] ^
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
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[WARNING] * Defines an {@link Aligner} for a pair of {@link Profile}s.
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[WARNING] * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
[WARNING] ^
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[WARNING] Javadoc Warnings
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.FatCatStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPPostProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPCalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPChainer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FCAlignHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/AFPOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/SigEva.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/StructureAlignmentOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatAligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/calc/class-use/FatCatParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairsMessage.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/PdbPairXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/MultipleAlignmentXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/xml/class-use/AFPChainFlipper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/PdbPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/client/class-use/StructureName.Source.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AfpChainWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/model/class-use/AFPChain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlternativeAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Gotoh.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AligNPE.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/StrCompAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentJoiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/FragmentPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AltAligComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/AlignmentProgressListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/pairwise/class-use/Alignable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/ScoresCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsemble.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/AbstractScoresCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/MultipleAlignmentEnsembleImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/Block.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSetImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/class-use/BlockSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcOptimizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/mc/class-use/MultipleMcMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/ReferenceSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/CoreSuperimposer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/multiple/util/class-use/MultipleAlignmentWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AlignUtils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/JointFragments.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IdxComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/IndexPair.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/AligMatEl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/helper/class-use/GapArray.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3Daligner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/seq/class-use/SmithWaterman3DParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlign.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsRelation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/quaternary/class-use/QsAlignResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/UserConfiguration.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/SynchronizedOutFile.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPAlignmentDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/URLConnectionTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AtomCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CliTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AlignmentTools.IdentityMap.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/RotationAxis.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/AFPChainScorer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ConfigurationException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/ResourceManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/util/class-use/CollectionTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/UserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeParameters.ScoringStrategy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/MatrixListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/StartupParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/OptimalCECPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCalculatorEnhanced.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/AbstractUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/ConfigStrucAligParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPMain.CPRange.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECalculator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeSideChainUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/GuiWrapper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CECPParameters.DuplicationHint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BioAssemblyIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Mutator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Site.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/EntityInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ExperimentalTechnique.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/DatabasePDBRevRecord.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/JournalArticle.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/URLIdentifier.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcidImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondImpl.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PassthroughIdentifier.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBHeader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SeqMisMatchImpl.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Element.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/GroupIterator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomPositionMap.GroupMatcher.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueRangeAndLength.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Atom.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomImpl.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Group.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/BondType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AugmentedResidueRange.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PdbId.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ChainImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/SubstructureIdentifier.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/DatabasePDBRevRecord.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/ResidueNumber.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/AtomIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StandardAminoAcid.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/StructureImpl.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/Author.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/class-use/PDBRecord.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/EigenvalueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/QRDecomposition.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/SingularValueDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/CholeskyDecomposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/jama/class-use/Matrix.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/GroupContactSet.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/BoundingBox.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/contact/class-use/AtomContactSet.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/xtal/io/class-use/TransfAlgebraicAdapter.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ReducedChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompDescriptor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ResidueType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/AllChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemComp.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/chem/class-use/ChemCompGroupFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/LocalProteinDomainParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/DomainProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/class-use/SerializableCache.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ClusterDomains.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/ShortSegmentRemover.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutValues.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/GetDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Segment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPDistanceMatrix.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Domain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/Cut.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutSites.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/CutDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/PDPParameters.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/domain/pdp/class-use/SegmentComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodInstallation.EcodParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/ecod/class-use/EcodDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPosition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositions.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/MomentsOfInertia.SymmetryClass.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/CalcPoint.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionSVD.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionAbstract.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQCP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/SuperPositionQuat.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/Matrices.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/geometry/class-use/UnitQuaternions.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/TertiaryBasePairParameters.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/MismatchedBasePairParameters.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/basepairs/class-use/BasePairParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/Subunit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitExtractor.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClustererParameters.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitClusterer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cluster/class-use/SubunitCluster.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ProteinComplexSignature.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/misc/class-use/ChainSignature.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixExtender.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.StringOverflowStrategy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Rotation.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SymmetryPerceptionMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelixLayers.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryResults.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySubunits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/PermutationGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryParameters.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Helix.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryScores.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSuperpositionScorer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/SystematicSolver.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/RotationSolver.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/C2RotationSolver.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/HelicalRepeatUnit.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetryDetector.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/QuatSymmetrySolver.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/core/class-use/Stoichiometry.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmIterative.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/ResidueGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.SymmetryType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.RefineMethod.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CESymmParameters.OrderDetectorMethod.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryAxes.Axis.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmetryRefiner.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/RefinerFailedException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/AngleOrderDetectorPlus.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SymmOptimizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/CeSymmResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentRefiner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/OrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/GraphComponentOrderDetector.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/SphereSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Prism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/IcosahedralSampler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Icosahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/DistanceBox.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Polyhedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/RectangularPrism.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Octahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/geometry/class-use/Tetrahedron.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/RotationAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/AxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/axis/class-use/HelixAxisAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/BlastClustReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/SymmetryTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PermutationGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/utils/class-use/PowerSet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/symmetry/internal/class-use/SequenceFunctionRefiner.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/DSSPParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/Ladder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BetaBridge.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/HBond.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucState.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucElement.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/BridgeType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/secstruc/class-use/SecStrucCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathSegment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFactory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDatabase.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathNode.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathInstallation.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/cath/class-use/CathFragment.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/CartesianProduct.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyTransformation.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BiologicalAssemblyBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OperatorResolver.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/BioAssemblyInfo.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/quaternary/class-use/OrderedPair.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaStructureParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/GroupToSDF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/ChargeAdder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileReader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBParseException.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureSequenceMatcher.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureFiletype.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaAFPChainConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileParsingParameters.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/MMTFFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBBioAssemblyParser.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/PDBFileParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/EntityFinder.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CifFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureProvider.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.FetchBehavior.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/LocalPDBDirectory.ObsoleteBehavior.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BcifFileReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SeqRes2AtomAligner.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FastaAFPChainConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/SSBondImpl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/FileConvert.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/StructureIOFile.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/CAConverter.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/class-use/BondMaker.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureReader.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfStructureWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfSummaryDataBean.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/mmtf/class-use/MmtfActions.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/util/class-use/PDBTemporaryStorageUtils.LinkRecord.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsXMLParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainEntry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsResidue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/sifts/class-use/SiftsChainToUniprotMapping.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/AbstractCifFileSupplier.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConsumerImpl.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/CifStructureSupplierImpl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/io/cif/class-use/MetalBondConverter.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatUserArgumentProcessor.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/fatcat/class-use/FatCatRigid.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeUserArgumentProcessor.CeStartupParams.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/align/ce/class-use/CeCPUserArgumentProcessor.CeCPStartupParams.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoMmtfWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/class-use/DemoCeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/ScopDescription.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/scop/class-use/LocalScopDatabase.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/demo/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure/target/apidocs/org/biojava/nbio/structure/package-use.html...
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@@ -6434,11 +6470,11 @@
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/serialized-form.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/DivergingColorPalettePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPanelSelectionModel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/PaletteIcon.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/QualitativeColorPalettePanel.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/ColorPaletteChooserDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/class-use/SequentialColorPalettePanel.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-jcolorbrewer/target/apidocs/org/jcolorbrewer/ui/package-use.html...
@@ -6493,18 +6529,18 @@
[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.
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[WARNING] Loading source files for package org.biojava.nbio.structure.gui.util.color...
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-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.structure.symmetry.jmolScript...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -6705,137 +6741,137 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/package-tree.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/serialized-form.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoQuatSymmetryJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoRotationAxis.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/AlignmentGuiDemo.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ParameterGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DisplayAFP.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AboutDialog.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SystemInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JMatrixPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/BiojavaJmol.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/WrapLayout.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/RenderStyle.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/ScaleableMatrixPanel.GradientRenderer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/StructureViewer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SequenceDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/Selection.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/class-use/SelectionImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlternativeAlignmentFrame.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBDirPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java:46: warning: invalid input: '&'
[WARNING] /** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
[WARNING] ^
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBServerPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopSelectPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignedPosition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/CoordManager.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/MenuCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/PDBUploadPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/class-use/ScopInstallationInstance.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/DefaultMatrixMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/SqrtColorMapper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LinearColorInterpolator.InterpolationDirection.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/LogColorMapper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientMapper.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/HSVColorSpace.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ContinuousColorMapperTransform.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/GradientPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorUtils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/gui/util/color/class-use/ColorInterpolator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/webstart/class-use/WebStartMain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/AutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalculationRunnable.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MemoryMonitor.Surface.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyAlignmentLoadListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfoParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AbstractAlignmentJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/JmolPanel.JmolLoggerAdapter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/AtomInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AFPChainCoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanelMouseMotionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoAlignmentFromFasta.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoStructureFromFasta.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoMultipleMC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/ShowStructureInJmol.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoSW3DAligner.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoFATCAT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/CookBook.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoCeSymm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/class-use/DemoShowBiolAssembly.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/demo/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-structure-gui/target/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/package-use.html...
@@ -6905,17 +6941,17 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
+[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename...
[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.twobit...
[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.cytoband...
[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.geneid...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.genename...
-[WARNING] Loading source files for package org.biojava.nbio.genome.parsers.gff...
[WARNING] Loading source files for package org.biojava.nbio.genome...
+[WARNING] Loading source files for package org.biojava.nbio.genome.uniprot...
+[WARNING] Loading source files for package org.biojava.nbio.genome.homology...
+[WARNING] Loading source files for package org.biojava.nbio.genome.query...
[WARNING] Loading source files for package org.biojava.nbio.genome.util...
[WARNING] Loading source files for package org.biojava.nbio.genome.io.fastq...
-[WARNING] Loading source files for package org.biojava.nbio.genome.query...
-[WARNING] Loading source files for package org.biojava.nbio.genome.uniprot...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7008,52 +7044,52 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Feature.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Writer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/Location.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePosition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneChromosomePositionParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneNamesParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/twobit/class-use/TwoBitFacade.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/Cytoband.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/CytobandParser.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/cytoband/class-use/StainType.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/GeneFeatureHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/class-use/App.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/BlastHomologyHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/class-use/GFF3FromUniprotBlastHits.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/SplitFasta.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ChromosomeMappingTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/util/class-use/ProteinMappingTools.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqTools.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/Fastq.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/StreamListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqVariant.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqBuilder.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqWriter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/IlluminaFastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/FastqReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/OutputHitsGFF.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/query/class-use/BlastXMLQuery.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/uniprot/class-use/UniprotToFasta.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/ParseListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SolexaFastqWriter.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/homology/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-genome/target/apidocs/org/biojava/nbio/genome/io/fastq/package-use.html...
@@ -7113,10 +7149,10 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
[WARNING] Loading source files for package org.biojava.nbio.protmod...
-[WARNING] Loading source files for package org.biojava.nbio.protmod.io...
[WARNING] Loading source files for package org.biojava.nbio.protmod.structure...
+[WARNING] Loading source files for package org.biojava.nbio.protmod.io...
+[WARNING] Loading source files for package org.biojava.nbio.phosphosite...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7200,30 +7236,30 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/Component.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationOccurrenceType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationLinkage.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationConditionImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationImpl.Builder.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCondition.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModificationRegistry.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ProteinModification.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/class-use/ModificationCategory.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtomLinkage.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ProteinModificationIdentifier.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompound.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/ModifiedCompoundImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureUtil.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureAtom.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/structure/class-use/StructureGroup.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ProteinModificationXmlReader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ModifiedCompoundXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/ComponentXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureGroupXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/class-use/StructureAtomXMLConverter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Site.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/class-use/Dataset.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/phosphosite/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-modfinder/target/apidocs/org/biojava/nbio/protmod/io/package-use.html...
@@ -7273,10 +7309,10 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.ws.hmmer...
+[WARNING] Loading source files for package demo...
[WARNING] Loading source files for package org.biojava.nbio.ws.alignment...
[WARNING] Loading source files for package org.biojava.nbio.ws.alignment.qblast...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.ws.hmmer...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7323,26 +7359,26 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentService.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/class-use/RemotePairwiseAlignmentOutputProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputAlignmentFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/MapToStringTransformer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastOutputProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastMatrixEnum.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastJob.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastAlignmentProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputParameterEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastAlignmentParameterEnum.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastOutputFormatEnum.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/NCBIQBlastService.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/NCBIQBlastServiceDemo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/class-use/HmmerDemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/class-use/BlastProgramEnum.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerScan.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerResult.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/HmmerDomain.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/hmmer/class-use/RemoteHmmerScan.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/demo/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ws/target/apidocs/org/biojava/nbio/ws/alignment/qblast/package-use.html...
@@ -7392,9 +7428,9 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.ronn...
-[WARNING] Loading source files for package org.biojava.nbio.data.sequence...
[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.data.sequence...
+[WARNING] Loading source files for package org.biojava.nbio.ronn...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7421,20 +7457,20 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Timer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/Jronn.Range.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/RonnConstraint.Threshold.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonnModel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/SequenceUtil.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/class-use/FastaSequence.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/class-use/PredictDisorder.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ORonn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Model.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/ModelLoader.Threshold.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/class-use/NullOutputStream.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/demo/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/data/sequence/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-protein-disorder/target/apidocs/org/biojava/nbio/ronn/package-use.html...
@@ -7485,11 +7521,11 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
+[WARNING] Loading source files for package demo...
[WARNING] Loading source files for package org.biojava.nbio.aaproperties...
[WARNING] Loading source files for package org.biojava.nbio.aaproperties.xml...
[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat...
[WARNING] Loading source files for package org.biojava.nbio.aaproperties.profeat.convertor...
-[WARNING] Loading source files for package demo...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7624,25 +7660,26 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-summary.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/constant-values.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptideProperties.SingleLetterAACode.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Constraints.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/PeptidePropertiesImpl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/CommandPrompt.PropertyName.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/AminoAcidProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/Utils.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/class-use/IPeptideProperties.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Isotope.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Name2Count.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/SchemaGenerator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidComposition.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/Element.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/AminoAcidCompositionTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ModifiedAminoAcidCompoundSet.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/ElementTable.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/CaseFreeAminoAcidCompoundSet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/xml/class-use/MyValidationEventHandler.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/IProfeatProperties.DISTRIBUTION.html...
[WARNING] /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java:106: warning: invalid input: '&'
@@ -7722,15 +7759,14 @@
[WARNING] ^
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatProperties.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/class-use/ProfeatPropertiesImpl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Charge.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarizability.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Polarity.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2Hydrophobicity.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SolventAccessibility.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/class-use/BioJavaAADemo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2NormalizedVanDerWaalsVolume.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convert2SecondaryStructure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/convertor/class-use/Convertor.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/demo/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-aa-prop/target/apidocs/org/biojava/nbio/aaproperties/profeat/package-use.html...
@@ -7804,13 +7840,13 @@
[WARNING] Javadoc Warnings
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
-[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
+[WARNING] Loading source files for package org.biojava.nbio.survival.data...
[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.figure...
+[WARNING] Loading source files for package org.biojava.nbio.survival.kaplanmeier.metadata...
[WARNING] Loading source files for package org.biojava.nbio.survival.cox...
+[WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators...
[WARNING] Loading source files for package org.biojava.nbio.survival.cox.stats...
[WARNING] Loading source files for package org.biojava.nbio.survival.cox.matrix...
-[WARNING] Loading source files for package org.biojava.nbio.survival.cox.comparators...
-[WARNING] Loading source files for package org.biojava.nbio.survival.data...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -7887,57 +7923,57 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/GroupResults.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatusSelect.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/NumbersAtRiskPanel.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfLower.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.ConfType.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Error.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/SurvFitKM.Method.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KMFigureInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/KaplanMeierFigure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/ExpressionFigure.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/figure/class-use/CensorStatus.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MetaDataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/ClinicalMetaDataOutcome.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/DiscreteQuantizerInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/kaplanmeier/metadata/class-use/MeanQuantizer.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/ResidualsCoxph.Type.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxScore.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCC.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/StrataInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvFitInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTest.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/WaldTestInfo.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxCoefficient.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxR.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMart.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/SurvivalInfoIndex.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxVariables.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxMethod.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/RiskInfo.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/class-use/CoxHelper.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/AgScore.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/ChiSq.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Cholesky2.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/stats/class-use/Chsolve2.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/StdArrayIO.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/MeanModelComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesVariableComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxVariablesOverallModelFitComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/SurvivalInfoValueComparator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/class-use/CoxComparatorInterface.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/ChangeValue.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/WorkSheet.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/HeaderInfo.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/data/class-use/CompactCharSequence.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/class-use/Matrix.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/comparators/package-use.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-survival/target/apidocs/org/biojava/nbio/survival/cox/matrix/package-use.html...
@@ -7997,11 +8033,11 @@
[WARNING] warning: The -footer option is no longer supported and will be ignored.
[WARNING] It may be removed in a future release.
[WARNING] Loading source file /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/src/main/java/package-info.java...
+[WARNING] Loading source files for package demo...
[WARNING] Loading source files for package org.biojava.nbio.ontology...
-[WARNING] Loading source files for package org.biojava.nbio.ontology.io...
[WARNING] Loading source files for package org.biojava.nbio.ontology.utils...
[WARNING] Loading source files for package org.biojava.nbio.ontology.obo...
-[WARNING] Loading source files for package demo...
+[WARNING] Loading source files for package org.biojava.nbio.ontology.io...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
@@ -8098,47 +8134,47 @@
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/utils/package-tree.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/constant-values.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/serialized-form.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/App.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/demo/class-use/ParseGO.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyFactory.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Term.Impl.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyTerm.Impl.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/IntegerOntology.IntTerm.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/AbstractTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/RemoteTerm.Impl.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Synonym.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/OntologyOps.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/InvalidTermException.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/biojava-ontology/target/apidocs/org/biojava/nbio/ontology/class-use/Ontology.Impl.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorDn.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorC1.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorPointGroup.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryGui.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/gui/class-use/SymmetryDisplay.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/BrowserOpener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/JNLPProxy.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/AligUIManager.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/DefaultAutoSuggestProvider.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/scop/class-use/ScopMirror.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentJmolDisplay.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureAlignmentDisplay.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MenuCreator.DotPlotListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MySaveFileListener.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyDistMaxListener.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentGUI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentTextPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MultipleAlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/DotPlotPanel.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/StructureLoaderThread.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyTableRowSorter.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ConfigPDBInstallPanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ChooseDirAction.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/JPrintPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/HelpDialog.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentCalc.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyOpenPdbFileListener.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/SelectPDBPanel.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/AlignmentGui.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/ShowPDBIDListener.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/class-use/MyExportListener.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/JAutoSuggest.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/autosuggest/class-use/SCOPAutoSuggestProvider.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MultipleAlignmentJmol.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/StructureAlignmentJmol.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/MyJmolStatusListener.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/jmol/class-use/RasmolCommandListener.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanel.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleStatusDisplay.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAligPanel.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/MultipleAlignmentCoordManager.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/AligPanelMouseMotionListener.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/geneid/class-use/GeneIDXMLReader.html...
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-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/ChromPos.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/genename/class-use/GeneName.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/gui/aligpanel/class-use/StatusDisplay.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/align/webstart/class-use/ConfigXMLHandler.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/class-use/JmolViewerImpl.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/AlignmentPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/events/class-use/JmolAlignedPositionListener.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/StructurePairSelector.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceScalePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/AlignmentCalc.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SelectMultiplePanel.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/gui/util/class-use/SequenceMouseListener.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorH.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorI.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGenerator.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/ColorConverter.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorT.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/structure/symmetry/jmolScript/class-use/JmolSymmetryScriptGeneratorCn.html...
+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureI.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneMarkGTFReader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GCStats.html...
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+[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/LocIterator.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GFF3Reader.html...
[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureList.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/GeneIDGFF2Reader.html...
-[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/parsers/gff/class-use/FeatureHelper.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/class-use/App.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqReader.html...
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[WARNING] Generating /build/reproducible-path/biojava6-live-6.1.0+dfsg/target/site/apidocs/org/biojava/nbio/genome/io/fastq/class-use/SangerFastqWriter.html...
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@@ -12370,28 +12406,28 @@
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
-[INFO] biojava ............................................ SUCCESS [ 25.759 s]
-[INFO] biojava-core ....................................... SUCCESS [ 9.438 s]
-[INFO] biojava-forester ................................... SUCCESS [ 12.138 s]
-[INFO] biojava-alignment .................................. SUCCESS [ 3.147 s]
-[INFO] biojava-structure .................................. SUCCESS [ 12.404 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.583 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [ 4.893 s]
-[INFO] biojava-genome ..................................... SUCCESS [ 3.002 s]
-[INFO] biojava-modfinder .................................. SUCCESS [ 2.163 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 1.854 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 1.850 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [ 2.382 s]
-[INFO] biojava-survival ................................... SUCCESS [ 2.513 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 2.239 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.120 s]
+[INFO] biojava ............................................ SUCCESS [ 46.534 s]
+[INFO] biojava-core ....................................... SUCCESS [ 18.783 s]
+[INFO] biojava-forester ................................... SUCCESS [ 21.499 s]
+[INFO] biojava-alignment .................................. SUCCESS [ 6.010 s]
+[INFO] biojava-structure .................................. SUCCESS [ 23.303 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 3.427 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 8.806 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 5.437 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 3.872 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 3.100 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 2.770 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [ 4.168 s]
+[INFO] biojava-survival ................................... SUCCESS [ 4.321 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 3.803 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 1.933 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 01:27 min
-[INFO] Finished at: 2025-02-25T04:17:45Z
+[INFO] Total time: 02:39 min
+[INFO] Finished at: 2024-01-23T22:41:13Z
[INFO] ------------------------------------------------------------------------
-[0m[0mmake[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
+[0m[0mmake[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen
dh_auto_test
/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/biojava6-live-6.1.0\+dfsg/debian/maven-repo --batch-mode test
OpenJDK Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
@@ -12451,295 +12487,295 @@
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
+[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.fasta.TestFASTAReader
-[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.218 s - in org.biojava.nbio.core.util.SequenceToolsTest
-[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
+[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.util.TestUncompressInputStream
-[INFO] Running org.biojava.nbio.core.util.EqualsTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.core.util.EqualsTest
-[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.92 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
-[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.804 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.259 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
-[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.224 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.core.util.SoftHashMapTest
-[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.986 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 s - in org.biojava.nbio.core.util.FlatFileCacheTest
-[INFO] Running org.biojava.nbio.core.util.HashcoderTest
-[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.core.util.HashcoderTest
-[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.2 s - in org.biojava.nbio.core.util.XMLHelperTest
-[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
-
- 22
- 43.22
- some text
- 2021-08-15
-
-
+[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.404 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Running org.biojava.nbio.core.search.io.HspTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
-[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
-[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
+getAlignment
+hashCode
+equals
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.core.search.io.HspTest
+[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
-[INFO] Running org.biojava.nbio.core.sequence.DNATest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.34 s - in org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+createObjects
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.core.sequence.DNATest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
+getFileExtensions
+setFile
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.561 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
+[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+getFileExtensions
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.core.sequence.location.LocationTest
+setFile
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.1 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
+[INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.803 s - in org.biojava.nbio.core.util.StringManipulationHelperTest
+[INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
-[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.006 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
+[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.3 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest
+[INFO] Running org.biojava.nbio.core.util.XMLHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
-[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.582 s - in org.biojava.nbio.core.util.XMLHelperTest
+[INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest
+
+ 22
+ 43.22
+ some text
+ 2021-08-15
+
+
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.core.sequence.RNASequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.421 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest
+[INFO] Running org.biojava.nbio.core.util.SoftHashMapTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.4 s - in org.biojava.nbio.core.util.SoftHashMapTest
+[INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.578 s - in org.biojava.nbio.core.util.FlatFileCacheTest
+[INFO] Running org.biojava.nbio.core.util.EqualsTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.469 s - in org.biojava.nbio.core.util.EqualsTest
+[INFO] Running org.biojava.nbio.core.util.HashcoderTest
+[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.128 s - in org.biojava.nbio.core.util.HashcoderTest
+[INFO] Running org.biojava.nbio.core.util.SequenceToolsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
-[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
+[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.551 s - in org.biojava.nbio.core.util.SequenceToolsTest
+[INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.biojava.nbio.core.sequence.EditSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.422 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest
+[INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 s - in org.biojava.nbio.core.util.CRC64ChecksumTest
+[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.core.sequence.SequenceViewTest
-[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.core.util.TestUncompressInputStream
+[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.8 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 s - in org.biojava.nbio.core.sequence.ExonComparatorTest
+[INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 s - in org.biojava.nbio.core.sequence.RNASequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.core.sequence.views.WindowViewTests
+[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.339 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.DNATest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.101 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 s - in org.biojava.nbio.core.sequence.DNATest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
-[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest
+[INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
-[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.728 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.location.LocationParserTest
+[INFO] Running org.biojava.nbio.core.sequence.location.LocationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
-[INFO] Running org.biojava.nbio.core.sequence.StrandTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.StrandTest
-[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.core.sequence.location.LocationTest
+[INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 s - in org.biojava.nbio.core.sequence.TranslationTest
-[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.TranslationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.699 s - in org.biojava.nbio.core.sequence.TranslationTest
+[INFO] Running org.biojava.nbio.core.sequence.StrandTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.core.sequence.StrandTest
[INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
-[INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest
+[INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.196 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.nbio.core.sequence.SequenceViewTest
+[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest
-[INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.core.sequence.ExonSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
-[INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.EditSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.065 s - in org.biojava.nbio.core.sequence.GeneSequenceTest
-[INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
+[INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest
+[INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest
+[INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.sequence.TestSequenceEquals
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.186 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.158 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest
-[INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest
+[INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest
+[INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.304 s - in org.biojava.nbio.core.sequence.io.ABITracerTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.core.alignment.SimpleProfileTest
-[INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest
-[INFO] Running org.biojava.nbio.core.search.io.HspTest
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.512 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getAlignment
-hashCode
-equals
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.core.search.io.HspTest
-[INFO] Running org.biojava.nbio.core.search.io.SearchIOTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest
+[INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.038 s - in org.biojava.nbio.core.search.io.SearchIOTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-createObjects
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest
+[INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-getFileExtensions
-setFile
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.79 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest
-[INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-getFileExtensions
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest
+[INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-setFile
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.017 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest
-[INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet
+[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.115 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest
+[INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.core.fasta.TestFASTAReader
[INFO]
[INFO] Results:
[INFO]
@@ -12790,86 +12826,86 @@
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator
[INFO] Running org.biojava.nbio.phylo.TestForesterWrapper
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.phylo.TestForesterWrapper
-[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 s - in org.biojava.nbio.phylo.TestForesterWrapper
+[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.alignment.SmithWatermanTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.456 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
-[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
-[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 s - in org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.io.TestStockholmParser
-[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.228 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Running org.biojava.nbio.alignment.SmithWatermanTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.GuideTreeTest
-[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
-[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.alignment.SmithWatermanTest
+[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
+[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.323 s - in org.biojava.nbio.alignment.TestDNAAlignment
[INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.105 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
-[INFO] Running org.biojava.nbio.alignment.TestDNAAlignment
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.164 s - in org.biojava.nbio.alignment.TestSubOptimalMSA
+[INFO] Running org.biojava.nbio.alignment.GuideTreeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.934 s - in org.biojava.nbio.alignment.TestDNAAlignment
-[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 s - in org.biojava.nbio.alignment.GuideTreeTest
+[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
-[INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest
-[INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.12 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
+[INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest
-[INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 s - in org.biojava.nbio.alignment.SimpleProfilePairTest
+[INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.alignment.LocalAlignmentTest
-[INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest
+[INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.234 s - in org.biojava.nbio.alignment.NeedlemanWunschTest
-[INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading
+[INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest
-[INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 s - in org.biojava.nbio.alignment.io.TestStockholmParser
+[INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest
+[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.145 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest
+[INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest
[INFO]
[INFO] Results:
[INFO]
@@ -12900,353 +12936,353 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestExperimentalTechniques
-[INFO] Running org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
+[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
+[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.067 s - in org.biojava.nbio.structure.HetatomImplTest
-[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.153 s - in org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.973 s - in org.biojava.nbio.structure.TestURLIdentifier
-[INFO] Running org.biojava.nbio.structure.TestKeywords
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.297 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
+[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
+[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.727 s - in org.biojava.nbio.structure.TestKeywords
-[INFO] Running org.biojava.nbio.structure.TestAtomCache
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.369 s - in org.biojava.nbio.structure.TestAtomCache
-[INFO] Running org.biojava.nbio.structure.TestStructureImpl
+[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.259 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestStructureImpl
-[INFO] Running org.biojava.nbio.structure.TestCalc
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
+[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
+[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.structure.TestCalc
-[INFO] Running org.biojava.nbio.structure.ChemCompTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.192 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.241 s - in org.biojava.nbio.structure.ChemCompTest
-[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.271 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
+[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
+[INFO] Running org.biojava.nbio.structure.TestStructureImpl
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.105 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster
-[INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor
-[INFO] Running org.biojava.nbio.structure.TestPdbId
-[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.TestPdbId
-[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
-[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
-[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.007 s - in org.biojava.nbio.structure.AtomPositionMapTest
-[INFO] Running org.biojava.nbio.structure.SiteTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.structure.TestStructureImpl
+[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.biojava.nbio.structure.SiteTest
-[INFO] Running org.biojava.nbio.structure.PDBStatusTest
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.PDBStatusTest
-[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestParsingCalcium
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.TestVeryLongFileName
+[INFO] Running org.biojava.nbio.structure.TestKeywords
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
-[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
-[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.128 s - in org.biojava.nbio.structure.TestKeywords
+[INFO] Running org.biojava.nbio.structure.Test2JA5
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.Test2JA5
+[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
-[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.084 s - in org.biojava.nbio.structure.ResidueRangeTest
+[INFO] Running org.biojava.nbio.structure.Test4hhb
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.74 s - in org.biojava.nbio.structure.TestEntityHeuristics
-[INFO] Running org.biojava.nbio.structure.TestAltLocs
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.821 s - in org.biojava.nbio.structure.Test4hhb
+[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.341 s - in org.biojava.nbio.structure.TestAltLocs
-[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.65 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.biojava.nbio.structure.ResidueNumberTest
+[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.011 s - in org.biojava.nbio.structure.contact.TestContactCalc
+[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.184 s - in org.biojava.nbio.structure.SourceCompoundTest
-[INFO] Running org.biojava.nbio.structure.io.TestShortLines
+Interface
+ - 4.0
+Interface
+ - 5.477225575051661
+Interface
+ - 5.477225575051661
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
+[INFO] Running org.biojava.nbio.structure.TestNucleotides
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestNucleotides
+[INFO] Running org.biojava.nbio.structure.TestAtomIterator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestAtomIterator
+[INFO] Running org.biojava.nbio.structure.TestEntityHeuristics
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.249 s - in org.biojava.nbio.structure.io.TestShortLines
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.05 s - in org.biojava.nbio.structure.TestEntityHeuristics
+[INFO] Running org.biojava.nbio.structure.ChemCompTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.065 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.466 s - in org.biojava.nbio.structure.ChemCompTest
+[INFO] Running org.biojava.nbio.structure.ElementTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.biojava.nbio.structure.ElementTest
+[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.816 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
-[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 5.35 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.918 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
-[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.707 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
+[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.014 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
+[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.876 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
-[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
-[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestSiftsParsing
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
-[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.044 s - in org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestExperimentalTechniques
+[INFO] Running org.biojava.nbio.structure.PDBStatusTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.013 s - in org.biojava.nbio.structure.PDBStatusTest
+[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestDNAAlignment
+[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.476 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
-[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
-[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.087 s - in org.biojava.nbio.structure.TestStructureSerialization
+[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.553 s - in org.biojava.nbio.structure.io.TestHeaderOnly
-[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
-[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
-[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.357 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[INFO] Running org.biojava.nbio.structure.SiteTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
-[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.SiteTest
+[INFO] Running org.biojava.nbio.structure.TestCalc
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.io.TestDBRefParsing
-[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
-[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
-[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestHardBioUnits
-[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
-[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.structure.TestCalc
+[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.3 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
-[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.TestTitleParsing
-[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.025 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.855 s - in org.biojava.nbio.structure.PdbFileFormat30Test
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-Using PDB_DIR=/tmp as temporary file directory
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.56 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.544 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.766 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
-[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.047 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.037 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
+[INFO] Running org.biojava.nbio.structure.HetatomImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.616 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
-[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.structure.HetatomImplTest
+[INFO] Running org.biojava.nbio.structure.TestAtomCache
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.896 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
-[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestStructureCrossReferences
-[INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.801 s - in org.biojava.nbio.structure.TestAtomCache
+[INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.006 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters
+[INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 s - in org.biojava.nbio.structure.align.util.RotationAxisTest
-[INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.088 s - in org.biojava.nbio.structure.align.util.AtomCacheTest
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.004 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.012 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter
-[INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes
+[INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm
+[INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser
+[INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.011 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc
+[INFO] Running org.biojava.nbio.structure.TestBond
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestBond
+[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
+[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[INFO] Running org.biojava.nbio.structure.TestAltLocs
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer
-[INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
+[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 0.578 s - in org.biojava.nbio.structure.TestAltLocs
+[INFO] Running org.biojava.nbio.structure.AtomPositionMapTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.011 s - in org.biojava.nbio.structure.AtomPositionMapTest
+[INFO] Running org.biojava.nbio.structure.TestParsingCalcium
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.013 s - in org.biojava.nbio.structure.TestParsingCalcium
+[INFO] Running org.biojava.nbio.structure.TestPdbId
+[1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC]
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.087 s - in org.biojava.nbio.structure.TestPdbId
+[INFO] Running org.biojava.nbio.structure.SourceCompoundTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion
-[INFO] Running org.biojava.nbio.structure.align.client.TestStructureName
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.039 s - in org.biojava.nbio.structure.SourceCompoundTest
+[INFO] Running org.biojava.nbio.structure.TestChargeAdder
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestChargeAdder
+[INFO] Running org.biojava.nbio.structure.TestURLIdentifier
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 s - in org.biojava.nbio.structure.align.client.TestStructureName
-[INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.014 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency
-[INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.007 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment
-[INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.743 s - in org.biojava.nbio.structure.TestURLIdentifier
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands
+[INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest
-[INFO] Running org.biojava.nbio.structure.ElementTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ElementTest
-[INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestLoadStructureFromURL
-[INFO] Running org.biojava.nbio.structure.TestDNAAlignment
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.005 s - in org.biojava.nbio.structure.TestDNAAlignment
-[INFO] Running org.biojava.nbio.structure.Test2JA5
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.007 s - in org.biojava.nbio.structure.Test2JA5
-[INFO] Running org.biojava.nbio.structure.ResidueRangeTest
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.34 s - in org.biojava.nbio.structure.io.TestHeaderOnly
+[INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestHardBioUnits
+[INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.051 s - in org.biojava.nbio.structure.ResidueRangeTest
-[INFO] Running org.biojava.nbio.structure.TestAtomIterator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestAtomIterator
-[INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign
-[INFO] Running org.biojava.nbio.structure.TestStructureSerialization
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.79 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.054 s - in org.biojava.nbio.structure.TestStructureSerialization
-[INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.024 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.401 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.3 s - in org.biojava.nbio.structure.geometry.TestSuperPosition
-[INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP
+[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.117 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils
+[INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding
+[INFO] Running org.biojava.nbio.structure.io.TestTitleParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestTitleParsing
+[INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP
-[INFO] Running org.biojava.nbio.structure.TestVeryLongFileName
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.819 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles
+[INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s - in org.biojava.nbio.structure.TestVeryLongFileName
-[INFO] Running org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.biojava.nbio.structure.ResidueNumberTest
-[INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest
+[INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.423 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.biojava.nbio.structure.xtal.TestCrystalCell
-[INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.278 s - in org.biojava.nbio.structure.io.TestMMCIFWriting
+[INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.02 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest
+[INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.019 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing
+[INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.011 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB
+[INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.82 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering
-[INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.025 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo
-[INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.669 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest
+[INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.012 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders
+[INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestSiftsParsing
+[INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures
+[INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 s - in org.biojava.nbio.structure.io.TestParseOnAsymId
+[INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.446 s - in org.biojava.nbio.structure.TestEntityResIndexMapping
-[INFO] Running org.biojava.nbio.structure.TestChargeAdder
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestChargeAdder
-[INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test
+Using PDB_DIR=/tmp as temporary file directory
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.842 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.934 s - in org.biojava.nbio.structure.PdbFileFormat30Test
-[INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder
+[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.419 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId
+[INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-Interface
- - 4.0
-Interface
- - 5.477225575051661
-Interface
- - 5.477225575051661
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder
-[INFO] Running org.biojava.nbio.structure.contact.TestContactCalc
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.008 s - in org.biojava.nbio.structure.contact.TestContactCalc
-[INFO] Running org.biojava.nbio.structure.TestCloning
-[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestCloning
-[INFO] Running org.biojava.nbio.structure.TestBond
-[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBond
-[INFO] Running org.biojava.nbio.structure.TestNucleotides
-[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.007 s - in org.biojava.nbio.structure.TestNucleotides
-[INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.633 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes
+[INFO] Running org.biojava.nbio.structure.io.TestShortLines
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.03 s - in org.biojava.nbio.structure.asa.TestAsaCalc
-[INFO] Running org.biojava.nbio.structure.Test4hhb
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.487 s - in org.biojava.nbio.structure.io.TestShortLines
+[INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 s - in org.biojava.nbio.structure.Test4hhb
-[INFO] Running org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
+[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.534 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles
+[INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.225 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider
-[INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.008 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.structure.io.TestDBRefParsing
+[INFO] Running org.biojava.nbio.structure.TestCloning
+[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.01 s - in org.biojava.nbio.structure.TestCloning
+[INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences
+[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.009 s - in org.biojava.nbio.structure.TestStructureCrossReferences
[INFO]
[INFO] Results:
[INFO]
@@ -13294,20 +13330,20 @@
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.structure.gui.StructureViewerTest
-[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
-[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.structure.gui.RenderStyleTest
-[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 s - in org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.structure.gui.StructureViewerTest
[INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 s - in org.biojava.nbio.structure.gui.TestAtomInfo
+[INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest
+[INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 s - in org.biojava.nbio.structure.gui.RenderStyleTest
+[INFO] Running org.biojava.nbio.structure.gui.ViewerTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.structure.gui.ViewerTest
[INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.078 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator
[INFO]
[INFO] Results:
[INFO]
@@ -13335,51 +13371,51 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.io.fastq.FastqTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
+[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.108 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
-[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
-[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.043 s - in org.biojava.nbio.genome.TestGenomeMapping
+[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.883 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Running org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.genome.FeatureListTest
[INFO] Running org.biojava.nbio.genome.TestIssue355
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s - in org.biojava.nbio.genome.TestIssue355
+[INFO] Running org.biojava.nbio.genome.TestLocation
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.genome.TestLocation
[INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
-[INFO] Running org.biojava.nbio.genome.TestLocation
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.biojava.nbio.genome.TestLocation
-[INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 s - in org.biojava.nbio.genome.TestChromosomeMappingTools
+[INFO] Running org.biojava.nbio.genome.TestGenomeMapping
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 s - in org.biojava.nbio.genome.TestGenomeMapping
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.413 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.FastqTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.473 s - in org.biojava.nbio.genome.GeneFeatureHelperTest
-[INFO] Running org.biojava.nbio.genome.FeatureListTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 s - in org.biojava.nbio.genome.FeatureListTest
+[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.genome.io.fastq.ConvertTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest
+[INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest
[INFO]
[INFO] Results:
[INFO]
@@ -13407,20 +13443,20 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.071 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.219 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
+[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.563 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
-[INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
+[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.079 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest
+[INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.283 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest
-[INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.046 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.442 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest
[INFO]
[INFO] Results:
[INFO]
@@ -13449,7 +13485,7 @@
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
-[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.057 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
+[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.122 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan
[INFO]
[INFO] Results:
[INFO]
@@ -13481,9 +13517,9 @@
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.563 s - in org.biojava.nbio.ronn.JronnTest
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.513 s - in org.biojava.nbio.ronn.JronnTest
[INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.046 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.091 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest
[INFO]
[INFO] Results:
[INFO]
@@ -13511,32 +13547,6 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.454 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.371 s - in org.biojava.nbio.aaproperties.xml.ElementTest
-[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
-[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
-SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
-SLF4J: Defaulting to no-operation (NOP) logger implementation
-SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
-NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
-SequenceName,A,N,MolecularWeight
-NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262
-SequenceName,A,N,MolecularWeight
-NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.363 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
[INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
@@ -13553,22 +13563,48 @@
SAOV_0114,0.101,0.0525,53660.5723
SAOV_0094,0.0537,0.0767,45884.0164
SAA6008_00126,0.0955,0.0414,95002.026
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.369 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.766 s - in org.biojava.nbio.aaproperties.CommandPromptTest
+[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.535 s - in org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.aaproperties.xml.ElementTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.62 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest
+[INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
+SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
+SLF4J: Defaulting to no-operation (NOP) logger implementation
+SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest
[INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest
[INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
-[INFO] Running org.biojava.nbio.aaproperties.CookBookTest
+[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.87 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest
+[INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 s - in org.biojava.nbio.aaproperties.CookBookTest
+SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint
+NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715
+SequenceName,A,N,MolecularWeight
+NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262
+SequenceName,A,N,MolecularWeight
+NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.697 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest
[INFO]
[INFO] Results:
[INFO]
@@ -13615,21 +13651,21 @@
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
-[INFO] Running org.biojava.nbio.ontology.TestParseOBO
+[INFO] Running org.biojava.nbio.ontology.TestParseSBO
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 s - in org.biojava.nbio.ontology.TestParseOBO
-[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Running org.biojava.nbio.ontology.TestParseOBO
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.ontology.TestOboFileParsing
-[INFO] Running org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.167 s - in org.biojava.nbio.ontology.TestParseOBO
+[INFO] Running org.biojava.nbio.ontology.TestOboFileParsing
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in org.biojava.nbio.ontology.TestParseSBO
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 s - in org.biojava.nbio.ontology.TestOboFileParsing
[INFO]
[INFO] Results:
[INFO]
@@ -13658,25 +13694,25 @@
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
[INFO] biojava ............................................ SUCCESS [ 0.002 s]
-[INFO] biojava-core ....................................... SUCCESS [09:50 min]
-[INFO] biojava-forester ................................... SUCCESS [ 0.038 s]
+[INFO] biojava-core ....................................... SUCCESS [09:51 min]
+[INFO] biojava-forester ................................... SUCCESS [ 0.575 s]
[INFO] biojava-alignment .................................. SUCCESS [03:00 min]
-[INFO] biojava-structure .................................. SUCCESS [16:21 min]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.451 s]
+[INFO] biojava-structure .................................. SUCCESS [16:20 min]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.025 s]
[INFO] biojava-structure-gui .............................. SUCCESS [01:00 min]
[INFO] biojava-genome ..................................... SUCCESS [03:00 min]
-[INFO] biojava-modfinder .................................. SUCCESS [ 40.088 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 10.046 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.034 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 40.112 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 10.088 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.082 s]
[INFO] biojava-aa-prop .................................... SUCCESS [01:20 min]
-[INFO] biojava-survival ................................... SUCCESS [ 0.036 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 30.029 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.111 s]
+[INFO] biojava-survival ................................... SUCCESS [ 0.057 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 30.061 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.137 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 36:13 min
-[INFO] Finished at: 2025-02-25T04:53:59Z
+[INFO] Total time: 36:14 min
+[INFO] Finished at: 2024-01-23T23:17:30Z
[INFO] ------------------------------------------------------------------------
[0m[0m create-stamp debian/debhelper-build-stamp
dh_prep
@@ -13893,26 +13929,26 @@
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for biojava 6.1.0:
[INFO]
-[INFO] biojava ............................................ SUCCESS [ 0.384 s]
-[INFO] biojava-core ....................................... SUCCESS [ 0.043 s]
-[INFO] biojava-forester ................................... SUCCESS [ 0.040 s]
-[INFO] biojava-alignment .................................. SUCCESS [ 0.028 s]
-[INFO] biojava-structure .................................. SUCCESS [ 0.032 s]
-[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.023 s]
-[INFO] biojava-structure-gui .............................. SUCCESS [ 0.028 s]
-[INFO] biojava-genome ..................................... SUCCESS [ 0.028 s]
-[INFO] biojava-modfinder .................................. SUCCESS [ 0.023 s]
-[INFO] biojava-ws ......................................... SUCCESS [ 0.024 s]
-[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.030 s]
-[INFO] biojava-aa-prop .................................... SUCCESS [ 0.024 s]
-[INFO] biojava-survival ................................... SUCCESS [ 0.029 s]
-[INFO] biojava-ontology ................................... SUCCESS [ 0.023 s]
-[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.033 s]
+[INFO] biojava ............................................ SUCCESS [ 1.167 s]
+[INFO] biojava-core ....................................... SUCCESS [ 0.152 s]
+[INFO] biojava-forester ................................... SUCCESS [ 0.116 s]
+[INFO] biojava-alignment .................................. SUCCESS [ 0.077 s]
+[INFO] biojava-structure .................................. SUCCESS [ 0.526 s]
+[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.087 s]
+[INFO] biojava-structure-gui .............................. SUCCESS [ 0.138 s]
+[INFO] biojava-genome ..................................... SUCCESS [ 0.070 s]
+[INFO] biojava-modfinder .................................. SUCCESS [ 0.061 s]
+[INFO] biojava-ws ......................................... SUCCESS [ 0.069 s]
+[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.051 s]
+[INFO] biojava-aa-prop .................................... SUCCESS [ 0.061 s]
+[INFO] biojava-survival ................................... SUCCESS [ 0.084 s]
+[INFO] biojava-ontology ................................... SUCCESS [ 0.066 s]
+[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.059 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 0.978 s
-[INFO] Finished at: 2025-02-25T04:54:02Z
+[INFO] Total time: 3.371 s
+[INFO] Finished at: 2024-01-23T23:17:37Z
[INFO] ------------------------------------------------------------------------
[0m[0m mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/reproducible-path/biojava6-live-6.1.0\+dfsg --non-explore
Analysing pom.xml...
@@ -14118,14 +14154,14 @@
dh_install
jh_installjavadoc
debian/rules override_dh_installdocs
-make[1]: Entering directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
-dpkg: warning: --compare-versions used with obsolete relation operator '>'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird betreten
+dpkg: Warnung: --compare-versions mit veraltetem Beziehungs-Operator »>« verwendet
dh_installdocs
# Deleting calls to urchinTracker to enhance privacy.
for F in $(find . -name "*.html"); do \
sed -i 's/^$//' $F; \
done
-make[1]: Leaving directory '/build/reproducible-path/biojava6-live-6.1.0+dfsg'
+make[1]: Verzeichnis „/build/reproducible-path/biojava6-live-6.1.0+dfsg“ wird verlassen
dh_installchangelogs
dh_lintian
dh_perl
@@ -14148,8 +14184,8 @@
dpkg-gencontrol: warning: package libbiojava6-java-doc: substitution variable ${maven:DocDepends} unused, but is defined
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'libbiojava6-java-doc' in '../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb'.
-dpkg-deb: building package 'libbiojava6-java' in '../libbiojava6-java_6.1.0+dfsg-4_all.deb'.
+dpkg-deb: Paket »libbiojava6-java-doc« wird in »../libbiojava6-java-doc_6.1.0+dfsg-4_all.deb« gebaut.
+dpkg-deb: Paket »libbiojava6-java« wird in »../libbiojava6-java_6.1.0+dfsg-4_all.deb« gebaut.
dpkg-genbuildinfo --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.buildinfo
dpkg-genchanges --build=binary -O../biojava6-live_6.1.0+dfsg-4_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -14157,12 +14193,14 @@
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3141/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/25528 and its subdirectories
-I: Current time: Mon Feb 24 16:59:34 -12 2025
-I: pbuilder-time-stamp: 1740459574
+I: removing directory /srv/workspace/pbuilder/3141 and its subdirectories
+I: Current time: Wed Jan 24 13:23:39 +14 2024
+I: pbuilder-time-stamp: 1706052219