[Debian-med-packaging] Bug#1026746: biojava5-live: FTBFS: [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.

Tue Dec 20 17:25:07 GMT 2022

Source: biojava5-live
Version: 5.4.0+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221220 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dpkg: warning: --compare-versions used with obsolete relation operator '>'
> # 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 \
> 	    -e 's, at JSON_SIMPLE_PACKAGE@,org.json.simple,' \
> 	    {} \; -print
> ./biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
> dh_auto_build
> 	/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=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US
> OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
> [0m[0m[INFO] Scanning for projects...
> [WARNING] 
> [WARNING] Some problems were encountered while building the effective model for org.biojava:biojava-structure-gui:jar:5.4.0
> [WARNING] 'dependencies.dependency.systemPath' for net.sourceforge.jmol:jmol:jar should use a variable instead of a hard-coded path /usr/share/java/Jmol.jar @ line 48, column 16
> [WARNING] 
> [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
> [WARNING] 
> [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
> [WARNING] 
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Build Order:
> [INFO] 
> [INFO] biojava                                                            [pom]
> [INFO] biojava-core                                                       [jar]
> [INFO] biojava-forester                                                   [jar]
> [INFO] biojava-alignment                                                  [jar]
> [INFO] biojava-structure                                                  [jar]
> [INFO] biojava-jcolorbrewer                                               [jar]
> [INFO] biojava-structure-gui                                              [jar]
> [INFO] biojava-genome                                                     [jar]
> [INFO] biojava-modfinder                                                  [jar]
> [INFO] biojava-ws                                                         [jar]
> [INFO] biojava-protein-disorder                                           [jar]
> [INFO] biojava-aa-prop                                                    [jar]
> [INFO] biojava-survival                                                   [jar]
> [INFO] biojava-ontology                                                   [jar]
> [WARNING] The artifact org.apache.maven.plugins:maven-antrun-plugin:jar:1.3 has been relocated to org.apache.maven.plugins:maven-antrun-plugin:jar:1.8
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [INFO] 
> [INFO] ------------------------< org.biojava:biojava >-------------------------
> [INFO] Building biojava 5.4.0                                            [1/14]
> [INFO] --------------------------------[ pom ]---------------------------------
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [INFO] 
> [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava ---
> [INFO] Not executing Javadoc as the project is not a Java classpath-capable package
> [INFO] 
> [INFO] ----------------------< org.biojava:biojava-core >----------------------
> [INFO] Building biojava-core 5.4.0                                       [2/14]
> [INFO] --------------------------------[ jar ]---------------------------------
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [INFO] 
> [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-core ---
> [INFO] Copying 24 resources
> [INFO] 
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-core ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 187 source files to /<<PKGBUILDDIR>>/biojava-core/target/classes
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Some input files use or override a deprecated API that is marked for removal.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/SingleLinkageClusterer.java: Recompile with -Xlint:removal for details.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.java: Recompile with -Xlint:unchecked for details.
> [INFO] 
> [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ biojava-core ---
> [INFO] Copying 46 resources
> [INFO] 
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-core ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 34 source files to /<<PKGBUILDDIR>>/biojava-core/target/test-classes
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/test/java/org/biojava/nbio/core/sequence/TranslationTest.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: /<<PKGBUILDDIR>>/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java uses unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java: Recompile with -Xlint:unchecked for details.
> [INFO] 
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-core ---
> [INFO] Tests are skipped.
> [INFO] 
> [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-core ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-core/target/biojava-core-5.4.0.jar
> [INFO] 
> [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-core ---
> [INFO] Adding the --ignore-source-errors option
> [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.exceptions...
> [WARNING] Loading source files for package org.biojava.nbio.core.util...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.transcription...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.loader...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.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.template...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.views...
> [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.edits...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.features...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.reference...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.template...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.util...
> [WARNING] Loading source files for package org.biojava.nbio.core.sequence.io.embl...
> [WARNING] Loading source files for package org.biojava.nbio.core.alignment...
> [WARNING] Loading source files for package org.biojava.nbio.core.alignment.template...
> [WARNING] Loading source files for package org.biojava.nbio.core.alignment.matrices...
> [WARNING] 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] Constructing Javadoc information...
> [WARNING] Building index for all the packages and classes...
> [WARNING] Standard Doclet version 17.0.5+8-Debian-2
> [WARNING] Building tree for all the packages and classes...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAindexFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexFileParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/AAIndexProvider.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ABITrace.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/ABITracerCompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractCompoundTranslator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/AbstractFeature.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AbstractLocation.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations()
> [WARNING] * {@link #getAllSubLocations()}.
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/AbstractReference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/AbstractSequence.AnnotationType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/AccesionedLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Accessioned.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/AccessionID.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner
> [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:68: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:133: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:157: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/AlignedSequence.Step.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java:41: warning: Tag @link: reference not found: Aligner
> [WARNING] * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNACompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityDNARNAHybridCompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AmbiguityRNACompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/ArrayListProxySequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/BasicSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
> [WARNING] * Class is immutable & so this is unsupported
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
> [WARNING] * Class is immutable & so this is unsupported
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:67: warning: invalid input: '&'
> [WARNING] * Class is immutable & so this is unsupported
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java:75: warning: invalid input: '&'
> [WARNING] * Class is immutable & so this is unsupported
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResult.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastTabularParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/BlastXMLParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java:524: warning: invalid input: '<'
> [WARNING] * @exception  IllegalArgumentException  If readAheadLimit is < 0
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/CaseInsensitiveCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/CDSSequence.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:34: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
> [WARNING] * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:85: warning: invalid usage of tag {@link http://www.sequenceontology.org/gff3.shtml
> [WARNING] * {@link http://www.sequenceontology.org/gff3.shtml}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java:86: warning: invalid usage of tag {@link http://biowiki.org/~yam/bioe131/GFF.ppt
> [WARNING] * {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ChromosomeSequence.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java:131: warning: @param argument "begin" is not a parameter name.
> [WARNING] * @param begin
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java:132: warning: @param argument "end" is not a parameter name.
> [WARNING] * @param end
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/ClasspathResource.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/CodonCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ComplementCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ComplementSequenceView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Compound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/CompoundNotFoundException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/CompoundTranslator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/ConcurrencyTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/CRC64Checksum.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DataSource.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/DBReferenceInfo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/DefaultAAIndexProvider.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/demo/DemoSixFrameTranslation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/DNACompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/DNASequence.DNAType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/DNASequenceCreator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/DNAToRNATranslator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.AbstractEdit.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Delete.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Insert.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/Edit.Substitute.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblId.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblRecord.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/embl/EmblReference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/Equals.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ExonSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaGeneWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java:127: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Amr AL-Hossary
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaReaderHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaSequenceParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FastaWriterHelper.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java:99: warning: @param argument "dnaSequences" is not a parameter name.
> [WARNING] * @param dnaSequences
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureInterface.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java:72: warning: @return tag cannot be used in method with void return type.
> [WARNING] public void setDescription(String description);
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeatureRetriever.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/FileDownloadUtils.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:276: warning: invalid input: '&'
> [WARNING] * Recursively delete a folder & contents
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:251: warning: invalid input: '&'
> [WARNING] * Recursively delete a folder & contents
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:159: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Peter Rose
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:205: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author BalusC,
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:241: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Jacek Grzebyta
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:251: warning: invalid input: '&'
> [WARNING] * Recursively delete a folder & contents
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java:276: warning: invalid input: '&'
> [WARNING] * Recursively delete a folder & contents
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name.
> [WARNING] * @param fastaFile
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java:58: warning: @param argument "fastaFile" is not a parameter name.
> [WARNING] * @param fastaFile
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java:59: warning: @param argument "fastaFile" is not a parameter name.
> [WARNING] * @param fastaFile
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/FlatFileCache.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/FourBitSequenceReader.FourBitArrayWorker.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Frame.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/FuzzyPoint.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:36: warning: Tag @param cannot be used in field documentation.  It can only be used in the following types of documentation: class/interface, constructor, method.
> [WARNING] * @param sequence
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java:37: warning: Tag @return cannot be used in field documentation.  It can only be used in the following types of documentation: method, inline text.
> [WARNING] * @return
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:63: warning: invalid input: '<'
> [WARNING] * @author Karl Nicholas <github:karlnicholas>
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java:64: warning: invalid input: '<'
> [WARNING] * @author Jacek Grzebyta <github:jgrzebyta>
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java:141: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Amr AL-Hossary
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/GenbankReference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriter.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java:85: warning: @param argument "lineSeparator" is not a parameter name.
> [WARNING] * @param lineSeparator
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:98: warning: @inheritDoc used but setAccession(String) does not override or implement any method.
> [WARNING] public void setAccession(String accession) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:133: warning: @inheritDoc used but setComment(String) does not override or implement any method.
> [WARNING] public void setComment(String comment) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:106: warning: @inheritDoc used but setDescription(String) does not override or implement any method.
> [WARNING] public void setDescription(String description) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:115: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method.
> [WARNING] public void setIdentifier(String identifier) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:124: warning: @inheritDoc used but setName(String) does not override or implement any method.
> [WARNING] public void setName(String name) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:81: warning: @inheritDoc used but setVersion(int) does not override or implement any method.
> [WARNING] public void setVersion(int version) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:81: warning: @inheritDoc used but setVersion(int) does not override or implement any method.
> [WARNING] public void setVersion(int version) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:98: warning: @inheritDoc used but setAccession(String) does not override or implement any method.
> [WARNING] public void setAccession(String accession) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:106: warning: @inheritDoc used but setDescription(String) does not override or implement any method.
> [WARNING] public void setDescription(String description) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:115: warning: @inheritDoc used but setIdentifier(String) does not override or implement any method.
> [WARNING] public void setIdentifier(String identifier) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:124: warning: @inheritDoc used but setName(String) does not override or implement any method.
> [WARNING] public void setName(String name) throws ParserException {
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java:133: warning: @inheritDoc used but setComment(String) does not override or implement any method.
> [WARNING] public void setComment(String comment) throws ParserException {
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/GeneSequence.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java:63: warning: @param argument "parentDNASequence" is not a parameter name.
> [WARNING] * @param parentDNASequence
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/Hashcoder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hit.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Hsp.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/InputStreamProvider.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.BondLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.GroupLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OneOfLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcLocations.OrderLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/InsdcParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/IntronSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String)
> [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/util/IOUtils.ReaderProcessor.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java:181: warning: Tag @link: reference not found: IOUtils#processReader(String)
> [WARNING] * {@link IOUtils#processReader(String)}. Each time a line is encountered
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/IUPACParser.IUPACTable.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java:264: warning: @param argument "nucleotides" is not a parameter name.
> [WARNING] * @param nucleotides The nucleotide set to use when building BioJava
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<'
> [WARNING] * Allows creation of the store from List<Sequence<C>>. CompoundSet
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&'
> [WARNING] * attempting to skip onto the next sequence as & when it is asked to
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:69: warning: invalid input: '<'
> [WARNING] * Allows creation of the store from List<Sequence<C>>. CompoundSet
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java:220: warning: invalid input: '&'
> [WARNING] * attempting to skip onto the next sequence as & when it is asked to
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:55: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java:71: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/LightweightProfile.StringFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:74: warning: Tag @link: reference not found: #getAllSubLocations()
> [WARNING] * {@link #getAllSubLocations()}.
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Location.Tools.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java:169: warning: @param argument "location" is not a parameter name.
> [WARNING] * @param location The location which currently expresses the outer
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/LocationHelper.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&'
> [WARNING] * Assumes that the first element is the start & clones it
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:116: warning: @param argument "location" is not a parameter name.
> [WARNING] * @param location The location which currently expresses the outer
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java:310: warning: invalid input: '&'
> [WARNING] * Assumes that the first element is the start & clones it
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/Messages.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfile.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableProfilePair.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/MutableSequencePair.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/NucleotideCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/demo/ParseFastaFileDemo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/ParserException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/PlainFastaHeaderParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/Point.Resolver.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/PrettyXMLWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:61: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:104: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:116: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:125: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:135: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:144: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:160: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:170: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:180: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java:239: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/Profile.StringFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfilePair.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/ProfileView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/ProteinSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/ProxySequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/Qualifier.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QualityFeature.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/QuantityFeature.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/ReferenceInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/Result.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/ResultFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/ReversedSequenceView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/RNACompoundSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/RNASequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/RNASequenceCreator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/RnaSequenceView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/ScaledSubstitutionMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/SearchIO.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/Sequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SequenceLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore
> [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString()
> [WARNING] * filled with the results of {@link Compound#toString()}. Does not
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:153: warning: @param argument "writer" is not a parameter name.
> [WARNING] * @param writer The writer to send data to
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:165: warning: Tag @link: reference not found: Compound#toString()
> [WARNING] * filled with the results of {@link Compound#toString()}. Does not
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:247: warning: Tag @link: reference not found: SequenceBackingStore
> [WARNING] * elements in a new instance of {@link SequenceBackingStore} which behaves
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:288: warning: invalid input: '&'
> [WARNING] * ATG, TGT & GTA
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:346: warning: invalid input: '&'
> [WARNING] * length & compound sets used. The code will also bail out the moment
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java:362: warning: invalid input: '&'
> [WARNING] * length & compound sets used. The code will also bail out the moment
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceMixin.SequenceIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceCollection.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/SequenceOptimizationHints.SequenceUsage.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SequencePair.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:44: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:53: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:62: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:71: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength()
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:80: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java:89: warning: invalid input: '<'
> [WARNING] * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength()
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java:35: warning: @param argument "dataInput" is not a parameter name.
> [WARNING] * @param dataInput
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceProxyView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/SequenceTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/SequenceView.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleAlignedSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimpleLocation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/SimplePoint.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfile.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleProfilePair.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/SimpleSequencePair.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
> [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java:171: warning: Tag @link: reference not found: SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
> [WARNING] * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/SingleLinkageClusterer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/SoftHashMap.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StartCodonSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/StopCodonSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/Strand.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/StringManipulationHelper.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java:70: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author andreas
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java:106: warning: invalid input: '<'
> [WARNING] * @throws IllegalArgumentException if scale < 1
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:77: warning: invalid input: '&'
> [WARNING] * Returns Blosum 100 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:85: warning: invalid input: '&'
> [WARNING] * Returns Blosum 30 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:93: warning: invalid input: '&'
> [WARNING] * Returns Blosum 35 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:101: warning: invalid input: '&'
> [WARNING] * Returns Blosum 40 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:109: warning: invalid input: '&'
> [WARNING] * Returns Blosum 45 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:117: warning: invalid input: '&'
> [WARNING] * Returns Blosum 50 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java:125: warning: invalid input: '&'
> [WARNING] * Returns Blosum 55 matrix by Henikoff & Henikoff
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.CaseInsensitiveTriplet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/Table.Codon.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/TaxonomyID.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/TextFeature.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.Builder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/TranscriptSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/TranslationException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/TwoBitSequenceReader.TwoBitArrayWorker.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/UncompressInputStream.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/WindowedSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/XMLHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/XMLWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/demo/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/demo/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/matrices/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/alignment/template/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/search/io/blast/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/compound/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/edits/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/features/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/package-tree.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/io/template/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/loader/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/location/template/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/reference/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/storage/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/template/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/views/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/exceptions/class-use/Messages.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SingleLinkageClusterer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/SequenceTools.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/util/class-use/InputStreamProvider.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/Strand.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/IntronSequence.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/MultipleSequenceAlignment.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StartCodonSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceCollection.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceOptimizationHints.SequenceUsage.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DNASequence.DNAType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/StopCodonSequence.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/GeneSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/CDSSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/DataSource.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/RNASequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ExonSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/ChromosomeSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/BasicSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/class-use/SequenceComparator.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/CaseInsensitiveCompound.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/Table.CaseInsensitiveTriplet.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-core/target/apidocs/org/biojava/nbio/core/sequence/transcription/class-use/DNAToRNATranslator.html...
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> [WARNING] 100 warnings
> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-core/target/biojava-core-5.4.0-javadoc.jar
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> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [INFO] 
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> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-forester/target/biojava-forester-5.4.0.jar
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/AccessionParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/AdjactantDirectedCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/AncestralTaxonomyInference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/AncestralTaxonomyInferenceException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Annotation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/AnnotationParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/annotator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/AptxUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/AptxUtil.GraphicsExportType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Archaeopteryx.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/ArchaeopteryxA.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/ArchaeopteryxE.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:544: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Herve Menager
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:574: warning: Tag @author cannot be used in method documentation.  It can only be used in the following types of documentation: overview, module, package, class/interface.
> [WARNING] * @author Herve Menager
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/AsciiHistogram.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/BasicBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/BasicCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/BasicDescriptiveStatistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/BasicDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/BasicDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/BasicGenomeWideCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/BasicGoRelationship.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/BasicGoSubset.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/BasicGoTerm.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/BasicGoXRef.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/BasicMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/BasicPhylogeniesWebserviceClient.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/BasicProtein.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/BasicSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/species/BasicSpecies.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/BasicTable.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/BasicTableParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/BinaryCharacters.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/BinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/BinaryDomainCombination.DomainCombinationType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/BinaryDomainCombination.OutputFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/Blast.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/tools/BootstrapResampler.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/BranchColor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/BranchCountingBasedScoringMethod.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<'
> [WARNING] *            SortedMap<PhylogenyNode, Double> in which the external node
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/BranchData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/BranchLengthBasedScoringMethod.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/BranchWidth.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/BranchWidthParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/CharacterStateMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/CharacterStateMatrix.BinaryStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/CharacterStateMatrix.Format.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/CharacterStateMatrix.GainLossStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/CharacterStateMatrix.NucleotideStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/Chart.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/check_fasta.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/ClustalOmega.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/ColorParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/CombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/CommandLineArguments.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Confidence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/ConfidenceAssessor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/ConfidenceParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Configuration.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Configuration.EXT_NODE_DATA_RETURN_ON.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Configuration.UI.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Constants.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/count_support.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/Coverage.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/CoverageCalculationMethod.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/CoverageCalculationOptions.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/CoverageCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/CoverageExtender.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Date.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/DateParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/decorator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/decoratorX.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/DeleteableMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/DescriptiveStatistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/DevelopmentTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DirectedBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DirectedCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/DistanceMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/DistanceMatrix.Format.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Distribution.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/DistributionParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/DolloParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/dom_dup.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/Domain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/DomainArchitecture.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainCountsDifferenceUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainLengths.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainLengthsTable.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainParsimonyCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarity.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/surfacing/DomainSimilarity.java:255: warning: invalid input: '<'
> [WARNING] * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarity.DomainSimilarityScoring.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarity.DomainSimilaritySortField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarity.PRINT_OPTION.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarityCalculator.Detailedness.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/DomainSimilarityCalculator.GoAnnotationOutput.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/EasyWriter.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Event.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/EventParser.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/ExternalForwardIterator.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/iterators/ExternalForwardIterator.java:42: warning: @param argument "tree" is not a parameter name.
> [WARNING] * @param tree
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/ExternalNodeBasedCoverage.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/ExternalProgram.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/FailedConditionCheckException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/fasta_split.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/FastaParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/FitchParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/FontChooser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/ForesterConstants.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/ForesterConstants.PhylogeneticTreeFormats.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/ForesterUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/GapContribution.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/GeneralMsaParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/GeneralTable.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/GenomeWideCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/get_distances.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/get_genome_counts_per_char.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/get_loss_nodes.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/get_shared_chars.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/get_subtree_specific_chars.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/goac.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/GoRelationship.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/GoTerm.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmPfamOutputParser.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/io/parsers/HmmPfamOutputParser.java:618: warning: @param argument "ignored_engulfed_domains" is not a parameter name.
> [WARNING] * @param ignored_engulfed_domains
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmPfamOutputParser.FilterType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmPfamOutputParser.ReturnType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmscanPerDomainTableParser.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/io/parsers/HmmscanPerDomainTableParser.java:604: warning: @param argument "ignored_engulfed_domains" is not a parameter name.
> [WARNING] * @param ignored_engulfed_domains
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmscanPerDomainTableParser.FilterType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/HmmscanPerDomainTableParser.ReturnType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Identifier.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/IdentifierParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/IllegalFormatUseException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/ImageLoader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/InferenceManager.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/datastructures/IntMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/inverted_dcs.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/IteratingPhylogenyParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/LevelOrderTreeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/LogBranchLengthBasedScoringMethod.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/Mafft.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/MainFrame.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/MainFrameApplet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/MainFrameApplication.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/MainPanel.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/map_lengths.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/Mapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/MappingResults.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/mcc.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/meta_ontologizer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/MetaOntologizer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/ModelingUtils.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/MolecularSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/MolecularSequence.TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/Msa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/msa_compactor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/Msa.MSA_FORMAT.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/MsaCompactor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/MsaFormatException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/MsaInferrer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/MsaMethods.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/MsaProperties.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/MsaRenderer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/MultipleUris.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/NeighborJoining.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/NeighborJoiningF.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/NeighborJoiningR.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/neTest.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/neTest.DoublePointer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/NexusCharactersParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/NexusConstants.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/NexusFormatException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/NexusPhylogeniesParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/NHXFormatException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/NHXParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/NHXParser.TAXONOMY_EXTRACTION.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/NHXtags.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/nj.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeDataField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeVisualData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeVisualData.FontType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeVisualData.NodeFill.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/NodeVisualData.NodeShape.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/obo_tool.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/OBOparser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/OBOparser.ReturnType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/OntologizerResult.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/OntologizerResult.TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Options.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Options.CLADOGRAM_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Options.NODE_LABEL_DIRECTION.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/Options.PHYLOGENY_GRAPHICS_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/PairwiseDistanceCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/PairwiseDomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/PairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/PairwiseGenomeComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/util/ParserUtils.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/PaupLogParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/pccx.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/pfam_go.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/pfam2go_extractor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/pfamacc2go.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/pfamacc2pfamid.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/PfamToGoMapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/PfamToGoParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/phylo2coloredgraphics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/phylo2graphics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/PhylogeneticInferrer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/PhylogeneticInferrer.MSA_PRG.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/Phylogeny.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/Phylogeny.java:90: warning: @param argument "n" is not a parameter name.
> [WARNING] * @param n
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyBranch.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/PhylogenyData.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/data/PhylogenyData.java:54: warning: @param argument "PhylogenyData" is not a parameter name.
> [WARNING] * @param PhylogenyData
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/PhylogenyDataUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/PhylogenyDecorator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/PhylogenyDecorator.FIELD.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/factories/PhylogenyFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyMethods.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyMethods.PhylogenyNodeField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyNode.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:99: warning: @param argument "n" is not a parameter name.
> [WARNING] * @param n
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:292: warning: @param argument "n" is not a parameter name.
> [WARNING] * @param n
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/PhylogenyNode.java:778: warning: @param argument "n" is not a parameter name.
> [WARNING] * @param n
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/PhylogenyNodeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/PhylogenyParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/util/PhylogenyParserException.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/io/parsers/util/PhylogenyParserException.java:48: warning: @param argument "arg0" is not a parameter name.
> [WARNING] * @param arg0
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/PhylogenyWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/PhylogenyWriter.FORMAT.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/PhyloInferenceDialog.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/phylostrip.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/phyloxml_converter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlHandler.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlMapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/PhyloXmlNodeWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/PhyloXmlUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Point.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/PointParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Polygon.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/PolygonParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/PostOrderStackObject.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/PostorderTreeIterator.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/phylogeny/iterators/PostorderTreeIterator.java:45: warning: @param argument "t" is not a parameter name.
> [WARNING] * @param t
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/PreorderTreeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/ProcessPool.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/ProcessRunning.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/PropertiesMap.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Property.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Property.AppliesTo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/PropertyParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/Protein.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/ProteinDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/ProteinId.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/datastructures/Queue.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/RandomThing.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Reference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/ReferenceParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/reinv_count.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/RenderableMsaSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/RenderableVector.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/ResampleableMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/ResidueRenderer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/RestUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/rio.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/RIO.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/RIO.REROOTING.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/RIOException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/RunnableProcess.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/SankoffParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/Sarray.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/ScoringMethodForExternalNode.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:47: warning: invalid input: '<'
> [WARNING] *            SortedMap<PhylogenyNode, Double> in which the external node
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/pccx/ScoringMethodForExternalNode.java:55: warning: @param argument "annotate_phylogeny" is not a parameter name.
> [WARNING] * @param annotate_phylogeny
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDI.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDI.java:85: warning: Tag @see: reference not found: #infer(boolean)
> [WARNING] * @see #infer(boolean)
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDIException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDIR.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:80: warning: Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:101: warning: Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:117: warning: Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:130: warning: Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/sdi/SDIR.java:146: warning: Tag @see: reference not found: #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDIutil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDIutil.ALGORITHM.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/SDIutil.TaxonomyComparisonBase.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Sequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/SequenceAccessionTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/SequenceDatabaseEntry.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/SequenceDataRetriver.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/SequenceDbWsTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/SequenceParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/SequenceRelation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/SequenceWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/SequenceWriter.SEQ_FORMAT.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/shared_chars_in_ext_nodes.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/simple_node_processor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/SimpleDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/species/Species.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/Sset.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/subtree_feature_count.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/support_statistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/support_transfer.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/application/support_transfer.java:55: warning: Parameter "args" is documented more than once.
> [WARNING] * @param args[1]
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/application/support_transfer.java:60: warning: Parameter "args" is documented more than once.
> [WARNING] * @param args[2]
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/application/support_transfer.java:62: warning: Parameter "args" is documented more than once.
> [WARNING] * @param args[3]
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/SupportCount.html...
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> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:592: warning: @param argument "protein_length_stats_by_dc" is not a parameter name.
> [WARNING] * @param protein_length_stats_by_dc
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:672: warning: @param argument "consider_directedness_and_adjacency_for_bin_combinations" is not a parameter name.
> [WARNING] * @param consider_directedness_and_adjacency_for_bin_combinations
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/surfacing/SurfacingUtil.java:673: warning: @param argument "all_binary_domains_combination_gained" is not a parameter name.
> [WARNING] * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/SymmetricalDistanceMatrixParser.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/TaxonomyParser.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/TestGo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/TestGSDI.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/TestPccx.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/TestPhylogenyReconstruction.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/TestRIO.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/TestSurfacing.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/development/Time.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/tol/TolParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/tol/TolXmlHandler.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/tol/TolXmlMapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/TreeColorSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/TreeFontSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/TreePanel.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/TreePanelUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/TreeSplitMatrix.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/tools/TreeSplitMatrix.java:73: warning: @param argument "target" is not a parameter name.
> [WARNING] * @param target
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/TxSearch.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-forester/src/main/java/org/forester/ws/wabi/TxSearch.java:41: warning: invalid input: '&mode'
> [WARNING] * See: http://xml.nig.ac.jp/wabi/Method?serviceName=TxSearch&mode=methodList
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/TxSearch.RANKS.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/TxSearch.TAX_NAME_CLASS.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/TxSearch.TAX_RANK.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/UniProtEntry.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/UniProtTaxonomy.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/Uri.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/UriParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/UrlTreeReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/WabiTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/WebservicesManager.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/WebservicesManager.WsPhylogenyFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/WebserviceUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/wiki_examples.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/WindowsUtils.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/XmlElement.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/package-tree.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/datastructures/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/tools/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nexus/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/nhx/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/phyloxml/data/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/tol/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/tol/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/util/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/parsers/util/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/io/writers/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/factories/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/package-summary.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sdi/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/species/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/species/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/hmmer/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/hmmer/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/package-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/package-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/constant-values.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/serialized-form.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoRelationship.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoRelationship.Type.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/TestGo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoNameSpace.GoNamespaceType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoTerm.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoSubset.Type.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/Mapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoId.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoUtils.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoTerm.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/PfamToGoMapping.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/OBOparser.ReturnType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/GoXRef.Type.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoXRef.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/class-use/BasicGoSubset.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/class-use/MetaOntologizer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/go/etc/class-use/OntologizerResult.TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/class-use/SupportCount.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/class-use/ConfidenceAssessor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/class-use/PhylogenyDecorator.FIELD.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/tools/class-use/TreeSplitMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInferenceException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/class-use/AncestralTaxonomyInference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/analysis/class-use/TaxonomyDataManager.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengthsTable.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CountsBasedPairwiseDomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/MappingResults.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseGenomeComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsBasedPairwiseSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainParsimonyCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainLengths.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicGenomeWideCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.PRINT_OPTION.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilaritySortField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarity.DomainSimilarityScoring.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.GoAnnotationOutput.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainSimilarityCalculator.Detailedness.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SurfacingConstants.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/PairwiseDomainSimilarity.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/AdjactantDirectedBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/CombinationsBasedPairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicBinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/TestSurfacing.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/SimpleDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/BasicCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DirectedCombinableDomains.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/ProteinCountsBasedPairwiseDomainSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainCountsDifferenceUtil.COPY_CALCULATION_MODE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/surfacing/class-use/DomainArchitectureBasedGenomeSimilarityCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicProtein.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/Protein.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/ProteinId.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/Domain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.OutputFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/BinaryDomainCombination.DomainCombinationType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/protein/class-use/BasicDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example4.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example5.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example3.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example2.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/examples/class-use/Example1.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/test/class-use/Test.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/hmmer/class-use/Test.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtEntry.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/UniProtTaxonomy.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/EbiDbEntry.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDatabaseEntry.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/seqdb/class-use/SequenceDbWsTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/WabiTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/RestUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_RANK.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.TAX_NAME_CLASS.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/ws/wabi/class-use/TxSearch.RANKS.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/phylostrip.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/obo_tool.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/gene_tree_preprocess.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/support_transfer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/pccx.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/pfam_go.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/fasta_split.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2pfamid.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/annotator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/gsdi.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/pfamacc2go.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/surfacing.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/decorator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/mcc.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/dom_dup.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/nj.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/pfam2go_extractor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/support_statistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/meta_ontologizer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/phyloxml_converter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/msa_compactor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/decoratorX.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/goac.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/check_fasta.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/table2fasta.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/count_support.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/confadd.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/application/class-use/rio.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/ExternalProgram.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/CommandLineArguments.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/EasyWriter.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/SystemCommandExecutor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/BasicDescriptiveStatistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/TaxonomyColors.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/IllegalFormatUseException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/StringInt.DescendingIntComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/ForesterConstants.PhylogeneticTreeFormats.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTable.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/SequenceAccessionTools.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/BasicTableParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/GeneralTable.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/CommandProcessBuilder.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/DescriptiveStatistics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/WindowsUtils.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/AsciiHistogram.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/util/class-use/FailedConditionCheckException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/ResampleableMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/ClustalOmega.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/DeleteableMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/Msa.MSA_FORMAT.html...
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/BasicMsa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaMethods.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/MsaFormatException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa/class-use/Mafft.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/class-use/MolecularSequence.TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/sequence/class-use/BasicSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/subtree_feature_count.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/inverted_dcs.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/get_distances.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/domainloss_replacement.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/wiki_examples.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/shared_chars_in_ext_nodes.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2coloredgraphics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/map_lengths.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/phylo2graphics.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/get_loss_nodes.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/genome_counts_for_once_appearing_dcs.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/set_comparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/aaa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/tax_code_cleaner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/simple_node_processor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/reinv_count.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/get_subtree_specific_chars.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/aa.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/core_chars.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/get_shared_chars.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/applications/class-use/get_genome_counts_per_char.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.PHYLOGENY_GRAPHICS_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.NODE_LABEL_DIRECTION.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Options.CLADOGRAM_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeFontSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/UrlTreeReader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanel.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/FontChooser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreePanelUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrame.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplication.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Constants.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.UI.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Configuration.EXT_NODE_DATA_RETURN_ON.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/AptxUtil.GraphicsExportType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/Archaeopteryx.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/ArchaeopteryxA.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainPanel.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/TreeColorSet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/class-use/MainFrameApplet.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/RunnableProcess.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/SequenceDataRetriver.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ImageLoader.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessRunning.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/ProcessPool.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/InferenceManager.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhyloInferenceDialog.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/AncestralTaxonomyInferrer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferenceOptions.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/PhylogeneticInferrer.MSA_PRG.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/tools/class-use/Blast.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebservicesManager.WsPhylogenyFormat.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/PhylogeniesWebserviceClient.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/WebserviceUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/webservices/class-use/BasicPhylogeniesWebserviceClient.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableDomainArchitecture.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableMsaSequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderablePhylogenyData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/archaeopteryx/phylogeny/data/class-use/RenderableVector.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/tools/class-use/BootstrapResampler.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/FitchParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/DolloParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/parsimony/class-use/SankoffParsimony.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/class-use/TestPhylogenyReconstruction.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.NucleotideStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.GainLossStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.Format.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/CharacterStateMatrix.BinaryStates.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/character/class-use/BasicCharacterStateMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/DistanceMatrix.Format.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/matrix/distance/class-use/BasicSymmetricalDistanceMatrix.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/PairwiseDistanceCalculator.PWD_DISTANCE_METHOD.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sset.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoining.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningF.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/Sarray.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/evoinference/distance/class-use/NeighborJoiningR.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/class-use/RIOException.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/class-use/TestRIO.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/rio/class-use/RIO.REROOTING.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/Chart.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaProperties.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/GapContribution.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/msa_compactor/class-use/MsaCompactor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.PhylogenyNodeField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyMethods.DESCENDANT_SORT_PRIORITY.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyBranch.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/Phylogeny.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/class-use/PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/PhylogenyFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/factories/class-use/ParserBasedPhylogenyFactory.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostorderTreeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PhylogenyNodeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PreorderTreeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/LevelOrderTreeIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/PostOrderStackObject.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/iterators/class-use/ExternalForwardIterator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/MultipleUris.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Uri.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BinaryCharacters.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeDataField.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Accession.Source.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Reference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchWidth.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Polygon.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Taxonomy.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Sequence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Point.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchColor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Property.AppliesTo.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/ProteinDomain.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/SequenceRelation.SEQUENCE_RELATION_TYPE.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Event.EventType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PropertiesMap.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Confidence.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Date.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/DomainArchitecture.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Annotation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeShape.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.NodeFill.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/NodeVisualData.FontType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Distribution.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/BranchData.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/Identifier.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/phylogeny/data/class-use/PhylogenyDataUtil.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/class-use/CoverageExtender.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/class-use/ExternalNodeBasedCoverage.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/org/forester/pccx/class-use/BranchCountingBasedScoringMethod.html...
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> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-forester/target/biojava-forester-5.4.0-javadoc.jar
> [INFO] 
> [INFO] -------------------< org.biojava:biojava-alignment >--------------------
> [INFO] Building biojava-alignment 5.4.0                                  [4/14]
> [INFO] --------------------------------[ jar ]---------------------------------
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [INFO] 
> [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-alignment ---
> [INFO] Copying 2 resources
> [INFO] 
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-alignment ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 53 source files to /<<PKGBUILDDIR>>/biojava-alignment/target/classes
> [INFO] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java uses or overrides a deprecated API that is marked for removal.
> [INFO] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java: Recompile with -Xlint:removal for details.
> [INFO] 
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> [INFO] 
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ biojava-alignment ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 24 source files to /<<PKGBUILDDIR>>/biojava-alignment/target/test-classes
> [INFO] 
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ biojava-alignment ---
> [INFO] Tests are skipped.
> [INFO] 
> [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ biojava-alignment ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-alignment/target/biojava-alignment-5.4.0.jar
> [INFO] 
> [INFO] --- maven-javadoc-plugin:3.0.1:jar (default-cli) @ biojava-alignment ---
> [INFO] Adding the --ignore-source-errors option
> [ERROR] Error fetching link: /<<PKGBUILDDIR>>/biojava-core/target/apidocs/package-list. Ignored it.
> [ERROR] Error fetching link: /<<PKGBUILDDIR>>/biojava-forester/target/apidocs/package-list. Ignored it.
> [WARNING] Javadoc Warnings
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> [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 org.biojava.nbio.alignment.routines...
> [WARNING] Loading source files for package org.biojava.nbio.alignment.template...
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> [WARNING] Constructing Javadoc information...
> [WARNING] Building index for all the packages and classes...
> [WARNING] Standard Doclet version 17.0.5+8-Debian-2
> [WARNING] Building tree for all the packages and classes...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/AbstractMatrixAligner.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java:49: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java:40: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java:46: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java:35: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:125: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:206: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:542: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java:615: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.PairInProfileScorerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.PairwiseSequenceAlignerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.PairwiseSequenceScorerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.ProfileProfileAlignerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/Alignments.RefinerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:45: warning: invalid input: '<'
> [WARNING] * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:70: warning: @param argument "cutsPerSection" is not a parameter name.
> [WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java:83: warning: @param argument "cutsPerSection" is not a parameter name.
> [WARNING] * @param cutsPerSection the number of cuts added to each section during each pass
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java:37: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/CallablePairwiseSequenceScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:36: warning: Tag @link: reference not found: Profile
> [WARNING] * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java:37: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/Comparison.html...
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:41: warning: @param argument "s1" is not a parameter name.
> [WARNING] * @param s1
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java:43: warning: @param argument "s2" is not a parameter name.
> [WARNING] * @param s2
> [WARNING] ^
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/demo/CookbookMSA.html...
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java:119: warning: invalid usage of tag {@link #pamDistance(MultipleSequenceAlignment
> [WARNING] * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java:37: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java:37: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java:37: warning: invalid input: '<'
> [WARNING] * space complexity is a modest (a multiple < 2) increase in time.
> [WARNING] ^
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> [WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java:34: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:34: warning: Tag @link: reference not found: Profile
> [WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java:35: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/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] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:34: warning: Tag @link: reference not found: Profile
> [WARNING] * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java:35: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/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] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java:35: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] * @param <S> each element of the alignment {@link Profile} is of type S
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java:37: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/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] ^
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java:44: warning: Tag @link: reference not found: AlignedSequence
> [WARNING] * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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> [WARNING] /<<PKGBUILDDIR>>/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java:163: warning: @param argument "dbReference" is not a parameter name.
> [WARNING] * @param dbReference the string without the initial annotation identifier ( #=GS DR )
> [WARNING] ^
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> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] ^
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> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/DistanceMatrixCalculator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/ForesterWrapper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/Comparison.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/class-use/TreeConstructorType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/NeedlemanWunsch.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/StandardRescoreRefiner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SmithWaterman.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.RefinerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.ProfileProfileAlignerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceScorerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairwiseSequenceAlignerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/Alignments.PairInProfileScorerType.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleProfileProfileAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SimpleGapPenalty.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalIdentityInProfileScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/GuideTree.Node.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/SubstitutionMatrixScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/class-use/FractionalSimilarityInProfileScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AnchoredPairwiseSequenceAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Subproblem.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Anchor.QueryIndexComparator.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Cut.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/AlignerHelper.Last.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/class-use/GuanUberbacher.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractMatrixAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/MatrixAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairInProfileScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallableProfileProfileAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Aligner.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/RescoreRefiner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractPairwiseSequenceAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PairwiseSequenceScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/AbstractProfileProfileAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/HierarchicalClusterer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GapPenalty.Type.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/GuideTreeNode.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/PartitionRefiner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceScorer.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/CallablePairwiseSequenceAligner.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/ProfileProfileScorer.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/class-use/Scorer.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileAnnotation.StockholmFileAnnotationReference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmStructure.DatabaseReference.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/class-use/StockholmFileParser.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/demo/package-use.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/package-use.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/io/package-use.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/routines/package-use.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/alignment/template/package-use.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/org/biojava/nbio/phylo/package-use.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/overview-tree.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/index.html...
> [WARNING] Building index for all classes...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/allclasses-index.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/allpackages-index.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/index-all.html...
> [WARNING] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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] /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/overview-summary.html...
> [WARNING] Generating /<<PKGBUILDDIR>>/biojava-alignment/target/apidocs/help-doc.html...
> [WARNING] 58 warnings
> [INFO] Building jar: /<<PKGBUILDDIR>>/biojava-alignment/target/biojava-alignment-5.4.0-javadoc.jar
> [INFO] 
> [INFO] -------------------< org.biojava:biojava-structure >--------------------
> [INFO] Building biojava-structure 5.4.0                                  [5/14]
> [INFO] --------------------------------[ jar ]---------------------------------
> [WARNING] The POM for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian is missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian: Plugin org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:debian or one of its dependencies could not be resolved: Cannot access central (https://repo.maven.apache.org/maven2) in offline mode and the artifact org.jvnet.jaxb2.maven2:maven-jaxb22-plugin:jar:debian has not been downloaded from it before.
> [WARNING] The artifact java3d:vecmath:jar:debian has been relocated to javax.vecmath:vecmath:jar:debian
> [WARNING] The artifact com.sun.xml.bind:jaxb-impl:jar:debian has been relocated to org.glassfish.jaxb:jaxb-runtime:jar:debian
> [WARNING] The artifact javax.activation:activation:jar:debian has been relocated to com.sun.activation:javax.activation:jar:debian
> [INFO] 
> [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ biojava-structure ---
> [INFO] Copying 3 resources
> [INFO] Copying 61 resources
> [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html
> [INFO] 
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ biojava-structure ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 522 source files to /<<PKGBUILDDIR>>/biojava-structure/target/classes
> [INFO] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Some input files use or override a deprecated API that is marked for removal.
> [INFO] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java: Recompile with -Xlint:removal for details.
> [INFO] -------------------------------------------------------------
> [ERROR] COMPILATION ERROR : 
> [INFO] -------------------------------------------------------------
> [ERROR] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:[296,52] reference to newFileSystem is ambiguous
>   both method newFileSystem(java.nio.file.Path,java.lang.ClassLoader) in java.nio.file.FileSystems and method newFileSystem(java.nio.file.Path,java.util.Map<java.lang.String,?>) in java.nio.file.FileSystems match
> [INFO] 1 error
> [INFO] -------------------------------------------------------------
> [INFO] 
> [INFO] ------------------------------------------------------------------------
> [INFO] Skipping biojava
> [INFO] This project has been banned from the build due to previous failures.
> [INFO] ------------------------------------------------------------------------
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Summary for biojava 5.4.0:
> [INFO] 
> [INFO] biojava ............................................ SUCCESS [  0.411 s]
> [INFO] biojava-core ....................................... SUCCESS [  8.513 s]
> [INFO] biojava-forester ................................... SUCCESS [  9.559 s]
> [INFO] biojava-alignment .................................. SUCCESS [  3.084 s]
> [INFO] biojava-structure .................................. FAILURE [  2.753 s]
> [INFO] biojava-jcolorbrewer ............................... SKIPPED
> [INFO] biojava-structure-gui .............................. SKIPPED
> [INFO] biojava-genome ..................................... SKIPPED
> [INFO] biojava-modfinder .................................. SKIPPED
> [INFO] biojava-ws ......................................... SKIPPED
> [INFO] biojava-protein-disorder ........................... SKIPPED
> [INFO] biojava-aa-prop .................................... SKIPPED
> [INFO] biojava-survival ................................... SKIPPED
> [INFO] biojava-ontology ................................... SKIPPED
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time:  24.629 s
> [INFO] Finished at: 2022-12-20T09:39:51Z
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project biojava-structure: Compilation failure
> [ERROR] /<<PKGBUILDDIR>>/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:[296,52] reference to newFileSystem is ambiguous
> [ERROR]   both method newFileSystem(java.nio.file.Path,java.lang.ClassLoader) in java.nio.file.FileSystems and method newFileSystem(java.nio.file.Path,java.util.Map<java.lang.String,?>) in java.nio.file.FileSystems match
> [ERROR] -> [Help 1]
> [ERROR] 
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR] 
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
> [ERROR] 
> [ERROR] After correcting the problems, you can resume the build with the command
> [ERROR]   mvn <args> -rf :biojava-structure
> [0m[0mdh_auto_build: error: /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=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg/debian -Dmaven.repo.local=/<<BUILDDIR>>/biojava5-live-5.4.0\+dfsg/debian/maven-repo --batch-mode package javadoc:jar javadoc:aggregate -DskipTests -Dnotimestamp=true -Dlocale=en_US returned exit code 1
> make[1]: *** [debian/rules:38: override_dh_auto_build] Error 25

The full build log is available from:
http://qa-logs.debian.net/2022/12/20/biojava5-live_5.4.0+dfsg-4_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221220;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.