[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_41 #8196
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https://jenkins.debian.net/job/reproducible_builder_armhf_41/8196/------------------------------------------
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[javadoc] Loading source files for package org.forester.phylogeny.data...
[javadoc] Loading source files for package org.forester.phylogeny.factories...
[javadoc] Loading source files for package org.forester.phylogeny.iterators...
[javadoc] Loading source files for package org.forester.protein...
[javadoc] Loading source files for package org.forester.sdi...
[javadoc] Loading source files for package org.forester.sequence...
[javadoc] Loading source files for package org.forester.species...
[javadoc] Loading source files for package org.forester.surfacing...
[javadoc] Loading source files for package org.forester.test...
[javadoc] Loading source files for package org.forester.test.examples...
[javadoc] Loading source files for package org.forester.tools...
[javadoc] Loading source files for package org.forester.util...
[javadoc] Loading source files for package org.forester.ws.hmmer...
[javadoc] Loading source files for package org.forester.ws.seqdb...
[javadoc] Loading source files for package org.forester.ws.uniprot...
[javadoc] Loading source files for package org.forester.ws.wabi...
[javadoc] Constructing Javadoc information...
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.java:80: error: package org.jmol.api does not exist
[javadoc] import org.jmol.api.JmolViewer;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:56: error: package org.jmol.adapter.smarter does not exist
[javadoc] import org.jmol.adapter.smarter.SmarterJmolAdapter;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:57: error: package org.jmol.api does not exist
[javadoc] import org.jmol.api.JmolAdapter;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:59: error: package org.jmol.api does not exist
[javadoc] import org.jmol.api.JmolStatusListener;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:60: error: package org.jmol.api does not exist
[javadoc] import org.jmol.api.JmolViewer;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:61: error: package org.jmol.util does not exist
[javadoc] import org.jmol.util.Logger;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:70: error: cannot find symbol
[javadoc] private JmolViewer viewer;
[javadoc] ^
[javadoc] symbol: class JmolViewer
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:71: error: cannot find symbol
[javadoc] private JmolAdapter adapter;
[javadoc] ^
[javadoc] symbol: class JmolAdapter
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:72: error: cannot find symbol
[javadoc] JmolStatusListener statusListener;
[javadoc] ^
[javadoc] symbol: class JmolStatusListener
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:109: error: cannot find symbol
[javadoc] public JmolViewer getViewer() {
[javadoc] ^
[javadoc] symbol: class JmolViewer
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:113: error: cannot find symbol
[javadoc] public JmolAdapter getAdapter(){
[javadoc] ^
[javadoc] symbol: class JmolAdapter
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java:117: error: cannot find symbol
[javadoc] public JmolStatusListener getStatusListener(){
[javadoc] ^
[javadoc] symbol: class JmolStatusListener
[javadoc] location: class JmolPanel
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:33: error: package org.jmol.api does not exist
[javadoc] import org.jmol.api.JmolStatusListener;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:34: error: package org.jmol.constant does not exist
[javadoc] import org.jmol.constant.EnumCallback;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:36: error: cannot find symbol
[javadoc] public class MyJmolStatusListener implements JmolStatusListener {
[javadoc] ^
[javadoc] symbol: class JmolStatusListener
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:114: error: cannot find symbol
[javadoc] public void notifyCallback(EnumCallback arg0, Object[] arg1) {
[javadoc] ^
[javadoc] symbol: class EnumCallback
[javadoc] location: class MyJmolStatusListener
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/jmol/MyJmolStatusListener.java:120: error: cannot find symbol
[javadoc] public boolean notifyEnabled(EnumCallback arg0) {
[javadoc] ^
[javadoc] symbol: class EnumCallback
[javadoc] location: class MyJmolStatusListener
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:33: error: package javax.jnlp does not exist
[javadoc] import javax.jnlp.BasicService;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:34: error: package javax.jnlp does not exist
[javadoc] import javax.jnlp.FileContents;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:35: error: package javax.jnlp does not exist
[javadoc] import javax.jnlp.PersistenceService;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:36: error: package javax.jnlp does not exist
[javadoc] import javax.jnlp.ServiceManager;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:37: error: package javax.jnlp does not exist
[javadoc] import javax.jnlp.UnavailableServiceException;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:56: error: cannot find symbol
[javadoc] PersistenceService ps;
[javadoc] ^
[javadoc] symbol: class PersistenceService
[javadoc] location: class PersistentConfig
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:57: error: cannot find symbol
[javadoc] BasicService bs ;
[javadoc] ^
[javadoc] symbol: class BasicService
[javadoc] location: class PersistentConfig
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/webstart/PersistentConfig.java:60: error: cannot find symbol
[javadoc] throws UnavailableServiceException
[javadoc] ^
[javadoc] symbol: class UnavailableServiceException
[javadoc] location: class PersistentConfig
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:8: error: package javax.vecmath does not exist
[javadoc] import javax.vecmath.Point3d;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:88: error: cannot find symbol
[javadoc] private Point3d[] spherePoints;
[javadoc] ^
[javadoc] symbol: class Point3d
[javadoc] location: class AsaCalculator
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:255: error: cannot find symbol
[javadoc] private Point3d[] generateSpherePoints(int nSpherePoints) {
[javadoc] ^
[javadoc] symbol: class Point3d
[javadoc] location: class AsaCalculator
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:36: error: package com.google.common.collect does not exist
[javadoc] import com.google.common.collect.Iterables;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:37: error: package com.google.common.collect does not exist
[javadoc] import com.google.common.collect.Lists;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java:39: error: package com.google.common.io does not exist
[javadoc] import com.google.common.io.Resources;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:25: error: package com.google.common.io does not exist
[javadoc] import com.google.common.io.CharStreams;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:26: error: package com.google.common.io does not exist
[javadoc] import com.google.common.io.LineProcessor;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java:66: error: cannot find symbol
[javadoc] private static final class FastqParserLineProcessor implements LineProcessor<Object>
[javadoc] ^
[javadoc] symbol: class LineProcessor
[javadoc] location: class FastqParser
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java:25: error: package com.google.common.collect does not exist
[javadoc] import com.google.common.collect.Lists;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java:26: error: package com.google.common.collect does not exist
[javadoc] import com.google.common.collect.ImmutableList;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/survival/kaplanmeier/figure/ExpressionFigure.java:24: error: package org.apache.commons.math.stat.descriptive does not exist
[javadoc] import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/survival/cox/CoxCC.java:11: error: package org.apache.commons.math.stat.correlation does not exist
[javadoc] import org.apache.commons.math.stat.correlation.Covariance;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/survival/cox/CoxCC.java:12: error: package org.apache.commons.math.stat.descriptive does not exist
[javadoc] import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/survival/kaplanmeier/metadata/MeanQuantizer.java:8: error: package org.apache.commons.math.stat.descriptive does not exist
[javadoc] import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:16: error: package org.json.simple does not exist
[javadoc] import org.json.simple.JSONArray;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:17: error: package org.json.simple does not exist
[javadoc] import org.json.simple.JSONObject;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:18: error: package org.json.simple does not exist
[javadoc] import org.json.simple.JSONValue;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:38: error: package com.itextpdf.text does not exist
[javadoc] import com.itextpdf.text.Document;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:39: error: package com.itextpdf.text does not exist
[javadoc] import com.itextpdf.text.DocumentException;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:40: error: package com.itextpdf.text does not exist
[javadoc] import com.itextpdf.text.FontFactory;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:41: error: package com.itextpdf.text does not exist
[javadoc] import com.itextpdf.text.Rectangle;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:42: error: package com.itextpdf.awt does not exist
[javadoc] import com.itextpdf.awt.DefaultFontMapper;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:43: error: package com.itextpdf.text.pdf does not exist
[javadoc] import com.itextpdf.text.pdf.PdfContentByte;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/PdfExporter.java:44: error: package com.itextpdf.text.pdf does not exist
[javadoc] import com.itextpdf.text.pdf.PdfWriter;
[javadoc] ^
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/forester/archaeopteryx/ArchaeopteryxE.java:29: error: package org.apache.commons.codec.binary does not exist
[javadoc] import org.apache.commons.codec.binary.Base64;
[javadoc] ^
[javadoc] javadoc: warning - Error fetching URL: http://java.sun.com/j2se/1.6.0/docs/api/
[javadoc] Standard Doclet version 1.8.0_111
[javadoc] Building tree for all the packages and classes...
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see:illegal character: "123" in "{@link GroupType#WATERNAMES}"
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see:illegal character: "64" in "{@link GroupType#WATERNAMES}"
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:142: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:154: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:172: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:183: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:194: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:215: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:265: warning - @param argument "chainId" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/AtomPositionMap.java:273: warning - @param argument "chainId" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Calc.java:146: warning - Tag @link: reference not found: subtract
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/DBRef.java:199: warning - Tag @see: can't find setChainId(Character) in org.biojava.bio.structure.DBRef
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Element.java:405: warning - Tag @link: reference not found: T
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see: reference not found: {@link GroupType#WATERNAMES}
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @link: can't find WATERNAMES in org.biojava.bio.structure.GroupType
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Group.java:374: warning - Tag @see: reference not found: {@link GroupType#WATERNAMES}
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:69: warning - Tag @link: can't find getReplacement(String, boolean) in org.biojava.bio.structure.PDBStatus
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:223: warning - Tag @link: can't find getReplacement(String,boolean) in org.biojava.bio.structure.PDBStatus
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:108: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/PDBStatus.java:108: warning - @param argument "statusStrUpper" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/Structure.java:606: warning - @param argument "PDBCrystallographicInfo" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureIdentifier.java:33: warning - Tag @link: reference not found: ScopDomain ScopDomains
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureIdentifier.java:33: warning - Tag @link: reference not found: CathDomain CathDomains
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureImpl.java:742: warning - @param argument "PDBCrystallographicInfo" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureTools.java:297: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/StructureTools.java:1249: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see:illegal character: "123" in "{@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length"
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see:illegal character: "64" in "{@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length"
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/SVDSuperimposer.java:336: warning - Tag @see: reference not found: {@link #getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/CeCPMain.java:248: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/CeParameters.java:346: warning - @param argument "maxNrIterationsForOptimization" is not a parameter name.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:190: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/OptimalCECPMain.java:470: warning - Tag @link: can't find alignHeuristic(Atom[], Atom[], Object) in org.biojava.bio.structure.align.ce.OptimalCECPMain
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/StartupParameters.java:67: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/ce/StartupParameters.java:79: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/DisplayAFP.java:143: warning - @return tag has no arguments.
[javadoc] /build/1st/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava/bio/structure/align/gui/DotPlotPanel.java:67: warning - @param argument "background" is not a parameter name.
/srv/reproducible-results/rbuild-debian-HZy4kA6P/tmp.DoWRKn3Mjg: FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1720)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:404)
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