Source: biojava4-live Version: 4.2.11+dfsg-1 Severity: serious Justification: FTBFS on amd64 Tags: buster sid Usertags: ftbfs-20181229 ftbfs-buster
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<BUILDDIR>>/biojava4-live-4.2.11+dfsg' > cd biojava-jcolorbrewer && ant jar > Buildfile: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-jcolorbrewer/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-jcolorbrewer/classes > [mkdir] Created dir: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-jcolorbrewer/build.xml:93: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 9 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-jcolorbrewer/classes > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java > uses or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [copy] Warning: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-jcolorbrewer/src/main/resources > does not exist. > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist/biojava4-jcolorbrewer.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-forester && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-forester/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-forester/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-forester/build.xml:93: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 359 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-forester/classes > [javac] Note: Some input files use or override a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [copy] Warning: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-forester/src/main/resources > does not exist. > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist/biojava4-forester.jar > > BUILD SUCCESSFUL > Total time: 9 seconds > cd biojava-core && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-core/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-core/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-core/build.xml:93: warning: > 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set > to false for repeatable builds > [javac] Compiling 176 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-core/classes > [javac] Note: Some input files use or override a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] Note: Some input files use unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [copy] Copying 24 files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-core/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist/biojava4-core.jar > > BUILD SUCCESSFUL > Total time: 4 seconds > cd biojava-phylo && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-phylo/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-phylo/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-phylo/build.xml:93: warning: > 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set > to false for repeatable builds > [javac] Compiling 8 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-phylo/classes > [copy] Copying 2 files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-phylo/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist/biojava4-phylo.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-alignment && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-alignment/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-alignment/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-alignment/build.xml:93: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 45 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-alignment/classes > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java > uses or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [copy] Copying 1 file to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-alignment/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/dist/biojava4-alignment.jar > > BUILD SUCCESSFUL > Total time: 2 seconds > cd biojava-aa-prop && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-aa-prop/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/build.xml:93: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 32 source files to > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/build/biojava4-aa-prop/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:24: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessorType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:25: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlElement; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:26: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlRootElement; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:33: > error: cannot find symbol > [javac] @XmlRootElement(name="compoundtable", > namespace="http://biojava.org";) > [javac] ^ > [javac] symbol: class XmlRootElement > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:34: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: class XmlAccessorType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:26: > error: cannot find symbol > [javac] @XmlRootElement(name = "compoundcomposition", namespace > ="http://biojava.org";) > [javac] ^ > [javac] symbol: class XmlRootElement > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:27: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: class XmlAccessorType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlRootElement; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java:28: > error: cannot find symbol > [javac] @XmlRootElement(name="elements", namespace="http://biojava.org";) > [javac] ^ > [javac] symbol: class XmlRootElement > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:24: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessorType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:25: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAttribute; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:26: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlElement; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:36: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: class XmlAccessorType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:24: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessorType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:25: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAttribute; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:26: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:29: > error: cannot find symbol > [javac] @XmlType(name = "Iostope", propOrder = > {"name","neutronsNum","mass"}) > [javac] ^ > [javac] symbol: class XmlType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:30: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: class XmlAccessorType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:24: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAccessorType; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:25: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.XmlAttribute; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:27: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.FIELD) > [javac] ^ > [javac] symbol: class XmlAccessorType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:23: > error: package javax.xml.bind.annotation does not exist > [javac] import javax.xml.bind.annotation.*; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java:31: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.JAXBException; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java:113: > error: cannot find symbol > [javac] throws FileNotFoundException, JAXBException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java:143: > error: cannot find symbol > [javac] public static final double getMolecularWeight(String sequence, > File aminoAcidCompositionFile) throws FileNotFoundException, JAXBException{ > [javac] > ^ > [javac] symbol: class JAXBException > [javac] location: class PeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java:170: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java:190: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:29: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.JAXBException; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:83: > error: cannot find symbol > [javac] public double getMolecularWeight(ProteinSequence sequence, File > aminoAcidCompositionFile) throws JAXBException, FileNotFoundException; > [javac] > ^ > [javac] symbol: class JAXBException > [javac] location: interface IPeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:103: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException; > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: interface IPeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:133: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException; > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: interface IPeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java:150: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException; > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: interface IPeptideProperties > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:32: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.JAXBContext; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:33: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.JAXBException; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:34: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.Unmarshaller; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:90: > error: cannot find symbol > [javac] public double getMolecularWeight(ProteinSequence sequence, File > aminoAcidCompositionFile) throws JAXBException, FileNotFoundException { > [javac] > ^ > [javac] symbol: class JAXBException > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:101: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:123: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:134: > error: cannot find symbol > [javac] throws JAXBException, FileNotFoundException{ > [javac] ^ > [javac] symbol: class JAXBException > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:26: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.ValidationEvent; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:27: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.ValidationEventHandler; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:28: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.ValidationEventLocator; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:30: > error: cannot find symbol > [javac] public class MyValidationEventHandler implements > ValidationEventHandler{ > [javac] ^ > [javac] symbol: class ValidationEventHandler > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:35: > error: cannot find symbol > [javac] public boolean handleEvent(ValidationEvent ve) { > [javac] ^ > [javac] symbol: class ValidationEvent > [javac] location: class MyValidationEventHandler > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:23: > error: package javax.xml.bind does not exist > [javac] import javax.xml.bind.SchemaOutputResolver; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:29: > error: cannot find symbol > [javac] public class SchemaGenerator extends SchemaOutputResolver{ > [javac] ^ > [javac] symbol: class SchemaOutputResolver > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:34: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: variable XmlAccessType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:27: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: variable XmlAccessType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:40: > error: cannot find symbol > [javac] @XmlElement(name = "compound", required = true) > [javac] ^ > [javac] symbol: class XmlElement > [javac] location: class AminoAcidCompositionTable > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:36: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: variable XmlAccessType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:30: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.NONE) > [javac] ^ > [javac] symbol: variable XmlAccessType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:35: > error: cannot find symbol > [javac] @XmlAttribute(name = "name", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Isotope > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:40: > error: cannot find symbol > [javac] @XmlAttribute(name = "neutronsnum", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Isotope > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java:45: > error: cannot find symbol > [javac] @XmlAttribute(name = "mass", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Isotope > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:42: > error: cannot find symbol > [javac] @XmlAttribute(name = "name", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Element > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:47: > error: cannot find symbol > [javac] @XmlAttribute(name = "symbol") > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Element > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:52: > error: cannot find symbol > [javac] @XmlAttribute(name = "atomicnumber") > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Element > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:57: > error: cannot find symbol > [javac] @XmlAttribute(name = "mass", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Element > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java:62: > error: cannot find symbol > [javac] @XmlElement > [javac] ^ > [javac] symbol: class XmlElement > [javac] location: class Element > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:32: > error: cannot find symbol > [javac] @XmlAttribute(name = "symbol", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:37: > error: cannot find symbol > [javac] @XmlAttribute(name = "shortname") > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:42: > error: cannot find symbol > [javac] @XmlAttribute(name = "name") > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:47: > error: cannot find symbol > [javac] @XmlAttribute(name = "id") > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:27: > error: cannot find symbol > [javac] @XmlAccessorType(XmlAccessType.FIELD) > [javac] ^ > [javac] symbol: variable XmlAccessType > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:52: > error: cannot find symbol > [javac] @XmlElement(name = "element") > [javac] ^ > [javac] symbol: class XmlElement > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java:57: > error: cannot find symbol > [javac] @XmlElement(name = "isotope", required = false) > [javac] ^ > [javac] symbol: class XmlElement > [javac] location: class AminoAcidComposition > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:29: > error: cannot find symbol > [javac] @XmlAttribute(name = "name", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Name2Count > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java:31: > error: cannot find symbol > [javac] @XmlAttribute(name = "count", required = true) > [javac] ^ > [javac] symbol: class XmlAttribute > [javac] location: class Name2Count > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:138: > error: cannot find symbol > [javac] JAXBContext jc = > JAXBContext.newInstance(iTable.getClass()); > [javac] ^ > [javac] symbol: class JAXBContext > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:138: > error: cannot find symbol > [javac] JAXBContext jc = > JAXBContext.newInstance(iTable.getClass()); > [javac] ^ > [javac] symbol: variable JAXBContext > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:139: > error: cannot find symbol > [javac] Unmarshaller u = jc.createUnmarshaller(); > [javac] ^ > [javac] symbol: class Unmarshaller > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: > error: cannot find symbol > [javac] JAXBContext jc2 = > JAXBContext.newInstance(aTable.getClass()); > [javac] ^ > [javac] symbol: class JAXBContext > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:147: > error: cannot find symbol > [javac] JAXBContext jc2 = > JAXBContext.newInstance(aTable.getClass()); > [javac] ^ > [javac] symbol: variable JAXBContext > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:148: > error: cannot find symbol > [javac] Unmarshaller u2 = jc2.createUnmarshaller(); > [javac] ^ > [javac] symbol: class Unmarshaller > [javac] location: class PeptidePropertiesImpl > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:34: > error: method does not override or implement a method from a supertype > [javac] @Override > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: > error: cannot find symbol > [javac] if (ve.getSeverity() == ValidationEvent.FATAL_ERROR || > ve.getSeverity() == ValidationEvent.ERROR){ > [javac] ^ > [javac] symbol: variable ValidationEvent > [javac] location: class MyValidationEventHandler > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: > error: cannot find symbol > [javac] if (ve.getSeverity() == ValidationEvent.FATAL_ERROR || > ve.getSeverity() == ValidationEvent.ERROR){ > [javac] > ^ > [javac] symbol: variable ValidationEvent > [javac] location: class MyValidationEventHandler > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:37: > error: cannot find symbol > [javac] ValidationEventLocator locator = > ve.getLocator(); > [javac] ^ > [javac] symbol: class ValidationEventLocator > [javac] location: class MyValidationEventHandler > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:36: > error: method does not override or implement a method from a supertype > [javac] @Override > [javac] ^ > [javac] 83 errors > > BUILD FAILED > /<<BUILDDIR>>/biojava4-live-4.2.11+dfsg/biojava-aa-prop/build.xml:93: Compile > failed; see the compiler error output for details. > > Total time: 2 seconds > make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1 The full build log is available from: http://aws-logs.debian.net/2018/12/29/biojava4-live_4.2.11+dfsg-1_unstable.log 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! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
