[Debian-med-packaging] Bug#917667: biojava4-live: FTBFS: error: package javax.xml.bind.annotation does not exist
Lucas Nussbaum
lucas at debian.org
Sat Dec 29 21:34:26 GMT 2018
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.
More information about the Debian-med-packaging
mailing list