Your message dated Mon, 14 Jan 2019 16:20:32 +0000 with message-id <e1gj4yw-000cwm...@fasolo.debian.org> and subject line Bug#917655: fixed in biojava4-live 4.2.12+dfsg-1 has caused the Debian Bug report #917655, regarding biojava4-live: FTBFS: error: package javax.xml.bind.annotation does not exist to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 917655: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917655 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
--- End Message ---
--- Begin Message ---Source: biojava4-live Source-Version: 4.2.12+dfsg-1 We believe that the bug you reported is fixed in the latest version of biojava4-live, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 917...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated biojava4-live package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 14 Jan 2019 16:05:19 +0100 Source: biojava4-live Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc Architecture: source Version: 4.2.12+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: libbiojava4-java - Java API to biological data and applications (default version) libbiojava4-java-doc - [Biology] Documentation for BioJava libbiojava4.0-java - Java API to biological data and applications (version 4) Closes: 917655 917667 Changes: biojava4-live (4.2.12+dfsg-1) unstable; urgency=medium . * Team upload. . [ Jelmer Vernooij ] * Use secure copyright file specification URI. * Trim trailing whitespace. . [ Andreas Tille ] * New upstream version * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.3.0 . [ tony mancill ] * Add build-dep on libjaxb-api-java and libjaxb-java * Add jaxb-api and jaxb-impl JARs to classpaths in debian/build.xml Closes: #917655, #917667 * Drop --add-modules java.se.ee from javadoc task Checksums-Sha1: 47965ebeb70fb261dc9a71dccbb602b93c6c162a 2701 biojava4-live_4.2.12+dfsg-1.dsc 35482e33f668eb4de9b371c93ed510f612d09281 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz 36ffe36492b9192dd00207c1bb2dcfdcd4516d34 14656 biojava4-live_4.2.12+dfsg-1.debian.tar.xz Checksums-Sha256: 8b626077c6effdede0a13dc3be391c6bd9169e5fbd187ee57e555096f357b7d6 2701 biojava4-live_4.2.12+dfsg-1.dsc 63ea99c016b4bbb87a62c9cb05d0dbc352845851c200b676821037d76c6021c7 12178028 biojava4-live_4.2.12+dfsg.orig.tar.xz de7990c95ca082724d5e9dc00463af117eccced4984a40df5fb362ad1e237339 14656 biojava4-live_4.2.12+dfsg-1.debian.tar.xz Files: ea91613498fc2ba7cc15b9a7b994645e 2701 java optional biojava4-live_4.2.12+dfsg-1.dsc c66ea841163dc423be3713cf937cef2a 12178028 java optional biojava4-live_4.2.12+dfsg.orig.tar.xz c6a3be4364a0c8e52d99bf800e85bdf1 14656 java optional biojava4-live_4.2.12+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlw8p6MRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF83w//eyuc5jcx37wLloWdw8/OwQ/zIFYcDIws 36qqn41zvH2NUlEimk9nBVALbwJktDe4kxYipi3uuLibfX2j93iaY/BKi0i0XKfI L3Rk7gWbhkOTWgSeEMRQbOdtHyDfTEmfjAb9aNcvLP3nM7vZMuvtbP6PiX3/NmI0 bq6ATOqhdckMVN1hFy7u6GnEoyfHFmu5KWL3q9fv9vL2cBv0S88+2cDS56wxNotL 6PzQYZD8u+X8BmaKYB1aVRLwAieBPxb3WUWKStIhepjvd8wtPuHfEclSZMc2RpTQ mMI38pQAoIQPYz0BCuQWxF+P0zQRQ5F2dc+roH07upVJyVKuDxRu+ev/DS+odj+H aCqcomt4lwPpwywaqlAohJLSmo+Tux3XMUozB7CXcO96RAGSu33w2oIr/9Ap4YIN /+T2mg6SSybZigihTqbQjtqkifRgYCv6cLfTlGnU8JcW0GotNvOikhZhKcHYpm4D c4S8Qqn5hkVOK2r4rJaRxYPwSr4A2snuS3MeXfqUV2Wnr74PWN1d7KnNc2yLBwSX AhdYjAdOdWXtb2qy1CsCTZO/jhAi/We++znXbd9MV/LoqzX8O3Yt38Y9oF01w17D XGf7L0FVlxez/u1z4dm3Mca2mEB5uNSEqQ4QplThTrxd2twCw7GpqZKPCmzIXbQM 67OkdyFvLHA= =sl3V -----END PGP SIGNATURE-----
--- End Message ---
