Source: artemis
Version: 16.0.0+dfsg-5
Severity: serious
Tags: stretch sid
User: [email protected]
Usertags: qa-ftbfs-20161202 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<BUILDDIR>>/artemis-16.0.0+dfsg'
> idlj -Icorba corba/types.idl
> idlj -Icorba corba/nsdb.idl
> idlj -Icorba corba/nsdb_write.idl
> idlj -Icorba corba/seqdb.idl
> CLASSPATH=/usr/share/java/biojava.jar:/usr/share/java/j2ssh-core.jar:/usr/share/java/ibatis.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/postgresql-jdbc3.jar:/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/commons-net.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/EMBOSS/jemboss/lib/jemboss.jar:/<<BUILDDIR>>/artemis-16.0.0+dfsg
> javac -source 1.5 -target 1.5
> uk/ac/sanger/artemis/MegaBlastComparisonData.java
> warning: [options] bootstrap class path not set in conjunction with -source
> 1.5
> warning: [options] source value 1.5 is obsolete and will be removed in a
> future release
> warning: [options] target value 1.5 is obsolete and will be removed in a
> future release
> warning: [options] To suppress warnings about obsolete options, use
> -Xlint:-options.
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/Feature.java:1626:
> warning: '_' used as an identifier
> catch(OutOfDateException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/Feature.java:1630:
> warning: '_' used as an identifier
> catch(EntryInformationException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/Options.java:452:
> warning: '_' used as an identifier
> catch(Throwable _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/GFFStreamFeature.java:1031:
> warning: '_' used as an identifier
> catch(NumberFormatException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:1230:
> warning: '_' used as an identifier
> catch(ReadOnlyException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:1269:
> warning: '_' used as an identifier
> catch(ReadOnlyException _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:1986:
> warning: '_' used as an identifier
> public void itemStateChanged (ItemEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:1995:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2155:
> warning: '_' used as an identifier
> } catch (OutOfDateException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2157:
> warning: '_' used as an identifier
> } catch (EntryInformationException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2159:
> warning: '_' used as an identifier
> } catch (ReadOnlyException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2482:
> warning: '_' used as an identifier
> } catch (ReadOnlyException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2920:
> warning: '_' used as an identifier
> } catch (EntryInformationException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:2923:
> warning: '_' used as an identifier
> } catch (OutOfDateException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:3510:
> warning: '_' used as an identifier
> catch(OutOfRangeException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/EditMenu.java:3519:
> warning: '_' used as an identifier
> catch(OutOfRangeException _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:78:
> warning: '_' used as an identifier
> public void setKey (final Key _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:79:
> warning: '_' used as an identifier
> public void setLocation (final Location _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:80:
> warning: '_' used as an identifier
> public void setLocation (final Location _, Entry entry) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:81:
> warning: '_' used as an identifier
> public void setQualifiers (final QualifierVector _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:82:
> warning: '_' used as an identifier
> public void setQualifier (final Qualifier _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:83:
> warning: '_' used as an identifier
> public void removeQualifierByName (final String _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:88:
> warning: '_' used as an identifier
> public Qualifier getQualifierByName (final String _) {return null;}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/FeatureTree.java:94:
> warning: '_' used as an identifier
> public void setUserData (final Object _) {}
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/LineAttributes.java:271:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/variant/GraphPanel.java:333:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:115:
> error: cannot find symbol
> import htsjdk.samtools.SAMFileReader;
> ^
> symbol: class SAMFileReader
> location: package htsjdk.samtools
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Plot.java:237:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Plot.java:248:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Plot.java:304:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Plot.java:316:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Plot.java:383:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:159:
> error: cannot find symbol
> private Hashtable<String, SAMFileReader> samFileReaderHash = new
> Hashtable<String, SAMFileReader>();
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/AbstractGraphPanel.java:98:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java:129:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:490:
> error: cannot find symbol
> private SAMFileReader getSAMFileReader(final String bam) throws IOException
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:693:
> error: cannot find symbol
> private void iterateOverBam(final SAMFileReader inputSam,
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/plot/LineAttributes.java:294:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/FeatureEdit.java:391:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:511:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:575:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:599:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:615:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:629:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/AlignmentViewer.java:667:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/ViewMenu.java:1331:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java:68:
> warning: '_' used as an identifier
> } catch (InterruptedException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/DocumentEntryAutosaveThread.java:140:
> warning: '_' used as an identifier
> } catch (InterruptedException _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:593:
> warning: '_' used as an identifier
> public void itemStateChanged (ItemEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:601:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:702:
> warning: '_' used as an identifier
> public void itemStateChanged (ItemEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:709:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:759:
> warning: '_' used as an identifier
> public void itemStateChanged (ItemEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/SelectMenu.java:768:
> warning: '_' used as an identifier
> public void actionPerformed (ActionEvent _) {
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:159:
> error: cannot find symbol
> private Hashtable<String, SAMFileReader> samFileReaderHash = new
> Hashtable<String, SAMFileReader>();
>
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:494:
> error: cannot find symbol
>
> SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
> ^
> symbol: variable SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:523:
> error: cannot find symbol
> final SAMFileReader samFileReader;
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:571:
> error: cannot find symbol
> samFileReader = new SAMFileReader(fss, bamIndexFile, false);
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:576:
> error: cannot find symbol
> samFileReader = new SAMFileReader(bamFile, bamIndexFile);
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:581:
> error: cannot find symbol
> samFileReader = new SAMFileReader(urlBamFile, bamIndexFile, false);
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:592:
> error: cannot find symbol
> final SAMFileReader inputSam = getSAMFileReader(bamList.get(0));
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:650:
> error: cannot find symbol
> final SAMFileReader inputSam = getSAMFileReader(bam);
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/MappedReads.java:40:
> error: cannot find symbol
> import htsjdk.samtools.SAMFileReader;
> ^
> symbol: class SAMFileReader
> location: package htsjdk.samtools
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/MappedReads.java:49:
> error: cannot find symbol
> private Hashtable<String, SAMFileReader> samFileReaderHash;
> ^
> symbol: class SAMFileReader
> location: class MappedReads
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/MappedReads.java:80:
> error: cannot find symbol
> final Hashtable<String, SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class MappedReads
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/MappedReads.java:147:
> error: cannot find symbol
> final Hashtable<String, SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class MappedReads
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/MappedReads.java:217:
> error: cannot find symbol
> final Hashtable<String, SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class MappedReads
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:4148:
> error: cannot find symbol
> final SAMFileReader inputSam = getSAMFileReader(bam);
> ^
> symbol: class SAMFileReader
> location: class BamView
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Selector.java:165:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Selector.java:203:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Selector.java:212:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Selector.java:420:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/Selector.java:434:
> warning: '_' used as an identifier
> public void itemStateChanged(ItemEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:32:
> error: cannot find symbol
> import htsjdk.samtools.SAMFileReader;
> ^
> symbol: class SAMFileReader
> location: package htsjdk.samtools
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:76:
> error: cannot find symbol
> final Hashtable<String, SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class BamUtils
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:131:
> error: cannot find symbol
> final Hashtable<String, SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class BamUtils
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:181:
> error: cannot find symbol
> final Hashtable<String,
> SAMFileReader> samFileReaderHash,
> ^
> symbol: class SAMFileReader
> location: class BamUtils
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/ComparatorDialog.java:235:
> warning: '_' used as an identifier
> public void actionPerformed(ActionEvent _)
> ^
> (use of '_' as an identifier might not be supported in releases after Java
> SE 8)
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:145:
> error: cannot find symbol
> SAMFileReader inputSam = samFileReaderHash.get(bam);
> ^
> symbol: class SAMFileReader
> location: class BamUtils
> /<<BUILDDIR>>/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamUtils.java:190:
> error: cannot find symbol
> SAMFileReader inputSam = samFileReaderHash.get(bamFile);
> ^
> symbol: class SAMFileReader
> location: class BamUtils
> Note: Some input files use or override a deprecated API.
> Note: Recompile with -Xlint:deprecation for details.
> Note: Some input files use unchecked or unsafe operations.
> Note: Recompile with -Xlint:unchecked for details.
> 24 errors
> 60 warnings
> Makefile:247: recipe for target
> 'uk/ac/sanger/artemis/MegaBlastComparisonData.class' failed
> make[2]: *** [uk/ac/sanger/artemis/MegaBlastComparisonData.class] Error 1
The full build log is available from:
http://aws-logs.debian.net/2016/12/02/artemis_16.0.0+dfsg-5_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.
