[Debian-med-packaging] Bug#846671: artemis: FTBFS: BamView.java:115: error: cannot find symbol
Lucas Nussbaum
lucas at debian.org
Sat Dec 3 07:19:36 UTC 2016
Source: artemis
Version: 16.0.0+dfsg-5
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
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 warning: [options] source value 1.5 is obsolete and will be removed in a future release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 warning: [options] target value 1.5 is obsolete and will be removed in a future release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.
More information about the Debian-med-packaging
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