Your message dated Thu, 8 Dec 2016 15:30:19 +0100
with message-id
<CA+VnnnDsmEuB5m_0LaosbBmsvpHcZyY=xKXCU=1iev+fka6...@mail.gmail.com>
and subject line Bug was done - just needed to unmerge 846708
has caused the Debian Bug report #846671,
regarding artemis: FTBFS: BamView.java:115: error: cannot find symbol
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.)
--
846671: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=846671
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: artemis
Version: 16.0.0+dfsg-5
Severity: serious
Tags: stretch sid
User: debian...@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 warning: [options] source value 1.5 is obsolete and will be removed in a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 warning: [options] target value 1.5 is obsolete and will be removed in a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.
--- End Message ---
--- Begin Message ---
This bug was done in recent upload. Reopening was just done for unmerge
with 846708. SOrry for the noise.
--
http://fam-tille.de
--- End Message ---
