[Debian-med-packaging] Bug#846671: artemis: FTBFS: BamView.java:115: error: cannot find symbol

[Andreas Tille]

Hi all,

On Sat, Dec 03, 2016 at 08:19:36AM +0100, Lucas Nussbaum wrote:
> 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
> > ...
> >       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.

It seems the bug against fastqc as well as artemis have the same reason.
The only thing I remember is that there was a recent upgrade of
picard-tool.  Please put these bugs with high priority on your bug
squashing agenda.

Kind regards

       Andreas.

-- 
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