[Debian-med-packaging] Bug#808851: artemis: FTBFS: error: package ReferenceSequenceFileFactory does not exist

[Chris Lamb]

Source: artemis
Version: 16.0.0+dfsg-4
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

artemis fails to build from source in unstable/amd64:

  [..]

  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:76: error: cannot find symbol
          indexSeqFile = new IndexedFastaSequenceFile(fasta, fastaIndex);
                             ^
    symbol:   class IndexedFastaSequenceFile
    location: class IndexFastaStream
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:82: error: package ReferenceSequenceFileFactory does not exist
              ReferenceSequenceFileFactory.FASTA_EXTENSIONS.toString()+
                                          ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:154: error: package ReferenceSequenceFileFactory does not exist
      if(ReferenceSequenceFileFactory.FASTA_EXTENSIONS.contains(".dna"))
                                     ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:156: error: package ReferenceSequenceFileFactory does not exist
      ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".dna");
                                  ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:157: error: package ReferenceSequenceFileFactory does not exist
      ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".seq");
                                  ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:158: error: package ReferenceSequenceFileFactory does not exist
      ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".fas");
                                  ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:159: error: package ReferenceSequenceFileFactory does not exist
      ReferenceSequenceFileFactory.FASTA_EXTENSIONS.add(".ffn");
                                  ^
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/io/IndexFastaStream.java:269: error: cannot find symbol
      ReferenceSequence ref;
      ^
    symbol:   class ReferenceSequence
    location: class IndexFastaStream
  /home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java:84: error: cannot find symbol
          return new ReferenceSequence(sequence.getName(), 0, 
                     ^
    symbol:   class ReferenceSequence
    location: class CRAMReferenceSequenceFile
  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.
  32 errors
  1 warning
  Makefile:247: recipe for target 'uk/ac/sanger/artemis/MegaBlastComparisonData.class' failed
  make[2]: *** [uk/ac/sanger/artemis/MegaBlastComparisonData.class] Error 1
  make[2]: Leaving directory '/home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg'
  debian/rules:39: recipe for target 'override_dh_auto_build' failed
  make[1]: *** [override_dh_auto_build] Error 2
  make[1]: Leaving directory '/home/lamby/temp/cdt.20151223192441.GwNPu7NexT/artemis-16.0.0+dfsg'
  debian/rules:36: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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