[Debian-med-packaging] Bug#808851: Artemis FTBFS due to picard API changes

[Afif Elghraoui]

Control: tag -1 + help

This looks like it's due to API changes in the picard Java library. I
was able to avoid some of the errors by using htsjdk (thereby adding
dependency on libhtsjdk-java) instead of picard. We may also be able
drop the dependency on libsam-java.

However, there are still some errors:

/«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:119:
error: cannot find symbol
import htsjdk.samtools.SAMFileReader.ValidationStringency;
                                    ^
  symbol:   class ValidationStringency
  location: class SAMFileReader
/«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 ValidationStringency
  location: class BamView
/«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:529:
error: package net.sf.picard.util.Log does not exist
          net.sf.picard.util.Log.LogLevel.ERROR);
                                ^
/«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:528:
error: package net.sf.picard.util does not exist
      net.sf.picard.util.Log.setGlobalLogLevel(
                        ^
/«BUILDDIR»/artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/BamView.java:583:
error: cannot find symbol
    samFileReader.setValidationStringency(ValidationStringency.SILENT);
                                          ^
  symbol:   variable ValidationStringency
  location: class BamView
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.
5 errors
1 warning
make[2]: *** [uk/ac/sanger/artemis/MegaBlastComparisonData.class] Error 1


Artemis already uses log4j in other places and perhaps it can be used
here to replace the dropped picard logging functionality. Any help would
be appreciated. I'm going to push my latest work and also plan to
revisit this.

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name