Source: artemis Version: 16.0.0+dfsg-4 Severity: serious Justification: fails to build from source User: reproducible-builds@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-builds@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
`. `'` la...@debian.org / chris-lamb.co.uk
`-
artemis.16.0.0+dfsg-4.unstable.amd64.log.txt.gz
Description: Binary data
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