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