Your message dated Sat, 26 Mar 2016 19:34:02 +0000 with message-id <e1ajtye-0002gy...@franck.debian.org> and subject line Bug#808851: fixed in artemis 16.0.0+dfsg-5 has caused the Debian Bug report #808851, regarding artemis: FTBFS: error: package ReferenceSequenceFileFactory does not exist to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 808851: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=808851 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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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--- Begin Message ---Source: artemis Source-Version: 16.0.0+dfsg-5 We believe that the bug you reported is fixed in the latest version of artemis, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 808...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Afif Elghraoui <a...@debian.org> (supplier of updated artemis package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sat, 26 Mar 2016 12:26:38 -0700 Source: artemis Binary: artemis Architecture: source Version: 16.0.0+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Afif Elghraoui <a...@debian.org> Description: artemis - genome browser and annotation tool Closes: 808851 Changes: artemis (16.0.0+dfsg-5) unstable; urgency=medium . [ Steffen Moeller and Jon Ison ] * Introduced EDAM annotation . [ Sascha Steinbiss ] * Bump Standards-Version * Use secure Vcs-* . [ Sascha Steinbiss and Afif Elghraoui ] * Patch code to use new htsjdk API (Closes: #808851) Checksums-Sha1: 6751edb9994e607184fdcf26590289726f11dfd6 2209 artemis_16.0.0+dfsg-5.dsc ed6bcc260759d44797d9e055517f7fdbd45dc3b6 10564 artemis_16.0.0+dfsg-5.debian.tar.xz Checksums-Sha256: bdf3fb6fbc3554e45d13f6b4911d8398f366f87f2f00a695b63285994756ea27 2209 artemis_16.0.0+dfsg-5.dsc 4183476eb90f9333401eb80b8583be57dc29c16fe757fcbec3a7e64c20500df3 10564 artemis_16.0.0+dfsg-5.debian.tar.xz Files: e3d2b687bce1c3496512e56922a305df 2209 science optional artemis_16.0.0+dfsg-5.dsc e4b4189feba7244211277d685606d3a0 10564 science optional artemis_16.0.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJW9uMpAAoJEM6uatOv6Cb7e/4P/1N7i+aWp7QKW/8KbSELMukE lF0lbKHC8P5o3icadM7QLGkpKHyOLm98u+yrJipxbhl1qIOdLt+s5R1mMYXetBzv dg6CJBQ3HX9U9PJzHfHEDfT08OoMlnhxW4mcNBv/P8aarqb86J4zQ5hOPXrgoGpe McvsRjaeWCzSuyXWxDgXq9WJuK6yStMUv6DdOWxY192tm9flALR7xM4OywWKjotS wvrQDRiSwYA/pIGTGg6M/TNslbuzT1UISvXTbWfBdFRAWU0ICs9Ji6U0HKUMkFHo LYwgy1Uih2SV7UuFSshUIVECY+v20HQfoMGXxyY5bTsYYFGb1/+pQhEew03UNSkm +o1iCziEIh0ZlHPlOKLFwcYKT8Gk+9xO3ZZQt4Hlr9JQMGSaTKi5AbGtyQfvnVQJ cDWYk/VViUifloRbHJ/nYnJEWXvg/c0sBgNKIDFaToW7vG5oPVPHUzwwDXf2v9Gz o98rvXySMosX3trZLLwrOTGpr7UYdT6uib+K5lMwqMayhOAJDN1rmu1z+6Wm2fkj uaB6HrYMlFkPblTKUKeTjCrsmsTLUlC80mPEeL6pAUi6lVA8ZXdxPouP+QZOr39g AAygKZt4qU0eh5/HtFgPDdVsFJO3OUWp0ag78q/zdkBSKkVoPcIKe48xH/TQnASg 60XKv63mPEoe1gWhxfCt =W5lX -----END PGP SIGNATURE-----
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