Your message dated Sat, 26 Mar 2016 19:34:02 +0000
with message-id <[email protected]>
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 [email protected]
immediately.)
--
808851: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=808851
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: artemis
Version: 16.0.0+dfsg-4
Severity: serious
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs
X-Debbugs-Cc: [email protected]
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
`. `'` [email protected] / chris-lamb.co.uk
`-
artemis.16.0.0+dfsg-4.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Afif Elghraoui <[email protected]> (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 [email protected])
-----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
<[email protected]>
Changed-By: Afif Elghraoui <[email protected]>
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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=W5lX
-----END PGP SIGNATURE-----
--- End Message ---
