Your message dated Wed, 05 Jun 2013 15:49:06 +0000
with message-id <e1ukfxs-0007xa...@franck.debian.org>
and subject line Bug#697604: fixed in fastqc 0.10.1+dfsg-2
has caused the Debian Bug report #697604,
regarding Templates/Icons is not found
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
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--
697604: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=697604
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: fastqc
Version: 0.10.1+dfsg-1
Severity: grave
Non-interactive fastqc always fails with
java.lang.NullPointerException
at
uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:170)
at
uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:60)
at
uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:157)
at
uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:108)
at java.lang.Thread.run(Thread.java:679)
It's this line:
File templatesDir = new
File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons").getFile(),"UTF-8"));
So it tries to find /usr/share/fastqc/Templates/Icons and don't succeed.
I tried various things to add /usr/share/fastqc to CLASSPATH in
/usr/bin/fastqc but it's not enough.
I downloaded upstream FastQC and there was no such problem. The only
difference that I see is that in Debian a fastqc.jar is used while in
upstream it's unpacked in the root directory. My conclusion is that this
specific way with getSystemResource searches only the location where
main class resides. In Debian's case it's fastqc.jar and in upstream
it's FastQC directory.
The easiest solution is to include all /usr/share/fastqc/* in the jar
file. (Well, you could not use jar file at all but I don't think it's a
good idea.)
Regards,
Ognyan Kulev
--- End Message ---
--- Begin Message ---
Source: fastqc
Source-Version: 0.10.1+dfsg-2
We believe that the bug you reported is fixed in the latest version of
fastqc, 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 697...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osal...@debian.org> (supplier of updated fastqc 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: Wed, 05 Jun 2013 17:08:44 +0200
Source: fastqc
Binary: fastqc
Architecture: source all
Version: 0.10.1+dfsg-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osal...@debian.org>
Description:
fastqc - quality control for high throughput sequence data
Closes: 697604
Changes:
fastqc (0.10.1+dfsg-2) unstable; urgency=low
.
* Add patch to fix Templates and Contaminants loading
in non interactive mode (Closes: #697604)
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fastqc_0.10.1+dfsg-2.debian.tar.gz
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fastqc_0.10.1+dfsg-2_all.deb
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