Your message dated Wed, 05 Jun 2013 15:49:06 +0000 with message-id <[email protected]> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 697604: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=697604 Debian Bug Tracking System Contact [email protected] 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
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Olivier Sallou <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Olivier Sallou <[email protected]> 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) Checksums-Sha1: 06f80374949f9e68c953a06f96643594d19fa80c 2135 fastqc_0.10.1+dfsg-2.dsc 8b861ab424d6250db3120141902fedb0e60a81d7 7441 fastqc_0.10.1+dfsg-2.debian.tar.gz e7c3c1ba5cf33e08f1ffc65fbd3dddb6e48b5bf4 320340 fastqc_0.10.1+dfsg-2_all.deb Checksums-Sha256: 45b31a9abe1358a9c8ff5af66165e62d92fe222628b675daae7d0c21294efbc0 2135 fastqc_0.10.1+dfsg-2.dsc 8697fb38dc3f36859738c77b25bb150a022906d0664fc2e1da4f6499d9cb8aa2 7441 fastqc_0.10.1+dfsg-2.debian.tar.gz 98c0962642649c46f496a34cfcf3864e4892a92c3fc5d241f08cb43f8c7f91ef 320340 fastqc_0.10.1+dfsg-2_all.deb Files: 8240d32da2d53630990c919a17f94eec 2135 science optional fastqc_0.10.1+dfsg-2.dsc b8f307202e9aac03abf895308b2bad20 7441 science optional fastqc_0.10.1+dfsg-2.debian.tar.gz b8ddb1329f7b182b54a2c217c30413c4 320340 science optional fastqc_0.10.1+dfsg-2_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBCAAGBQJRr1eeAAoJEHjcaNsybYQ4PZkP+QFdPyFyUMQG5ofLqRduWgDL aRCCJa9dx4LlNcM1ZVOGN8zw3xP4K0h3qlDulZPozEz98iQtOSLQTkmPjcczmgnS NZeKceemzjKmb+fm0wFkz+i/cowRBMZM6l5e5ob3+Go3mVHAzlaLw/AL0sCLk0Vs i0RWAynE8KeZon2VNV4MAT+MMQbtoDFnu9bwCG8zj706rKiyupsiHDyNJJIhthS9 jGp67UHBR6seAXjkGRIs6gI/xg9oZYyIwjty/wmfsY2/yiai529Z54iMz+q+j0ha XbZ273U0kF0j4GfQI3vIfOpTCFfWMS3Y0JcV7CdOz/6rgvQrBglI7gt4I8o+lphB ZymuNGfK2B0pVV+vmpZSs+jntjpDFx3ZjkXoY4YDjvPl05TfMt7NyE4FNSLRouvk Zp9CKYz+Id03kWc7ux9X8PCdvFWfZQ52+HY+c0sfhbrnrAV+y7r8CSVepP2E0KaQ lLcxhNbPX2t49/7kPgudG/MiHCdv0DFqSVZijQQ2nJl+cnm6vLvQ3Aggdh+2Nqia /+qU+1GnpZssb02OEojq0KbFVRjZ5aVZDFYQpNyRVT/fiLdZ7QuWsVig/VsFcySV i0ra9PUf68YvyZ9Ga91UbTSsdN/JevYWyZFh90dYQ7JYLRHQT7h0dR8vy3R9GtUg acIOcAAnUO6B4tR4gOpD =ovd1 -----END PGP SIGNATURE-----
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