Le 11/8/12 8:40 AM, Olivier Sallou a écrit : > Le 11/7/12 3:29 PM, Andreas Tille a écrit : >> Hi, >> >> I stumbled upon this one and did some work on it in >> >> Vcs-Svn: >> http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/ >> >> It is close to lintian clean now but there is some CLASSPATH issue >> which is probably very easy for Java experts: >> >> $ fastqc >> Exception in thread "main" java.lang.NoClassDefFoundError: >> uk/ac/babraham/FastQC/FastQCApplication >> Caused by: java.lang.ClassNotFoundException: >> uk.ac.babraham.FastQC.FastQCApplication >> at java.net.URLClassLoader$1.run(URLClassLoader.java:217) >> at java.security.AccessController.doPrivileged(Native Method) >> at java.net.URLClassLoader.findClass(URLClassLoader.java:205) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:321) >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:266) >> Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. >> Program will exit. >> >> or when trying manually what the wrapper tries to do >> >> $ java -jar /usr/share/fastqc/fastqc.jar >> uk.ac.babraham.FastQC.FastQCApplication >> Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or >> couldn't be read By the way, should not fastqc.jar be placed in /usr/share/java with version symlink ? > I will have a look but: > It seems that the file with structure > uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file > /usr/share/fastqc/fastqc.jar (you can check content with jar -tf > /usr/share/fastqc/fastqc.jar) >> >> My suspicion is that simply specifying the Main-Class in debian/manifest >> is not sufficient. Something might be wrong with the Debian home brewn >> Makefile as quilt patch and ant+built.xml might do a better job to build >> the Jar functionally. Any hint for doing this properly? > Main-Class in manifest gives the default class to call when using java > -jar myjarfile. > If the jar needs other jar files, they need to be specified in Manifest > too or at command line in the classpath parameter. > > Olivier >> Note to obtain the source as easy as possible: Just use the uscan from >> >> >> http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=blob;f=scripts/uscan.pl >> >> to call >> >> uscan.pl --verbose --force-download --repack-compression xz >> >> which gives you a properly stripped source tarball. >> >> Kind regards and thanks for any help >> >> Andreas. >> >> On Wed, Apr 25, 2012 at 01:08:54AM +0200, Steffen Moeller wrote: >>> Package: wnpp >>> Severity: wishlist >>> Owner: Steffen Moeller <steffen_moel...@gmx.de> >>> >>> * Package name : fastqc >>> * URL : >>> http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ >>> * License : GPL-3 >>> Programming Lang: Java >>> Description : quality control for next generation sequencing data >>> >>> The Debian Med source code repository has some functional (not lintian >>> clean) package in >>> trunk/packages/babraham/fastqc. >>>
-- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/509b66e5.2060...@irisa.fr
