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 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/509b61d6.4070...@irisa.fr
