Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
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_moeller@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
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