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