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
> 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)
To get it work, you should fix the /usr/bin/fastq line 183 on exec to get:
exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
instead of
exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
and same thing for system call.
>>
>> My suspicion is that simply specifying the Main-Class in debian/manifest
>> is not sufficient. Something might be wrong with the Debian home brewn
>> Makefile as quilt patch and ant+built.xml might do a better job to build
>> the Jar functionally. Any hint for doing this properly?
> Main-Class in manifest gives the default class to call when using java
> -jar myjarfile.
> If the jar needs other jar files, they need to be specified in Manifest
> too or at command line in the classpath parameter.
>
> Olivier
>> Note to obtain the source as easy as possible: Just use the uscan from
>>
>>
>> http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=blob;f=scripts/uscan.pl
>>
>> to call
>>
>>uscan.pl --verbose --force-download --repack-compression xz
>>
>> which gives you a properly stripped source tarball.
>>
>> Kind regards and thanks for any help
>>
>>Andreas.
>>
>> On Wed, Apr 25, 2012 at 01:08:54AM +0200, Steffen Moeller wrote:
>>> Package: wnpp
>>> Severity: wishlist
>>> Owner: Steffen Moeller
>>>
>>> * Package name: fastqc
>>> * URL :
>>> http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
>>> * License : GPL-3
>>> Programming Lang: Java
>>> Description : quality control for next generation sequencing data
>>>
>>> The Debian Med source code repository has some functional (not lintian
>>> clean) package in
>>> trunk/packages/babraham/fastqc.
>>>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Index: fastqc-0.10.1+dfsg.orig/fastqc
===
--- fastqc-0.10.1+dfsg.orig.orig/fastqc 2012-11-08 08:55:51.0 +0100
+++ fastqc-0.10.1+dfsg.orig/fastqc 2012-11-08 09:24:41.0 +0100
@@ -177,10 +177,10 @@
if ($java_bin ne 'java') {
- system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
+ system $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar",
@files;
}
else {
- exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
+ exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
}
__DATA__
@@ -273,4 +273,4 @@
Any bugs in fastqc should be reported either to
simon.andr...@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
-
\ No newline at end of file
+
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 >>> >>> * 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-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
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 >> >> * 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-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
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 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? 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 > > * 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. > -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
