Re: Need some help for Java package
Hi Olivier, On Mon, Feb 10, 2014 at 10:01:33AM +0100, Olivier Sallou wrote: ok, I found that several things were missing. I have updated build.xml and added d/ipig.jlibs (to install generated jar to /usr/share/java). What could be missing is a main ipig program in /usr/bin doing a: java $JAVA_OPTS -jar /usr/share/java/iPiG.jar $@ I added it in debian dir with a rule to install it. fell free to keep or erase. Cool. Many thanks! I'll check out and see. Thanks a lot for all your help Andreas. -- http://fam-tille.de -- 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/20140210090546.ge3...@an3as.eu
Re: Need some help for Java package
On 02/10/2014 08:16 AM, olivier.sal...@codeless.fr wrote: On 02/09/2014 12:57 AM, Andreas Tille wrote: Hi, On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this I've got response from upstream that the code is available at http://ics.hutton.ac.uk/svn/tablet means an other package dependency packaging and may be others. I had a quick look at svn, and it contains too other jar files (flamingo, scri-commons) that may need themselves packaging. Olivier Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. It seems to be a different codebase anyway - so my suggested fallback to ask upstream remains. hi andreas, I asked upstream with a ticket about missing class. They added it in their svn codebase (so not needing to package the whole dependencies for a single class). So you need to reupdate the git codebase (pristine etc..) with latest from SVN (zip archive file has also been updated). With this added class, the code compiles correctly. I have updated patches to latest code, patching should be ok. Olivier Kind regards Andreas. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- 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/52f8a3de.1030...@irisa.fr
Re: Need some help for Java package
Hi Olivier, On Mon, Feb 10, 2014 at 11:03:10AM +0100, Olivier Sallou wrote: I asked upstream with a ticket about missing class. They added it in their svn codebase (so not needing to package the whole dependencies for a single class). Great! So you need to reupdate the git codebase (pristine etc..) with latest from SVN (zip archive file has also been updated). With this added class, the code compiles correctly. I have updated patches to latest code, patching should be ok. I can confirm that the package builds (changes pushed). I'm a bit worried about the lintian warning: W: giira: missing-classpath libglpk-java N: N:None of the jar files contained in the package declare a Class-Path in N:their manifest, but the package depends on at least one java library. N:That means that either the dependency is not needed or at least one of N:the JARs should include a classpath. N: N:It is important to keep the classpath up-to-date to allow the automatic N:detection of dependencies at run time. Having a Class-Path element in N:the manifest allows for painless transitions if the class path of the N:dependencies of the library ever changes. N: N:Failing to do that means that for every change in class path, all N:rdepends must update their wrapper scripts, which is a lot of work for N:nothing. N: N:Severity: normal, Certainty: possible N: N:Check: java, Type: binary Any hint where to add this classpath? Kind regards Andreas. -- http://fam-tille.de -- 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/20140210125122.gd6...@an3as.eu
Re: Need some help for Java package
On 02/10/2014 01:51 PM, Andreas Tille wrote: Hi Olivier, On Mon, Feb 10, 2014 at 11:03:10AM +0100, Olivier Sallou wrote: I asked upstream with a ticket about missing class. They added it in their svn codebase (so not needing to package the whole dependencies for a single class). Great! So you need to reupdate the git codebase (pristine etc..) with latest from SVN (zip archive file has also been updated). With this added class, the code compiles correctly. I have updated patches to latest code, patching should be ok. I can confirm that the package builds (changes pushed). I'm a bit worried about the lintian warning: W: giira: missing-classpath libglpk-java N: N:None of the jar files contained in the package declare a Class-Path in N:their manifest, but the package depends on at least one java library. N:That means that either the dependency is not needed or at least one of N:the JARs should include a classpath. N: N:It is important to keep the classpath up-to-date to allow the automatic N:detection of dependencies at run time. Having a Class-Path element in N:the manifest allows for painless transitions if the class path of the N:dependencies of the library ever changes. N: N:Failing to do that means that for every change in class path, all N:rdepends must update their wrapper scripts, which is a lot of work for N:nothing. N: N:Severity: normal, Certainty: possible N: N:Check: java, Type: binary Any hint where to add this classpath? I have added it in build.xml, updated in repo Kind regards Andreas. -- 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/52f8cdf1.70...@irisa.fr
Re: Need some help for Java package
On 02/09/2014 12:57 AM, Andreas Tille wrote: Hi, On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this I've got response from upstream that the code is available at http://ics.hutton.ac.uk/svn/tablet means an other package dependency packaging and may be others. I had a quick look at svn, and it contains too other jar files (flamingo, scri-commons) that may need themselves packaging. Olivier Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. It seems to be a different codebase anyway - so my suggested fallback to ask upstream remains. Kind regards Andreas. -- 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/52f87cdc.6040...@codeless.fr
Re: Need some help for Java package
Hi Olivier, On Sat, Feb 08, 2014 at 09:11:15AM +0100, olivier.sal...@codeless.fr wrote: I've gone furher, remove cplex, but there is still an issue. Code references: CigarParser.extractAllAlignDiffs() but there is no import in the code that would import CigarParser from a library or local code! and I cannot find on Internet any CigarParser class. This is related in a way or an other to samtools, but I do not see any CigarParser in libsam-java. I wonder how the source code is stable Any way, does anyone has an idea where this CigarParser may come from? I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this Kind regards Andreas. -- http://fam-tille.de -- 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/20140208155453.gb10...@an3as.eu
Re: Need some help for Java package
On 02/08/2014 04:54 PM, Andreas Tille wrote: Hi Olivier, On Sat, Feb 08, 2014 at 09:11:15AM +0100, olivier.sal...@codeless.fr wrote: I've gone furher, remove cplex, but there is still an issue. Code references: CigarParser.extractAllAlignDiffs() but there is no import in the code that would import CigarParser from a library or local code! and I cannot find on Internet any CigarParser class. This is related in a way or an other to samtools, but I do not see any CigarParser in libsam-java. I wonder how the source code is stable Any way, does anyone has an idea where this CigarParser may come from? I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. Olivier Kind regards Andreas. -- 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/52f66567.9090...@codeless.fr
Re: Need some help for Java package
Hi Olivier, On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. As I said I'll clarify this with giira upstream. However, I have a new issue to solve. I tried to adapt your way to deal with a missing build.xml but it seems I failed in git://anonscm.debian.org/debian-med/ipig.git I added the needed the Build-Depends for the following JARs: /usr/share/java/commons-compress.jar /usr/share/java/commons-net.jar /usr/share/java/jdom1.jar /usr/share/java/xercesImpl.jar These were deleted before (some with explicite versions but I guess this should work) and I guess I failed to create a working build.xml. Would you be patient enough to have another look? Kind regards Andreas. -- http://fam-tille.de -- 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/20140208213434.gf10...@an3as.eu
Re: Need some help for Java package
Hi, On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this I've got response from upstream that the code is available at http://ics.hutton.ac.uk/svn/tablet Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. It seems to be a different codebase anyway - so my suggested fallback to ask upstream remains. Kind regards Andreas. -- http://fam-tille.de -- 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/20140208235738.gi10...@an3as.eu
Need some help for Java package
Hi, I need to package a Java package without build system. I prepared the packaging at git://anonscm.debian.org/debian-med/giira.git and need to reconstruct the file GIIRA.jar which is part of http://sourceforge.net/projects/giira/files/GIIRA.zip Any idea how to create the jar file? (Feel free to commit straight to Git.) Kind regards Andreas. -- http://fam-tille.de -- 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/20140207231614.gh15...@an3as.eu
