[Debian-med-packaging] Java-help for BBMap needed

[Andreas Tille]

On Sun, Mar 20, 2016 at 04:27:55PM +0100, Felix Natter wrote:
> > project but has no dedicated Build-System - it does not even create a
> > JAR.  My very naive approach to create a JAR ended up in
> 
> The package your are developing uses "javahelper" helper,
> which takes care of compiling and generating a jar.

I was not aware of this since I assumed at least a Java typical build
system would be required.  I commited a change using jh_build now
instead of my own build commands.  Thanks a lot for the hint.

> (You can generate a package using "jh_makepkg" from that package.)
> 
> (If there are resources, you need to add them manually to the jar,
> though (see [1]))
> 
> Why do you override override_dh_auto_build without running
> dh_auto_build? That way you turn off javahelper's logic for compiling
> and jar'ing. [1] is an example for using javahelper.
> (you probably only need to create debian/javabuild [2] and not override
> dh_auto_build).
> 
> Also see /usr/share/doc/javahelper/tutorial.html.
> 
> [1] http://anonscm.debian.org/cgit/pkg-java/libjsyntaxpane-java.git/tree/debian/rules
> [2] http://anonscm.debian.org/cgit/pkg-java/libjsyntaxpane-java.git/tree/debian/javabuild

Thanks for the helpful hints.
 
> > ...
> > jar -cmf debian/manifest bbmap.jar `find current -name "*.class"`
> > current/stream/mpi/MPIWrapper.java:48: error: cannot find symbol
> > 				Shared.MPI_RANK=MPI.COMM_WORLD.getRank();
> 
> Not sure what you are doing here, Does the command (create jar from
> class files) really match with the error message (compilation failure)?

The jh_build call results in the same problem.
 
> >   symbol:   method getRank()
> >   location: variable COMM_WORLD of type Intracomm
> > current/stream/mpi/MPIWrapper.java:49: error: cannot find symbol
> > 				Shared.MPI_NUM_RANKS=MPI.COMM_WORLD.getSize();
> > 				                                   ^
> >   symbol:   method getSize()
> 
> It looks like bbmap requires the methods getRank() and getSize()
> on mpi.Intracomm, and this method does not seem to be available in
> mpj-0.42+dfsg.
> (I couldn't find it in mpj-0.44 either [3] [4])

Apropos mpj:  Its maintained by the Debian team for historical reasons.
I'd be happy to move it to pkg-java Git in case Debian Java team wants
to take over.
 
> [3] https://sourceforge.net/projects/mpjexpress/files/
> [4] http://mpjexpress.org/docs/javadocs/mpi/Intracomm.html
> 
> Maybe we should ask the mpjexpress folks which
> mpjexpress to use or how to fix/patch bbmap [5]?
> 
> Does anyone on this list know more about MPI for java?

I'd be really happy for any further hint.
 
> [5] https://anonscm.debian.org/git/debian-med/bbmap.git/tree/current/stream/mpi/MPIWrapper.java
> 
> Cheers and Best Regards,

Thanks for your help

     Andreas.

-- 
http://fam-tille.de