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

[Felix Natter]

Andreas Tille <andreas at an3as.eu> writes:

> Hi,

hello Andreas,

> I just injected some rudimentary packaging for BBMap[1] which is a Java
> 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.
(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

> ...
> 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)?

>   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])

[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?

[5] https://anonscm.debian.org/git/debian-med/bbmap.git/tree/current/stream/mpi/MPIWrapper.java

Cheers and Best Regards,
-- 
Felix Natter