Re: Java-help for BBMap needed
Andreas Tille <email@example.com> writes:
> I just injected some rudimentary packaging for BBMap 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 ))
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.  is an example for using javahelper.
(you probably only need to create debian/javabuild  and not override
Also see /usr/share/doc/javahelper/tutorial.html.
> jar -cmf debian/manifest bbmap.jar `find current -name "*.class"`
> current/stream/mpi/MPIWrapper.java:48: error: cannot find symbol
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
> 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
(I couldn't find it in mpj-0.44 either  )
Maybe we should ask the mpjexpress folks which
mpjexpress to use or how to fix/patch bbmap ?
Does anyone on this list know more about MPI for java?
Cheers and Best Regards,