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

[Andreas Tille]

Hi,

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

...
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();
				                              ^
  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()
  location: variable COMM_WORLD of type Intracomm
current/stream/mpi/MPIWrapper.java:82: error: cannot find symbol
			MPI.COMM_WORLD.bcast(bLength,1,MPI.INT,0); // can't probe a broadcast, so send message size first
			              ^
  symbol:   method bcast(int[],int,Datatype,int)
  location: variable COMM_WORLD of type Intracomm
current/stream/mpi/MPIWrapper.java:83: error: cannot find symbol
			MPI.COMM_WORLD.bcast(b,b.length,MPI.BYTE,0); // broadcast the actual message
			              ^
  symbol:   method bcast(byte[],int,Datatype,int)
  location: variable COMM_WORLD of type Intracomm

Any idea how to fix this?

Kind regards

      Andreas.

[1] https://anonscm.debian.org/git/debian-med/bbmap.git

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