Subject: “generate-jar-indices” phase fails on many packages

From: Ricardo Wurmus <[email-masked]>
Date: Tue, 5 Jun 2018 13:15:41 +0200

The “generate-jar-indices” phase fails on a couple of packages, such as

  java-picard (all variants)
  dropseq-tools
  java-cisd-jhdf5

The errors are either about duplicates as in java-picard-2.10.3:

    duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class

or about missing files as in dropseq-tools:

    java.io.FileNotFoundException: /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar

I have removed the phase in these packages, but that’s not ideal.

Can we make this phase more robust?

-- 
Ricardo