GNU bug report logs - #31721
“generate-jar-indices” phase fails on many packages

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Package: guix; Reported by: Ricardo Wurmus <ricardo.wurmus@HIDDEN>; dated Tue, 5 Jun 2018 11:17:01 UTC; Maintainer for guix is bug-guix@HIDDEN.

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From: Ricardo Wurmus <ricardo.wurmus@HIDDEN>
To: <bug-guix@HIDDEN>
Subject: =?utf-8?Q?=E2=80=9Cgenerate-jar-indices=E2=80=9D?= phase fails on
 many packages
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The =E2=80=9Cgenerate-jar-indices=E2=80=9D phase fails on a couple of packa=
ges, 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/q76y0ximcziplgfpbn26kbw4h3s14=
f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar

I have removed the phase in these packages, but that=E2=80=99s not ideal.

Can we make this phase more robust?

--=20
Ricardo




Acknowledgement sent to Ricardo Wurmus <ricardo.wurmus@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#31721; Package guix. Full text available.
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