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Re: “generate-jar-indices” phase fails on many packages
From: |
Danny Milosavljevic |
Subject: |
Re: “generate-jar-indices” phase fails on many packages |
Date: |
Thu, 7 Jun 2018 01:06:20 +0200 |
Hi Ricardo,
did you get a bug# for this? I can't see it on
https://debbugs.gnu.org/cgi/pkgreport.cgi?pkg=guix ...
> The errors are either about duplicates as in java-picard-2.10.3:
>
> duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class
That's... bad. What if those files differed? Which one would be used at
runtime?
> or about missing files as in dropseq-tools:
>
> java.io.FileNotFoundException:
> /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar
That's also bad. How does it run at all if its dependencies are missing?
> I have removed the phase in these packages, but that’s not ideal.
I think that's suboptimal in the above cases since those error messages report
real problems, or in the first case at least pointing to a potential problem.
> Can we make this phase more robust?
Right now, it just invokes
jar -i
with the finished jar file. That's as simple as it gets - and I specifically
did only that minimal implementation for this cycle in order to only fix our GC
problem with java packages.
The only thing I can think of that would improve things long term:
The phase can add relative paths to all the dependencies to META-INF/MANIFEST.MF
before invoking "jar -i".
Then "jar -i" will index those - and all java packages can use regular inputs
instead of propagated inputs. I've tested that locally already - and it
works fine.
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