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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