From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Danny Milosavljevic <dannym@scratchpost.org>
Cc: 31721@debbugs.gnu.org
Subject: bug#31721: “generate-jar-indices” phase fails on many packages
Date: Thu, 7 Jun 2018 09:20:37 +0200 [thread overview]
Message-ID: <877enbyse2.fsf@elephly.net> (raw)
In-Reply-To: <20180607010620.31fbf16c@scratchpost.org>
Danny Milosavljevic <dannym@scratchpost.org> writes:
>> 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?
I wonder where they come from. Is this from a dependency or are there
actually two such classes?
>> 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?
To satisfy the dropseq-tools build system the dependencies a symlinked
to the build directory. I suspect that the error is something to do
with that.
> 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.
Is it correct that this would ensure that in case of duplicate class
names this would pick the class from the current package?
--
Ricardo
next prev parent reply other threads:[~2018-06-07 7:21 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-06-05 11:15 bug#31721: “generate-jar-indices” phase fails on many packages Ricardo Wurmus
2018-06-06 23:06 ` Danny Milosavljevic
2018-06-07 7:20 ` Ricardo Wurmus [this message]
2018-06-07 8:27 ` bug#31721: " Gábor Boskovits
2018-06-07 8:46 ` Gábor Boskovits
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