Re: Help to detect java classes in drop-seq (covid-19 relevant) needed
Hi,
On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote:
>
> Thanks. This was pretty helpful. Now I need to package the
> remaining JAR which is not yet packaged from
>
> http://la4j.org/
I made some progress and also uploaded libla4j-java[1] to new. With
this I tried to build drop-seq[2] and stumbled upon two issues:
At first a lintian issue:
W: drop-seq-tools: classpath-contains-relative-path usr/share/java/dropseq-2.3.0.jar: lib/FastInfoset-1.2.12.jar, lib/FastInfoset.jar, lib/FastInf
N:
N: The classpath listed in the jar file refers to a potential missing jar
N: file. This could be the remnants of a build-time classpath that are not
N: relevant for a JAR bundled in a Debian package.
N:
N: Alternatively, the classpath may be correct, but the package is lacking
N: a jar file or a symlink to it.
N:
N: Note, Lintian assumes that all (relative) classpaths pointing to
N: /usr/share/java/ (but not subdirs thereof) are satisfied by dependencies
N: as long as there is at least one strong libX-java dependency.
N:
N: Severity: warning
N:
N: Check: languages/java
I have no idea what this means. A `grep -Ri fastinfoset` inside the source
tree remains empty.
The other one is a runtime error of the wrapper script:
$ drop-seq
Error: Could not find or load main class org.broadinstitute.dropseqrna.cmdline.DropSeqMain
Caused by: java.lang.NoClassDefFoundError: picard/cmdline/PicardCommandLine
Any idea what might be wrong here?
Thanks a lot for any help
Andreas.
[1] https://salsa.debian.org/med-team/libla4j-java
[2] https://salsa.debian.org/med-team/drop-seq
--
http://fam-tille.de
Reply to: