Groups > linux.debian.maint.java > #11629

Re: Help to detect java classes in drop-seq (covid-19 relevant) needed

Path	csiph.com!aioe.org!bofh.it!news.nic.it!robomod
From	Andreas Tille <andreas@an3as.eu>
Newsgroups	linux.debian.maint.java
Subject	Re: Help to detect java classes in drop-seq (covid-19 relevant) needed
Date	Thu, 21 May 2020 14:50:04 +0200
Message-ID	<A8SO8-1Qp-5@gated-at.bofh.it> (permalink)
References	<A8v59-4ls-11@gated-at.bofh.it> <A8zBM-77U-11@gated-at.bofh.it> <A8DvH-101-9@gated-at.bofh.it>
X-Original-To	Debian Java List <debian-java@lists.debian.org>
X-Mailbox-Line	From debian-java-request@lists.debian.org Thu May 21 12:46:54 2020
Old-Return-Path	<andreas@an3as.eu>
X-Amavis-Spam-Status	No, score=-5 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, MEDS2=2] autolearn=no autolearn_force=no
X-Policyd-Weight	using cached result; rate: -4.6
MIME-Version	1.0
Content-Type	text/plain; charset=us-ascii
Content-Disposition	inline
User-Agent	Mutt/1.10.1 (2018-07-13)
X-Mailing-List	<debian-java@lists.debian.org> archive/latest/22207
List-ID	<debian-java.lists.debian.org>
List-URL	<https://lists.debian.org/debian-java/>
List-Archive	https://lists.debian.org/msgid-search/20200521124639.GU12054@an3as.eu
Approved	robomod@news.nic.it
Lines	52
Organization	linux.* mail to news gateway
Sender	robomod@news.nic.it
X-Original-Cc	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
X-Original-Date	Thu, 21 May 2020 14:46:39 +0200
X-Original-Message-ID	<20200521124639.GU12054@an3as.eu>
X-Original-References	<20200520112049.GK12054@an3as.eu> <87eereshyx.fsf@gmx.net> <20200520200748.GN12054@an3as.eu>
Xref	csiph.com linux.debian.maint.java:11629

Show key headers only | View raw

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

Back to linux.debian.maint.java | Previous | Next — Previous in thread | Next in thread | Find similar

Thread

Help to detect java classes in drop-seq (covid-19 relevant) needed Andreas Tille <andreas@an3as.eu> - 2020-05-20 13:30 +0200
  Re: Help to detect java classes in drop-seq (covid-19 relevant) needed Felix Natter <fnatter@gmx.net> - 2020-05-20 18:20 +0200
    Re: Help to detect java classes in drop-seq (covid-19 relevant)  needed Andreas Tille <andreas@fam-tille.de> - 2020-05-20 22:30 +0200
      Re: Help to detect java classes in drop-seq (covid-19 relevant)  needed Andreas Tille <andreas@an3as.eu> - 2020-05-21 14:50 +0200
        Re: Help to detect java classes in drop-seq (covid-19 relevant) needed Felix Natter <fnatter@gmx.net> - 2020-05-21 21:40 +0200

csiph-web