Groups > linux.debian.maint.java > #11626

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

Path	csiph.com!4.us.feeder.erje.net!3.eu.feeder.erje.net!feeder.erje.net!usenet.goja.nl.eu.org!aioe.org!bofh.it!news.nic.it!robomod
From	Andreas Tille <andreas@an3as.eu>
Newsgroups	linux.debian.maint.java
Subject	Help to detect java classes in drop-seq (covid-19 relevant) needed
Date	Wed, 20 May 2020 13:30:03 +0200
Message-ID	<A8v59-4ls-11@gated-at.bofh.it> (permalink)
X-Mailbox-Line	From debian-java-request@lists.debian.org Wed May 20 11:21:04 2020
Old-Return-Path	<andreas@an3as.eu>
X-Amavis-Spam-Status	No, score=-3.48 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, MDO_CABLE_TV3=0.5, MEDS2=2, MURPHY_DRUGS_REL8=0.02, WORD_WITHOUT_VOWELS=1] autolearn=no autolearn_force=no
X-Policyd-Weight	using cached result; rate:hard: -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/22203
List-ID	<debian-java.lists.debian.org>
List-URL	<https://lists.debian.org/debian-java/>
List-Archive	https://lists.debian.org/msgid-search/20200520112049.GK12054@an3as.eu
Approved	robomod@news.nic.it
Lines	41
Organization	linux.* mail to news gateway
Sender	robomod@news.nic.it
X-Original-Date	Wed, 20 May 2020 13:20:49 +0200
X-Original-Message-ID	<20200520112049.GK12054@an3as.eu>
Xref	csiph.com linux.debian.maint.java:11626

Show key headers only | View raw

Hi,

I've started packaging of drop-seq[1] and replaced those JARs that are
replacable by Debian packaged versions.  I also have set CLASS_PATH in
d/rules, but it seems to be ignored.  I have dealt with similar cases by
patching it into build.xml but here I have not found the relevant place
to do so.  I'm aware that I did not yet added all needed classes to
CLASS_PATH, but currently I get


   dh_auto_build
        ant -Duser.name debian
Buildfile: /build/drop-seq-2.3.0+dfsg/build.xml
  [taskdef] Could not load definitions from resource testngtasks. It could not be found.

compile-src:
    [mkdir] Created dir: /build/drop-seq-2.3.0+dfsg/classes
    [javac] Compiling 201 source files to /build/drop-seq-2.3.0+dfsg/classes
    [javac] /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:28: error: package htsjdk.samtools does not exist
    [javac] import htsjdk.samtools.SAMException;
    [javac]                       ^
    [javac] /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:34: error: cannot find symbol
    [javac] public class TranscriptomeException extends SAMException
    [javac]                                             ^
    [javac]   symbol: class SAMException
...


but /usr/share/java/htsjdk.jar which is in CLASS_PATH contains this class.

Any hint how to take this hurdle would be welcome.

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/drop-seq

-- 
http://fam-tille.de

Back to linux.debian.maint.java | Previous | Next — 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