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Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

Hi Java programmers,

I wonder whether you could help to replace some outdated code in
libcolt-java which has some old code from src/hep.aida.* which is LGPL
but no military exception.  The code is old, was rewritten in
   http://java.freehep.org/ (???)
which has a free license and all our tries to reach the original author
for some clarification failed.  Debian Med and Debian Science need
libcolt-java for several reverse dependencies which unfortunately all
need to go in contrib because of a few files with old code.

Unfortunately nobody in the team is skilled anough in Java to do the job
(or at least confirm that it is as simple as I assume) and thus I wonder
whether there is some kind soul on Debian Java having a look into this.

Kind regards


----- Forwarded message from Andreas Tille <andreas@an3as.eu> -----

Date: Tue, 17 Feb 2015 09:50:35 +0100
From: Andreas Tille <andreas@an3as.eu>
To: debian-med@lists.debian.org
Subject: Re: Update on Trinityrnaseq packaging

Hi Michael,

On Tue, Feb 17, 2015 at 03:46:09AM +0000, Michael Crusoe wrote:
> On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille <andreas@an3as.eu> wrote:
> > > dependencies needing review & uploading to Debian:
> > > - [ ] libjung-java
> Ready for sponsoring

Uhmm, only for contrib since it depends libcolt-java. :-( :-( :-(
This libcolt issue is beating us over and over again.  My last longer
explanation was here:


For me it seems pretty clear that for some interested Java programmer
this issue could be solved in a dcent time frame by upgrading to
freehep.  Alternatively some interested non-programmer could try even
harder to push the original author changing the broken license.  But as
long as this is not solved at least four of our packages in interest
will end up in contrib only (which all the nasty consequences). :-(
> Has a dependency that I just packaged: r-bioc-ebseq (also needed for
> Trinity); of course that had its own dependency: r-cran-blockmodeling. Both
> are ready for sponsoring.

r-cran-blockmodeling uploaded to new.  It would be safer to ping me
again about r-bioc-ebseq once r-cran-blockmodeling might have hit
unstable to make sure I will not loose the chain of dependency amongst
the other things I'm doing.
> rsem itself needs manpages & testing

> > > - [ ] express
> Ready for sponsoring

I'll have a look.

Thanks for your effort



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