[Debian-med-packaging] Bug#645487: ensembl: includes GPL code without source

[Andreas Tille]

Hi,

On Wed, Nov 30, 2011 at 01:11:30PM +0100, Steffen Möller wrote:
> I would not bet on it. Most likely this needs some adjustments to the
> Ensembl code since the Jar of Ensembl is considerably older than what is
> now in Debian with a much smaller set of dependencies to additional jars.
> 
> Please leave it for after the Sprint.

I'm not very happy about leaving RC bugs open *and* unanswered over a
long time and even if I do not really agree with the drastic means the
reporter was proposing the thing should be settled in a reasonable time
frame and not just hang around for two additional monthes.  That's why I
was simply hoping for an answer of upstream like:

   a) We will test Debian packaged jalview in the next couple of days.
   b) No, the new jars will not work at all, just add the sources to fix
      the problem.
   c) Things are perfectly OK. Just follow your symlink-suggestion if
      you have time
   d) Things are perfectly OK. We will take over preparation of package
      update.

Just doing nothing is wrong and moving a package to
non-free/experimental is no excuse to just let a package bit rot.  I
realised that upstream has issued a new release (64) before the bug in
question was filed.  It would have been easy enough to check whether the
issue is simply fixed in this release (and if not just fix it upstream
because this is actually not a Debian specific problem).

In short: Debian Med is a team.  If there are reasons to not let us
simply fix a problem as we are doing it for any other package, just let
us know and let us develop a strategy how we can solve these.

Kind regards

      Andreas.

PS: I have reordered SVN to the structure suggested by our policy
    handling different versions in tags.  The rationale behind it is
    that otherwise the maintainer will forget to update the Vcs fields
    and our tools will point into the void (which just happened now).
 
> On 11/30/2011 10:42 AM, Andreas Tille wrote:
> > On Wed, Nov 30, 2011 at 10:37:11AM +0100, Steffen Möller wrote:
> >>> Regarding fixing the actual problem I would like to ask those people
> >>> directly involved with ensemble packaging (explicitely in CC) whether
> >>> it is OK, to finally drop the jar files in question from the source
> >>> package and rather symlink to
> >>>
> >>> jemboss: /usr/share/EMBOSS/jemboss/lib/jalviewApplet.jar
> >>> jalview: /usr/share/java/jalview.jar
> >>>
> >>> inside the package.  The only missing file would be jalviewAppletOld.jar
> >>> but guessing from the name this file might be unused anyway.  Please
> >>> either confirm that this would properly fix the situation and will not
> >>> break ensembl and if I should go for it or whether you want to fix this
> >>> yourself.
> 
> 

-- 
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