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

[William Spooner]

On 30 Nov 2011, at 12:41, Andreas Tille wrote:

> 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.


Hi Andreas,

I agree with your comments. The problem we have is knowing where to start with fixing this problem. That is why Steffen suggests waiting until the sprint, where there will be some face-time for him to help us. If this needs to be done sooner, then my response is c) please follow your symlink-suggestion if you have time. We can test at the sprint, and you can help us fix is needed. Jalview is not a vital component of Ensembl, and the package is experimental after all.

Many thanks for your understanding. The reason why I have not responded sooner is lack of understanding of the issue.

Best,

Will



> 
> 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.
>> 
>> 
> 
> -- 
> http://fam-tille.de

--
William Spooner
william.spooner at eaglegenomics.com
http://www.eaglegenomics.com