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

[Steffen Möller]

Hello Jonathan,

Thank you for spotting the omission.

On 11/30/2011 09:58 AM, Andreas Tille wrote:
> Hi,
>
> On Sun, Oct 16, 2011 at 09:49:25PM +0200, Andreas Tille wrote:
>> On Sun, Oct 16, 2011 at 03:51:18AM -0500, Jonathan Nieder wrote:
>>> Unfortunately no such file exists --- I guess it disappeared during
>>> some upgrade.  The jars in the source package only contain class
>>> files, no .java source files.
>>>
>>> Assuming that what debian/copyright says is correct, this would make
>>> the ensembl package non-distributable:
>> In how far would this make the package non-distributable?  Just
>> providing the binary without source is OK as long as you can provide
>> the source at request.  While you are correct that we should fix the
>> package I do not think that we need to take any more drastic action
>> like:
>>  
>>> notify the admins of snapshot.debian.org so the nondistributable
>>> versions can be removed. 
>> This would be pure overreaction.
> Despite your previous response to my mail I stick to my opinion that
> this is overreaction but if you feel obliged to contact admins of
> snapshot.debian.org to remove files where I actually do not see any need
> for I can not stop you.  IMHO the fact that the files never really were
> distributed in any Debian release but just hanging around in
> non-free/experimental makes your point quite weak and finally the
> sources are there - now even inside Debian.
>
> 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.
the snapshotting is rather helpful to accomodate legacy installations
of the MySQL databases, which just are not expected to be updated
to often. In that sense, removing the package from the snapshots is
in nobody's interest.

We knew Jalview coming to Debian for long. This limited our motivation
to spend too much time on it but we have rather moved it all to
experimental.
We have upstreams of Jalview with us on our Sprint for this and other
reasons, and contributors to Ensembl are also coming. We shall investigate
it when we are together.

Please contact the admins of Snapshot, but only to praise them for
their service.

Cheers,

Steffen