[Debichem-devel] jmol: diff for NMU version 12.2.32+dfsg2-1.1

[Andreas Tille]

Hi,

On Sat, Dec 10, 2016 at 03:37:00PM +0000, Ximin Luo wrote:
> tony mancill:
> > [..]
> > 
> > This upload was rejected due to a lintian error that existed in the
> > source package before I added the patch.  Since NMUs are supposed to
> > be very targeted, the rejection puts us in an odd place.

As a general remark: Feel free to do a "Team upload" and do the needed
changes which should not have the restriction to be very targeted

> > Will the
> > upload to experimental [1] find its way into unstable before the
> > freeze, or should I try again with 12.2.32?
> > 
> 
> Hi Tony and everyone else I added:
> 
> That depends on what DebiChem, Debian Med, and the Debian Java Team collectively want.
> 
> jmol has three reverse dependencies. The new upload, jmol 14, breaks all of them.
> 
> - biojava3-live can feasibly be dropped from Debian.

I have asked Olivier about this.

> - biojava4-live is currently being worked on by the upstream developer. We're waiting to hear back from them.

Olivier has just uploaded a recent BioJava 4 version.  I think this one
should be kept in Debian in any case.
 
> - jalview's current version doesn't work with jmol 14, but the new version does. I started packaging it, but it adds several other dependencies not in Debian. Most of them seem bio related:

>From my *personal* and *uneducated* view its better to have a recent
Jmol than an outdated Jalview.  While having also an updated Jalview
would be the optimal approach I'm not sure (in other words I doubt)
whether we will manage to package the missing dependencies:
 
>   https://anonscm.debian.org/cgit/pkg-java/jalview.git/tree/debian/TODO
> 
>   fr.orsay.lri.varna.*
>   htsjdk.samtools.*

This should be inside the libhtsjdk-java package.

>   org.biodas.jdas.*
>   org.jfree.graphics2d.svg.*
> 
> So we have a few options:
> 
> 1. Keep everything old in Debian, and SageMath out of Debian stable.

No.

> 2. Update Jmol in Debian, with a chance of SageMath entering Debian stable, but drop biojava4 and jalview from Debian stable. (They can remain broken in unstable, with a chance of fixing them later, ofc)
> 3. Update Jmol in Debian, and update biojava4 and jalview as well.

4. Update Jmol in Debian, and update biojava4 and drop outdated jalview
   (by at least starting the new dependencies and trying to upgrade
   jalview) and have the chance of SageMath entering Debian stable.
 
> If I work on (3) I don't think I will have any time to properly work on (2), but that is where my main personal interest lies. I'm also wondering what you all prefer, too.

May be 4 is a sensible compromise if we could live with backporting
the latest version of Jalview later.

Thanks for your work on these packages

    Andreas.

-- 
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