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Status of rostlab software in Debian (Was: Bug#905206: Seems to crash in fortran lib)


back in 2009 Laszlo Kajan did quite some effort to package several
projects from rostlab.org for official Debian.  There was a very good
cooperation between RostLab and Debian - mediated by Laszlo who was
introducing other members (who probably left Rostlab meanwhile to find
other jobs).

Since Laszlo moved away from Munich he lost contact to Rostlab and had
also no time to keep on maintaining the existing Software inside Debian.
So the Debian Med team took over the maintenance.  The packages were
regularly updated to latest versions released by Rostlab as well as to
the latest packaging standards in Debian.  This also included continuous
integration tests to verify the functionality of the programs.

It now turned out that one of the tests for profnet failed (you might
like to read the full story and the effort we did to track the issue
down in the according bug report https://bugs.debian.org/905206 ).
The reason seems to be inside a FORTRAN module
(see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=905206#69 ).
Unfortunately there is nobody in the team who can even decide whether
this might be caused by a broken gfortran compiler or whether the code
is broken.  Thus we can not guarantee the proper functionality of the
code for our users without help.

As you can read below Olivier Sallou from Debian Med team found reasons
to assume that the software stack based on profnet is superseeded
anyway.  It would be nice if you could confirm this.  In this case we
could stop our desperate efforts to get profnet fully functional again.

If you consider that packaging SNAP2 is more fruitful - may be other
software you would like to see inside Debian - we would rather
concentrate on this and would be happy to package your latest and
greatest code.

In general we would love to refresh the closer relation between RostLab
and Debian since Laszlo made us believe this would be quite fruitfully.
May be you would like to send a member of your lab to our next Sprint
which will happen somewhen in the beginning of next year in Berlin (to
be announced).  Such kind of sprint once was the entry point for Laszlo
into Debian.  Inside the Debian Med team we have quite a record for
teaching about Debian packaging which could be quite interesting for

I'd be really happy to revive the connection again.

Kind regards


On Tue, Oct 08, 2019 at 09:26:13AM +0200, Olivier Sallou wrote:
> On 10/4/19 3:07 PM, Andreas Tille wrote:
> > Hi Olivier,
> >
> > On Fri, Oct 04, 2019 at 02:14:02PM +0200, olivier sallou wrote:
> >>> Program received signal SIGSEGV: Segmentation fault - invalid memory
> >>> reference.
> >> I really do not see what error could be. Maybe a fortran issue after an
> >> upgrade (something that was working but not done the same way now....)
> >> Sorry, I have no skill to fix this kind of issue. Should be reported
> >> upstream
> > Since Laszlo changed his job we do not have real upstream contact.
> >  
> >> I see on their web site that it was superseeded by snap2 in 2015. So maybe
> >> time to let it go....
> > Fine for me.  Where exactly did you found this? 
> On https://rostlab.org/owiki/index.php/Snapfun:
> """
> 2015-07-23 : The Snapfun (SNAPweb service) has been superseded by an
> improved version of SNAP, named SNAP2. Requests for the SNAPweb service
> now point to SNAP2. If for some reason, you require the original SNAPweb
> service, please contact hecht@rostlab.org. More information about SNAP2
> is available here.
> """
> Snap2 links:
> https://rostlab.org/owiki/index.php/Snap2
> https://github.com/Rostlab/SNAP2
> >  I only found a snap^2
> > web interface.  What about the reverse depends of profnet?
> this is indeed an issue, but if "old" release is not maintained anymore
> and if we don't have local skills on this....
> This kind of issue goes beyond "maintainer" packaging, need skills in
> language and software itself.
> >
> > Kind regards
> >
> >       Andreas.
> >
> -- 
> Olivier Sallou
> Univ Rennes, Inria, CNRS, IRISA
> Irisa, Campus de Beaulieu
> Tel:
> gpg key id: 4096R/326D8438  (keyring.debian.org)
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438


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