Dear Andreas Tille, we really appreciate your efforts in packaging our software. I wanted to let you know that we’re currently in the process of fading out some of the oldest and most “problematic” modules of PredictProtein (e.g. PROFphd, PROFhtm… almost everything with “prof” in its name actually) and replace it by newer software (also moving from Perl to Python). Thus, you do not have to worry about those very old packages. We currently are figuring out what to replace, remove and/or add. Though, since you mentioned it in one of the previous emails: SNAP2 will most likely stay for a while longer. Regards Michael Bernhofer
Subject: Additional remark to: Status of rostlab software in Debian (Was: Bug#905206: Seems to crash in fortran lib) Date: 11. October 2019 at 09:38:55 CEST Hello again,
another package originated at RostLab is currently creating issues
as it is reported against the package profphd
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=942064#17).
The bug report quotes the following hint:
Make prof work with Debian Jessie by requiring perlbrew package
and have it install independent perl v5.10 instance. $[ has been
moved from perl core >=5.16.0 into arybase, and does not produce
the same side effects as in previous perl versions, therefore
breaking prof when run using perl v5.20 in Jessie.
Currently Debian is moving to Perl v5.30 and we have no power to port
all code that is even orphaned by its original authors. But before we
give up we want to make really sure what you think about it. I wonder
whether some member of your group might find some time to clarify the
need to keep this software or what the more up to date replacements
might be. We'd happily support you in packaging the latest and greatest
code from your lab.
Kind regards and thanks a lot for your cooperation
Andreas.
On Tue, Oct 08, 2019 at 04:47:12PM +0200, Andreas Tille wrote:
Hello,
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
you.
I'd be really happy to revive the connection again.
Kind regards
Andreas.
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
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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