Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

[Andreas Tille]

Hi Lincoln,

On Sun, Jan 15, 2017 at 04:25:46PM -0500, Lincoln Stein wrote:
> The bug in the memory adaptor that Scott found turns out to have been from
> using the old perl 1.6.9 installed by the Debian package. Updating to 1.7.1
> (1.007001) fixes the problem.
> 
> I have merged all GBrowse changes into git version 2.56 and have made a
> CPAN release. I think you can go ahead and package it.

thanks a lot for your work on this.

For the Debian packaging[1] I imported the new version and tried to
adapt the patches[2] (BTW, I have no idea whether any previous
maintainer of the package pointed to it but some of these might be
interesting to integrate into the upstream code).

Since I learned from Perl team (in CC) that I can exclude tests via

   debian/tests/pkg-perl/smoke-skip

I tried to use this feature.  Unfortunately this does not work as
expected - at least in the build process.  Could anybody with better
Perl skills than me please have a look at the failed build time tests?

Thanks to all who provided help so far to finally fix gbrowse for the
next Debian stable release

 Andreas.

[1] https://anonscm.debian.org/git/debian-med/gbrowse.git
[2] https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches

-- 
http://fam-tille.de

Re: pbcommand new upstream

[Afif Elghraoui]

على السبت 14 كانون الثاني 2017 ‫21:42، كتب Sascha Steinbiss:
> OK, thanks for the confirmation. I’ll update to the latest version of 
> pbcommand then.

Many thanks for updating pbcommand--but don't forget to push the final
changes and tag. :)

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: Second Conference of Research Software Engineers: Sep 07-08, 2017

[adam.bogacki]

Sorry, I can't make it - but my postgraduate degree was
entirely due to free softwara (aka debian)
so you have my best wishes for the proceedings.

Regards,

Adam Bogacki,
adam.boga...@clear.net.nz


- Original Message Follows -
> Hello all,
> 
> As you all probably know, there is a huge need for
> sustainable community maintenance of research software;
> and I think Debian is the logical foundation for such
> efforts due to its distributed nature and extensive
> technical & social infrastructure**
> 
> To help make this a reality I urge any Debian contributor
> who cares about science to participate in this year's
> Conference of Research Software Engineers:
> 
> http://www.rse.ac.uk/conf2017.html
> 
> Last year's program:
> http://www.rse.ac.uk/conf2016_programme
> 
> ** and shadow infrastructure!
> 
> Cheers,
> 
> -- 
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> 
> https://impactstory.org/u/-0002-2961-9670
> michael.cru...@gmail.com +1 480 627 9108
> +32 2 808 25 58
> 

Adam Bogacki

adam.boga...@clear.net.nz

pub  2048R/E4E5BF4C [expires: 2016/04/22]
 3863 A27B CB01 E57F C49A 2B57 A9E4 C5E7 E4E5 B4FC

Second Conference of Research Software Engineers: Sep 07-08, 2017

[Michael Crusoe]

Hello all,

As you all probably know, there is a huge need for sustainable community
maintenance of research software; and I think Debian is the logical
foundation for such efforts due to its distributed nature and extensive
technical & social infrastructure**

To help make this a reality I urge any Debian contributor who cares about
science to participate in this year's Conference of Research Software
Engineers:

http://www.rse.ac.uk/conf2017.html

Last year's program: http://www.rse.ac.uk/conf2016_programme

** and shadow infrastructure!

Cheers,

-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project 
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+1 480 627 9108
+32 2 808 25 58

Bug#851488: ITP: python-gffutils -- Work with GFF and GTF files in a flexible database framework

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-gffutils
  Version : 0.8.7.1
  Upstream Author : Ryan Dale 
* URL : http://daler.github.io/gffutils/
* License : MIT
  Programming Lang: Python
  Description : Work with GFF and GTF files in a flexible database framework

 A Python package for working with and manipulating the GFF and GTF format
  files typically used for genomic annotations.  Files are loaded into a
   sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with
 plain-text methods alone.

Dependency of bcbio, to be team maintained by Debian Med

Re: libzstd 1.1.2 contains embedded zlib fork

[Sascha Steinbiss]

Hi Kevin,

thanks for your email.

>> I was looking to update libzstd to the current upstream version 1.1.2.
>> Besides some minor changes to the patches I had to make, I also noticed that
>> it now includes an embedded copy of some zlib code, which -- according to the
>> inline comments -- was adapted to be ready to compile with the zlibwrapper.
>> It wasn’t clear to me whether this was really necessary; when these files are
>> removed from the affected Makefile (and some minor adjustments are made) the
>> build still finishes fine.
> 
> That's been there since 1.1 I think, and is AFAICT example code for an
> alternative, non-packaged API that mimics the zlib API. It could be packaged
> under libzstd-dev:usr/share/doc/libzstd-dev/examples or something, like I've
> seen with a few development packages. Otherwise, I think nuking the sources or
> just removing them from the makefile is fine. Though from memory, anything
> compiled from these is not installed, so no action is probably also OK.

OK. I've checked that the new packages contain (at least) the same files as the 
1.1.1 version, which is the case. So this indeed doesn’t touch the installed 
contents and I also agree that there shouldn’t be a problem.

[…]
> What does the DFSG say about sources that are
> not compiled? They're in d/copyright anyway, IIRC FTPMASTER bounced me last
> update for this exact issue, and I added them.

There are some new sources in zlibWrapper/ under zlib license by M. Adler. They 
are actually new in 1.1.2 and also compiled in the Makefile — thats why I was 
asking about them as I disabled them. To be on the safe side license-wise have 
added them to d/copyright as well, so I guess we should be fine.
Preparing an upload as we speak.

Cheers
Sascha


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