Re: List of software debuted at ISMB2016

[Andreas Tille]

Hi Michael

On Tue, Jul 12, 2016 at 07:57:17PM -0400, Michael Crusoe wrote:
> https://github.com/bioconda/bioconda-recipes/pull/1951
> 
> URLs and availability helpfully consolidated by the BioConda community.
> 
> I like their suggestion of a SVG badge (suitable for posters, slideshows,
> webpages, and handouts) to offer tool authors who get their software
> packaged.

+1

I've added some comments about cooperation + MoM as well as actual
licensing issues with GATK and TRF.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Please consider free license for segemehl

[Andreas Tille]

Hi again,

I have not yet received any response since three weeks.  I wonder
whether I was using a proper address.  It would be great if you could
comment on the license issue and I wonder whether the technical hints
I have given were helpful.

Kind regards

   Andreas.

On Mon, Jun 20, 2016 at 02:21:38PM +0200, Andreas Tille wrote:
> Hello,
> 
> I'm writing you on behalf of the Debian Med team which is a group inside
> Debian with the objective to package free software in the field of
> medicine and biology for official Debian.  We have assembled several
> known tools which you can see on our so called biology task page[1].
> Also Segemehl will show up on this page in the "Packaging has started
> and developers might try the packaging code in VCS" section after about
> 24 hours.
> 
> Since I've got a request from my colleagues to install segemehl I also
> intend to package this for Debian.  Unfortunately the licensing
> information at the website and inside the code is quite sparse.  The
> only hint I've found is if I call the executables it prints:
> 
>   SEGEMEHL is free software for non-commercial use 
>   (C) 2008 Bioinformatik Leipzig
> 
> >From a Debian point of view this is non-free since it puts a restriction
> on the usage of the software.  I wonder whether you might consider some
> free license like GPL, BSD or similar.
> 
> Since I had a look onto the source archive I'd like to give some
> additional hints:
> 
>1. The archive contains a file
> segemehl_0_2_0/segemehl/cscope.out
>   which most probably is not intended to be distributed.
>2. It would be also great if you could strip backup files
>   (*~) from the source tarball.
>3. There is an object file
> segemehl_0_2_0/segemehl/libs/remapping.o
>   which also made it probably unintended into the tarball
> 
> Finally it looks unusual that you are distributing all files under
> segemehl_0_2_0/segemehl instead of simply putting everything into just
> segemehl_0_2_0.
> 
> If you are interested I could provide manpages for the three executables
> created by the default build process.  These will be part of the Debian
> package (provided you will consider a free license and we can distribute
> the package inside Debian).
> 
> As a hint for a naming convention:  All three executables are ending
> with ".x" which is quite unusual.  While it might be help against name
> space pollution specifically for such generic names as "lack" you might
> consider droping this extension in a next version.
> 
> Kind regards
> 
>Andreas.
> 
> [1] https://blends.debian.org/med/tasks/bio
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de

Re: Sponsoring request: ITK-4.10 (addendum)

[Andreas Tille]

Hi Gert,

I admit I either need to find a powerful box *and* a connection with
better bandwidth for upload than I usually have.  I have put Steve who
did previous uploads explicitly in CC.  Steve, please state explicitly
that you have no time / resources to do the upload and I'll see what
I can do.

Kind regards

   Andreas.

On Tue, Jul 12, 2016 at 11:31:03AM +0200, Gert Wollny wrote:
> I might add, I'd appreciate if someone takes another look at the
> d/copyright file, it is a complete overhaul. 
> 
> * There are warnings about "missing-field-in-dep5-copyright", but this
> is source code in the "public domain" 
> * There are files that are both under "Apache-2.0" and VTK-copyright,
> and I'm not sure how to name the license here, since it is a 
> combination. 
> * Lintian also doesn't like the general license paragraph that explains
> that the package is GPL becaus of linking it against fftw. 
> 
> Best, 
> Gert 
> 
> 
> 

-- 
http://fam-tille.de

[GSoC] Next packages (Was: Clustalo Autopkgtests)

[Andreas Tille]

Hi Canberk,

On Wed, Jul 13, 2016 at 01:35:47AM +0300, Canberk Koç wrote:
> I commit to git.

Fine.  Next packages on the todo list are

 phyml  

 
 dialign
 clustalw

Kind regards

  Andreas.

-- 
http://fam-tille.de

List of software debuted at ISMB2016

[Michael Crusoe]

https://github.com/bioconda/bioconda-recipes/pull/1951

URLs and availability helpfully consolidated by the BioConda community.

I like their suggestion of a SVG badge (suitable for posters, slideshows,
webpages, and handouts) to offer tool authors who get their software
packaged.

Clustalo Autopkgtests

[Canberk Koç]

Hello Andreas,

I commit to git.

Best Regards


Canberk Koç
[image: https://]about.me/canberkkoc

Re: Doo likee top-grade Girl doingg resplendent blowjoob?

[Emilia Clark]

Sent from my iPhone

RFS: odil 0.7.1-1

[Julien Lamy]

Dear all,
I've updated the Git repository of Odil to the latest upstream version
(0.7.1). It builds and passes lintian on my side, so if everything looks
OK, could I get an upload?

Cheers,
-- 
Julien



signature.asc
Description: OpenPGP digital signature

Re: Sponsoring request: ITK-4.10 (addendum)

[Gert Wollny]

I might add, I'd appreciate if someone takes another look at the
d/copyright file, it is a complete overhaul. 

* There are warnings about "missing-field-in-dep5-copyright", but this
is source code in the "public domain" 
* There are files that are both under "Apache-2.0" and VTK-copyright,
and I'm not sure how to name the license here, since it is a 
combination. 
* Lintian also doesn't like the general license paragraph that explains
that the package is GPL becaus of linking it against fftw. 

Best, 
Gert 

Sponsoring request: ITK-4.10

[Gert Wollny]

Dear all, 

I've prepared the new version of ITK in the packaging svn [1].

Changes: 

* New upstream release
* d/rules: remove installation of VNL valgrind suppression file,
  it is no longer distributed.
* d/rules, d/control: switch to automatically created debug packages
* d/rules: separate arch-indep build, Thanks: Santiago Vila,
  Closes: #829347
* d/p/series: disable bsd_hdf5 patch, we don't build for KFreeBSD and
  also use the system version of HDF5
* d/p/itk-4.10-correct..: correct a circular include bug
* d/p/itk-4.10-enable-system-nifti: use system nifti library
* d/control: update castxml dependency to latest version
* d/copyright: overhaul: add excludes and update accordingly
* d/watch, d/rules: add dfsg orig tarball suffix and correct data file
  accordingly
* d/rules: disable unsigned_long wrapping on i386, because the compiler
  considers it to be the same like unsigned_int
* d/p/vnl_complex_test_accuracy: correct tests to not test equality but
  near-ness of floating point results, test fails otherwise on i386
* d/control*: set secure browser url

Some remarks: 

* Please note that the build takes a very long time (on the build
servers 20h 55m are reported for amd64 and 8h33m for i386). 

* If someone has cycles to spare you could test to enable hardening. 

* I've named the mangled source tarballs -dfsg instead of +dfsg because
somewhere the build-system tests for the + sign in the build path, and
doesn't build if it is found.

many thanks, 
Gert 


[1] svn://anonscm.debian.org/debian-
med/trunk/packages/insighttoolkit/trunk/

Re: [ftpmas...@ftp-master.debian.org: mypy_0.4.1-2_amd64.changes REJECTED]

[Afif Elghraoui]

Hello,

على الإثنين 11 تـمـوز 2016 ‫11:10، كتب Michael Crusoe:
>> Hmmm, is there any need for a new build?  If the package builds now fine
>> as is (which I did not tested) I would write this insied the bug report
>> (not reproducible any more).
> 
> Yes a new build is needed, there are no binary packages; I did a source
> only upload.
> 
> It builds for me in an updated pbuilder chroot but I don't know how to
> trigger the build daemons to try again.
> 

You'd have to contact the corresponding buildd admin(s) and ask them to
requeue the package for building.

"""
The admins responsible for buildd's for a particular arch can be reached
at a...@buildd.debian.org, for example i...@buildd.debian.org.
""" https://www.debian.org/devel/buildd/

regards
Afif

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