Re: Sponsoring request: mriconvert

[Andreas Tille]

Uploaded, thanks for your effort, Andreas.

On Thu, Jun 30, 2016 at 09:58:48PM +0200, Gert Wollny wrote:
> Hello all, 
> 
> yet another package with a fix for gcc-6  compilation: 
> 
>   * d/p/gcc-6: Fix compilation with Gcc-6, Closes: #811811
>   * cme fix dpkg-control 
> 
> Many thanks, 
> Gert 
> 
> 
> 

-- 
http://fam-tille.de

Re: Updated beagle

[Andreas Tille]

Hi Dylan,

On Thu, Jun 30, 2016 at 10:37:23PM +0200, Dylan wrote:
> Hi Andreas,
> Thank you for this upload.
> 
> Did you push your changes ? (Probably a d/changelog: UNRELEASED to unstable 
> ;-)
> I don't see them.

Pushed and tagged.

Thanks for watching me ;-)

   Andreas.

-- 
http://fam-tille.de

Re: Sponsoring request: libgtextutils; - next package I'll work on: libbpp-core

[Andreas Tille]

On Thu, Jun 30, 2016 at 09:40:07PM +0200, Fabian Klötzl wrote:
> On 29.06.2016 17:24, Andreas Tille wrote:
> > Fabian, in future could you please:
> >
> >1. Use quilt for patches
> 
> IIRC, the repo was structured in a weird way, so I rather not wanted to
> fiddle with that.

I agree that the repository did not had a default structure.  Since I
have not seen any good reason to derive from standard I have switched it
yesterday to a default layout.
 
> >2. Make some noise about your fix to prevent others doing
> >   the same work twice (if you did some noise but nobody
> >   was hearing - please make noise again and sorry if we
> >   did not respond).
> 
> I think, I was hoping to make some noise as soon as my pull request got
> merged [1]. But as that never happened, well …
> 
> [1]: https://github.com/agordon/libgtextutils/pull/6

I guess the code is not actively maintained upstream.

Thanks for your attempt to fix anyway

  Andreas.

-- 
http://fam-tille.de

Re: Updated beagle

[Dylan]

Hi Andreas,
Thank you for this upload.

Did you push your changes ? (Probably a d/changelog: UNRELEASED to unstable ;-)
I don't see them.

Best regards,
Dylan

2016-06-25 15:56 GMT+02:00 Andreas Tille :
> I'll do it.
>
> On Sat, Jun 25, 2016 at 03:18:37PM +0200, Dylan wrote:
>> Hi,
>> I have updated beagle. Could someone upload it to unstable?
>>
>> Thank you.
>>
>> Best regards,
>> Dylan
>>
>>
>
> --
> http://fam-tille.de
>

Re: InVesalius 3.0.1 with VTK6 support

[Thiago Franco Moraes]

I've added the keyword and comment fields to the .desktop file and commited
to Debian-med SVN. It seems to be correct because if I search the
invesalius's keywords in the krunner, it show InVesalius. But I'm not sure,
since I don't use Debian unstable and the Ubuntu lintian doesn't search for
this error in the .desktop file.

On Thu, Jun 30, 2016 at 3:05 PM Thiago Franco Moraes 
wrote:

> Hi Andreas,
>
> On Thu, Jun 30, 2016 at 11:56 AM Andreas Tille  wrote:
>
>> Hi Thiago,
>>
>> On Thu, Jun 30, 2016 at 10:18:00AM -0300, Thiago Franco de Moraes wrote:
>> >
>> > I've updated InVesalius 3 to the new version. This version has support
>> to VTK6. The changes are in the Debian-Med svn. It seems to be lintian
>> clean.
>>
>> VTK6 is very good news!  Thanks for your work on this.
>>
>>
> Thanks! I was out for some time because our project ended temporarily. Now
> we are back again. Because of that, the conversion to VTK6 was delayed.
>
>
>> The package was not fully lintian clean (under unstable lintian) but I've
>> fixed some small issues.  There is one left that might interest you also
>> as upstream since you might like to provide a proper desktop file:
>>
>>
>> I: invesalius: desktop-entry-lacks-keywords-entry
>> usr/share/applications/invesalius-3.0.desktop
>> N:
>> N:This .desktop file does either not contain a "Keywords" entry or it
>> does
>> N:not contain any keywords not already present in the "Name" or
>> N:"GenericName" entries.
>> N:
>> N:.desktop files are organized in key/value pairs (similar to .ini
>> files).
>> N:"Keywords" is the name of the entry/key in the .desktop file
>> containing
>> N:keywords relevant for this .desktop file.
>> N:
>> N:The desktop-file-validate tool in the desktop-file-utils package is
>> N:useful for checking the syntax of desktop entries.
>> N:
>> N:Refer to
>> N:
>> https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s05.html
>> ,
>> N:https://bugs.debian.org/693918, and
>> N:https://wiki.gnome.org/Initiatives/GnomeGoals/DesktopFileKeywords
>> for
>> N:details.
>> N:
>> N:Severity: wishlist, Certainty: certain
>> N:
>> N:Check: menu-format, Type: binary
>>
>>
>> I have uploaded despite this minor issue and may be we can fix this in a
>> later version.
>>
>
> Ok. I'll take a look into this problem.
>
>
>>
>> Thanks again
>>
>>
> Thank you for your work!
>
>
>>   Andreas.
>
>
>>
>> --
>> http://fam-tille.de
>>
>

Bug#828850: marked as done (ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression Analysis)

[Debian Bug Tracking System]

Your message dated Thu, 30 Jun 2016 18:00:31 +
with message-id 
and subject line Bug#828850: fixed in r-bioc-deseq2 1.12.3-1
has caused the Debian Bug report #828850,
regarding ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression 
Analysis
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
828850: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=828850
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: r-bioc-deseq2
  Version : 1.12.3
  Upstream Author : Michael Love 
* URL : https://bioconductor.org/packages/DESeq2
* License : LGPL-3+
  Programming Lang: R
  Description : R package for RNA-Seq Differential Expression Analysis

Differential gene expression analysis based on the negative binomial
distribution. Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential expression based
on a model using the negative binomial distribution.

Popular bioinformatics tool/library; team maintained by Debian Med
--- End Message ---
--- Begin Message ---
Source: r-bioc-deseq2
Source-Version: 1.12.3-1

We believe that the bug you reported is fixed in the latest version of
r-bioc-deseq2, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 828...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated r-bioc-deseq2 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Hash: SHA256

Format: 1.8
Date: Mon, 27 Jun 2016 13:42:38 -0700
Source: r-bioc-deseq2
Binary: r-bioc-deseq2
Architecture: source amd64
Version: 1.12.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-bioc-deseq2 - R package for RNA-Seq Differential Expression Analysis
Closes: 828850
Changes:
 r-bioc-deseq2 (1.12.3-1) unstable; urgency=medium
 .
   * Initial release (Closes: #828850)
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r-bioc-deseq2_1.12.3-1_amd64.deb
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 05913ad6ba6bc8b5b73e3b107fd53b1d 1324782 gnu-r optional 
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 2dcf23b3ae55656128c28f407a92becf 558352 debug extra 
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Re: InVesalius 3.0.1 with VTK6 support

[Andreas Tille]

Hi Thiago,

On Thu, Jun 30, 2016 at 10:18:00AM -0300, Thiago Franco de Moraes wrote:
> 
> I've updated InVesalius 3 to the new version. This version has support to 
> VTK6. The changes are in the Debian-Med svn. It seems to be lintian clean.

VTK6 is very good news!  Thanks for your work on this.

The package was not fully lintian clean (under unstable lintian) but I've
fixed some small issues.  There is one left that might interest you also
as upstream since you might like to provide a proper desktop file:


I: invesalius: desktop-entry-lacks-keywords-entry 
usr/share/applications/invesalius-3.0.desktop
N: 
N:This .desktop file does either not contain a "Keywords" entry or it does
N:not contain any keywords not already present in the "Name" or
N:"GenericName" entries.
N:
N:.desktop files are organized in key/value pairs (similar to .ini files).
N:"Keywords" is the name of the entry/key in the .desktop file containing
N:keywords relevant for this .desktop file.
N:
N:The desktop-file-validate tool in the desktop-file-utils package is
N:useful for checking the syntax of desktop entries.
N:
N:Refer to
N:
https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s05.html,
N:https://bugs.debian.org/693918, and
N:https://wiki.gnome.org/Initiatives/GnomeGoals/DesktopFileKeywords for
N:details.
N:
N:Severity: wishlist, Certainty: certain
N:
N:Check: menu-format, Type: binary


I have uploaded despite this minor issue and may be we can fix this in a
later version. 

Thanks again

  Andreas.

-- 
http://fam-tille.de

Re: Sponsoring request: libmems

[Andreas Tille]

Cool!  Thanks a lot for your great effort.  Uploaded, Andreas.

On Thu, Jun 30, 2016 at 03:56:44PM +0200, Gert Wollny wrote:
> Hi all, 
> 
> I've update libmems: 
> 
>   * d/p/05: Add patch to fix compilation with g++-6, Closes: #811870
>   * d/control: cme fix dpkg-control
> 
> Best, 
> Gert 
> 
> 

-- 
http://fam-tille.de

Re: Sponsoring request: libgtextutils; - next package I'll work on: libbpp-core

[Gert Wollny]

Am Mittwoch, den 29.06.2016, 18:15 +0200 schrieb Gert Wollny:
> Am Mittwoch, den 29.06.2016, 17:24 +0200 schrieb Andreas Tille:
> 
> 
> > 
> > -   return input_stream ;
> > +   return static_cast(input_stream) ;


Actually, after reading up on this [1] it seems that this is actually
correct, since with -std=c++11 std::istream defines an explicit bool()
operator that would be invoked by the static_cast. 

Nevertheless, returning "input_stream.good()" is equally correct in the
given code snipped. 

Best, 
Gert 

[1]  http://en.cppreference.com/w/cpp/io/basic_ios/operator_bool

Sponsoring request: libmems

[Gert Wollny]

Hi all, 

I've update libmems: 

  * d/p/05: Add patch to fix compilation with g++-6, Closes: #811870
  * d/control: cme fix dpkg-control

Best, 
Gert 

Re: Bug#828850: ITP: r-bioc-deseq2 -- R package for RNA-Seq Differential Expression Analysis

[Andreas Tille]

Uploaded.  Regarding cnvkit:  If I build in a pbuilder chroot this fails with:

...
help2man --no-info --version-option=version \
--name="a command-line toolkit for copy number analysis." \
./cnvkit > debian/cnvkit.1
debian/genmanpages.py 0.7.11
Traceback (most recent call last):
  File "debian/genmanpages.py", line 3, in 
from cnvlib import commands
ImportError: No module named cnvlib
debian/rules:37: recipe for target 'override_dh_auto_install' failed
...


I personally stopped autogeneration of manpages since most of it needs
post-processing anyway.  So either you set PYTHONPATH properly or install
the package call help2man (perhaps using the script I commited to SVN
in trunk/helper-scripts/createmanpages) and add it statically.

Kind regards

  Andreas.


On Tue, Jun 28, 2016 at 06:51:42AM -0700, Michael R. Crusoe wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Debian Med team 
> 
> * Package name: r-bioc-deseq2
>   Version : 1.12.3
>   Upstream Author : Michael Love 
> * URL : https://bioconductor.org/packages/DESeq2
> * License : LGPL-3+
>   Programming Lang: R
>   Description : R package for RNA-Seq Differential Expression Analysis
> 
> Differential gene expression analysis based on the negative binomial
> distribution. Estimate variance-mean dependence in count data from
> high-throughput sequencing assays and test for differential expression based
> on a model using the negative binomial distribution.
> 
> Popular bioinformatics tool/library; team maintained by Debian Med
> 
> 

-- 
http://fam-tille.de

Re: Please choose a free license for eigensoft

[Andreas Tille]

Hello again,

I have not received any response from your side.  I wonder whether the
mail addresses I used are active and if you are involved in the process
of deciding about a license.

Kind regards

Andreas.

On Mon, May 30, 2016 at 02:10:21PM +0200, Andreas Tille wrote:
> Hi,
> 
> I'm writing you on behalf of the Debian Med team which is a group inside
> Debian with the objective to package free software with relevance in
> biology and medicine for official Debian.  As you might possibly know we
> have created packages also from eigensoft as you can see on our so
> called tasks biology page[1].
> 
> Since I realised that there is a new version available I wanted to
> discuss the licensing issue with you before we are upgrading the
> package.  The problem is that the current licensing permits a
> distribution inside official Debiani.  According to the Debian Free
> Software Guidelines[2] which are widely accepted as Open Source
> definition the current license is not free since it is restricted to
> a specific (== non-commercial) use.
> 
> I wonder whether you might consider changing the licensing to some free
> license like GPL, BSD or MPL - just anything that has no such
> restricttion to non-commercial use.  You might like to know that several
> other authors of biologic software recently switched to free licenses
> (may be most prominently phylib).  The advantage for you inside Debian
> would be a higher visibility of eigensoft (since we distribute it with
> metapackages) and a way better quality assurance since Debian is running
> several tools to automatically detect problems inside the distributed
> software.
> 
> Another (unrelated) question is whether there are any publications
> connected to eigensoft.  As you can see in the entries of other packages
> on our tasks page[1] we usually add publications to the scientific
> software we are packaging.  Just let me know if you want me to add such
> a record for eigensoft.
> 
> Kind regards and thanks for your cooperation
> 
>   Andreas.
> 
> [1] http://blends.debian.org/med/tasks/bio#eigensoft
> [2] https://www.debian.org/social_contract#guidelines
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de