Re: Request for review & upload: salmon

2016-01-30 Thread Michael Crusoe 
Thank you!

Sâm, 30 ian. 2016, 22:56, Andreas Tille  a scris:

> On Sat, Jan 30, 2016 at 06:32:54PM +, Michael Crusoe wrote:
> >
> > Heh, a timely mistake. Fixed.
>
> So its uploaded now (after fixing yaml syntax).
>
> Thanks for your work on this
>
>   Andreas.
>
> --
> http://fam-tille.de
>
> --
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu

Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: new version of libspdlog-dev ready for sponsoring

2016-01-30 Thread Michael Crusoe 
Sorry, was testing all the way through with salmon & transrate; should be
available now.

On Sat, Jan 30, 2016 at 7:38 PM Andreas Tille  wrote:

> On Sat, Jan 30, 2016 at 05:26:11PM +, Michael Crusoe wrote:
> > git+ssh://git.debian.org/git/debian-med/spdlog.git
>
> Did you pushed?
>
> --
> http://fam-tille.de
>
> --
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu

Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: Request for review & upload: salmon

2016-01-30 Thread Michael Crusoe 
On Sat, Jan 30, 2016 at 8:10 PM Andreas Tille  wrote:

> On Sat, Jan 30, 2016 at 05:51:59PM +, Michael Crusoe wrote:
> > The Lintian warning is due to the eigen3 library; I've filed a bug about
> > that.
>
> Probably a lintian check for an empty debian/upstream/metadata should be
> craftet.  If there is no reference for this software please remove the
> file.
>

Heh, a timely mistake. Fixed.


>
> There is a remaining debian/TODO file - do you plan to do this before
> upload or did you just forgot to remove the file (or should it remain
> for future package versions)?
>

This is for a future packager.


> The Vcs-* fields are just the boilerplate pointing to SVN of ""
>

Fixed :-)


-- 
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu

Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

new version of libspdlog-dev ready for sponsoring

2016-01-30 Thread Michael Crusoe 
git+ssh://git.debian.org/git/debian-med/spdlog.git

Thanks!
-- 
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu

Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe

Re: new version of libspdlog-dev ready for sponsoring

2016-01-30 Thread Andreas Tille 
On Sat, Jan 30, 2016 at 05:43:53PM +, Michael Crusoe wrote:
> Sorry, was testing all the way through with salmon & transrate; should be
> available now.

No need to sorry - I'm guilty for the same in several occurances. ;-)

Uploaded.  Thanks for your work

  Andreas.

-- 
http://fam-tille.de

Re: Request for review & upload: salmon

2016-01-30 Thread Andreas Tille 
On Sat, Jan 30, 2016 at 05:51:59PM +, Michael Crusoe wrote:
> The Lintian warning is due to the eigen3 library; I've filed a bug about
> that.

Probably a lintian check for an empty debian/upstream/metadata should be
craftet.  If there is no reference for this software please remove the
file.

There is a remaining debian/TODO file - do you plan to do this before
upload or did you just forgot to remove the file (or should it remain
for future package versions)?

The Vcs-* fields are just the boilerplate pointing to SVN of ""

Hint:  I inject my packages into Git by using this script:

   
https://anonscm.debian.org/viewvc/debian-med/trunk/helper-scripts/inject-into-alioth-git?view=markup

If I failed to adjust Vcs-Git the script wil fail ...


As far as I can see debian/gbp.conf is default as we recommend in our
policy.  Feel free to drop it.

Kind regards

Andreas.

-- 
http://fam-tille.de

Re: ginkgocadx ...The good, the bad, and the ugly

2016-01-30 Thread Gert Wollny 
Hi,

just wanted to give you the heads up on how this goes: 

The good: 

I got it to build and it runs, thumbnails now work, and also the 
loading of the borked dicom file (thanks to Matheu's patch for GDCM).


The bad: 

This was all done on Gentoo, because the current versions of VTK and
GDCM don't cut it: 

* VTK < 6.2.1 has a bug that makes ginkgocadx crash when creating the
thumbnails. 

* GDCM-2.6.3 + patch can't currently be build in a clean unstable,
because the build dependencies pull in conflicting versions of
libopenmpi (1.6 and 1.10). 

The ugly: 

The ginkgocadx code is a mess, threading is poorly implemented with the
result that at exit the program either crashes or hangs. Luckily gcc
now implements a thread-checker that gives some hints what is going
wrong, but resolving this threading issue will still be difficult.  

-- 
This means we'll have to wait until the gdcm can be build again, and
I'll ask the VTK maintainer what he think about uploading either vtk
-6.2.1, or vtk-6.3. vtk-7.0 is just around the corner, and both (vtk
-6.3 and vtk-7.0) will need to pass through NEW ...

Best, 
Gert