Re: Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]

2015-08-13 Thread Steve M. Robbins
On August 13, 2015 01:47:37 PM Dmitry Smirnov wrote: > On Wednesday 12 August 2015 22:01:36 Steve M. Robbins wrote: > > Could those package maintainers update to v4, please? > > First ITK-4 needs to be re-build for GCC-5 transition. Yes, true. There is work in progress on that front [1]. I'm

Re: samtools 1.2 package layout change

2015-08-13 Thread Charles Plessy
Le Thu, Aug 13, 2015 at 03:03:34PM +0100, Tim Booth a écrit : > > I was looking to see if it was worth pulling the samtools 1.2 package > into Bio-Linux (Ubuntu LTS Backports) and I can see that the package for > 1.2 has all the utility scripts going into /usr/bin where before they > were in /usr/

Re: gcc-5 transition of GDCM

2015-08-13 Thread michkapopoff
Hi thanks for your insights. I guess python-pygccxml is not directly needed here in Debian Med. On ITK’s side, pygccxml is present in ITK’s repo as a subtree. So it is not needed as a dependency, and there is no plan to change this. I’ll leave the decision up to you. I personally recommend people

Re: MOM: reportbug fails

2015-08-13 Thread Andreas Tille
Hi, On Thu, Aug 13, 2015 at 09:44:05PM +0430, Malihe Asemani wrote: > Your report will be carbon-copied to debian-devel, per Debian policy. > Querying Debian BTS for reports on wnpp (source)... > Traceback (most recent call last): > ... > SOAPpy.Errors.HTTPError: > > Any Idea? A websearch unco

MOM: reportbug fails

2015-08-13 Thread Malihe Asemani
Hi Andreas, The reportbug command fails, every time I tried to report a bug for king-probe: mali@buildEnv:/home/mali/med/probe$ LC_ALL=C reportbug wnpp ^[[A/usr/lib/python2.7/dist-packages/gtk-2.0/gtk/__init__.py:57: GtkWarning: could not open display warnings.warn(str(e), _gtk.Warning) *** We

Re: Help needed to update to latest fastqc

2015-08-13 Thread Tim Booth
Hi Olivier, Looks like Bernd Rinn is making positive noises regarding a DFSG version of the library, so hopefully once he provides code you can take what I have done and make use of it. I committed to SVN because it's so much easier than pushing to GIT and I'm lazy, sorry. In my libsis-jhdf5-jav

samtools 1.2 package layout change

2015-08-13 Thread Tim Booth
Hi Charles, I was looking to see if it was worth pulling the samtools 1.2 package into Bio-Linux (Ubuntu LTS Backports) and I can see that the package for 1.2 has all the utility scripts going into /usr/bin where before they were in /usr/{lib,share}/samtools. A slew of Lintian warnings results.

Re: DWV (DICOM Web Viewer)

2015-08-13 Thread Yves
Hi Sébastien, I did not progress on this topic but I will try to find some time to study these examples. Thanks for the update! Best, Yves On 8 August 2015 at 11:05, Sébastien Jodogne wrote: > Hi Yves, > > > My name is Yves, I'm developing a pure javascript DICOM viewer called > dwv. > > It is

Re: gcc-5 transition of GDCM

2015-08-13 Thread Aron Xu
Actually I'm seeking to orphan the package as I don't use it myself anymore, but it's not a burden so far so that I haven't done it yet. If there are people interested in adopting or co-maintaining it'll be appreciated. There's no any form of repository at the moment and I can create one if no one

Re: gcc-5 transition of GDCM

2015-08-13 Thread Andreas Tille
Hi Michka, I keep the Debian maintainer Aron Xu in CC. Gccxml was maintained as a predependency of some Debian Med package by the according team. I'm not aware that python-pygccxml has any reverse dependencies in Debian Med but surely ITK is of interest. Could the ITK people please raise their

Re: Help needed to update to latest fastqc

2015-08-13 Thread olivier.sal...@codeless.fr
On 08/12/2015 08:43 PM, Tim Booth wrote: > Hi, > > After a fair amount of struggling I conclude that I do not have all the > code required to build this thing from source. > > The distribution of JHDF5 from > https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 > contains some Java sou

Re: Help needed to update to latest fastqc

2015-08-13 Thread olivier.sal...@codeless.fr
On 08/12/2015 12:44 PM, Tim Booth wrote: > Hi Andreas and Olivier, > > I'm going to have a crack at the FastQC update. I've been poking at the > HDF5 packages and here are my conclusions so far: I already had a look and started some work. In fact I expected to progress on it during Debconf, but