Re: Outreachy 2017 (Round 14)

2017-03-19 Thread Büşra Selin Pekişçi 
Hello Andreas,

I make request to participate Debian-Med at Alioth fyi.

Best Regards.

2017-03-17 23:46 GMT+03:00 Andreas Tille :

> Hi Büşra
>
> On Fri, Mar 17, 2017 at 11:21:44PM +0300, Büşra Selin Pekişçi wrote:
> > I made a testsuite for bug number #848329
> >  . I look at
> > program's website and there is no documentation so i made a simple test
> by
> > looking examples.
>
> Sounds good.
>
> > Now what should i do to commit code to you ? Thanks for
> > help.
>
> Did you created a login on alioth.debian.org as described in the Debian
> Med policy?  If yes please either apply for the Debian Med team or let
> me know your login name to make you a member of the team which will
> grant you commit permissions to the Debian Med packaging repositories.
>
> Then you can commit and I'll check your changes.
>
> Thanks for your work on this
>
>  Andreas.
>
> --
> http://fam-tille.de
>

Bug#858183: binNMU needed for r-bioc- packages broken by R 3.3.3.

2017-03-19 Thread Charles Plessy 
Package: release.debian.org
Severity: grave

Hello everybody,

the update of R to version 3.3.3 unexpectedly breaks some R packages, which
need to be reinstalled from source.  In Debian terms, given how we package R
packages, this can be solved by a binNMU.

A quick look at ci.debian.net shows that a large number of Bioconductor
packages (r-bioc-*) started to fail their tests at the end of February
following the upload of r-base version 3.3.2.20170227-1, which was a release
candidate of 3.3.3.  Some of the failures are direct, and some may be a ripple
effect.

On Bioconductor's support forum 
(https://support.bioconductor.org/p/93695/#93719),
it was suggested to reinstall the packages "BiocGenerics", "S4Vectors",
"IRanges", and "GenomicRanges".  I tried this on my computer (using sbuild 
--make-binNMU)
and their regression tests restarted to pass.  These packages are very central 
in
Bioconductor's dependency graph.

If time remains, how about starting with these four and see if the failures in 
the 
the other packages dissapear ?

nmu r-bioc-biocgenerics_0.20.0-1 . all . -m "Rebuild for R 3.3.3."
nmu r-bioc-s4vectors_0.12.1-2 . ANY . -m "Rebuild for R 3.3.3." 
nmu r-bioc-iranges_2.8.1-1-m . ANY . "Rebuild for R 3.3.3."
nmu r-bioc-genomicranges_1.26.2-1 . ANY -m "Rebuild for R 3.3.3."

Otherwise I can prepare a more extensive list of packages to rebuild.

Cheers,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

Re: ezDicom

2017-03-19 Thread Karsten Hilbert 
On Sun, Mar 19, 2017 at 07:48:37AM +0100, Mark 1234 wrote:

> There's a piece of abandon-ware called ezDicom that is a fantastic
> lightweight Dicom viewer:
> 
> https://sourceforge.net/projects/ezdicom/
> 
> The source code is provided in the link. The authors are not reachable
> (I tried several times).
> 
> I wonder if this could be a candidate for your project?

Hello Mark 1234,

thanks for your suggestion.

I have had a quick look at the source code and here are *my*
thoughts why ezdicom may not be an easy candidate for
inclusion into Debian:

- there's currently no upstream maintainer

- there are other dicom viewers available
(aeskulap, gingkocadx)
(not that they have upstream maintainers, though :-)

- it would need porting (maybe that's easy) from
  Delphi to FreePascal

- the source doesn't seem to cater to being
  compiled on Linux so may need to be ported/
  adjusted to Linux compatibility, too

- the license contains a no-endorsement clause
  which may need to be checked against DFSG

Notwithstanding, thanks for the pointer !

Karsten
-- 
GPG key ID E4071346 @ eu.pool.sks-keyservers.net
E167 67FD A291 2BEA 73BD  4537 78B9 A9F9 E407 1346

ezDicom

2017-03-19 Thread Mark 1234 
I just heard about the debian medical imaging package - really good idea!

There's a piece of abandon-ware called ezDicom that is a fantastic
lightweight Dicom viewer:

https://sourceforge.net/projects/ezdicom/

The source code is provided in the link. The authors are not reachable
(I tried several times).

I wonder if this could be a candidate for your project? I would love
to have it on Linux.