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Re: Alert about several medical imaging packages (Was: insighttoolkit4 is marked for autoremoval from testing)



On August 2, 2015 07:13:09 AM Andreas Tille wrote:
> Hi,
> 
> you might have noticed that we have gathered several gcc-5 related bugs.
> The situation in several medical imaging packages is specifically hard
> since it is a longer chain of dependencies and these seem to be
> specifically hard to solve.  

Hi Andreas,

I appreciate your concern about these packages and raising the alarm is 
probably useful.  To avoid the appearance that nothing is happening, I suppose 
it would be useful to report on my activities and plans.

CastXml: is now in sid and testing, building on all architectures.

ITK: I have gotten latest version (4.8.0) into VCS as reported [1].  With help 
from Paul Novotny and Gert Wollny two of the issues in [1] are solved and I've 
been making progress with the last, which is to tweak the CMake flags.  I was 
also intentionally delaying the upload until after the GCC switch (now 
complete) so that we don't have to change the SONAME artificially. 

Gccxml: I have taken your idea of a compatibility wrapper around castxml, 
implemented the suggestions of Brad King [2] and am in the process of testing 
it with all the packages that build using gccxml.  

mummy and activiz.net: I have not looked in detail at either, yet.  However, I 
have recently used both -- and debugged both -- in my paid employment.  So I 
have a reasonable idea of how they work.  The released activiz.net does not 
work with recent VTK, but Corentin Desfarges reports [3] that the git repo has 
updates.  So my expectation is that we'd have to package the latest git 
version.  


Above is roughly the order in which I plan to work on things.  My progress is 
admittedly slow.  Some of the above may well get removed temporarily from 
testing, but I believe we can eventually get back the ones we need.  Some may 
be permanently removed; e.g. in my view, ITK v3 is old enough that I propose 
we allow it to be removed.  I'd also like to remove cableswig because it was 
mainly used in pre-castxml days for ITK, but presently mummy needs it to.  I'm 
hoping that upstream mummy would update to remove this usage.


In the short term, my goals are:

ITK:
 1. Check the build with gcc 5 on all architectures.
 2. Enable more of the system libs, ensuring they build on all architectures.
 3. Review the list of modules to see if we need more enabled.
 4. Upload.

Gccxml:
 1. Check the list of dependent packages [4] build with the script
 2. Upload.

If you can help with any of the above, get in touch!

Thanks,
-Steve



[1] https://lists.debian.org/debian-med/2015/07/msg00152.html
[2] http://public.kitware.com/pipermail/castxml/2015-July/000014.html
[3] https://lists.debian.org/debian-med/2015/07/msg00055.html
[4] Packages that build-depend on gccxml:
activiz.net
cableswig
gdcm
mummy
pygccxml
pyplusplus
python-ctypeslib
spring   

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