[Neurodebian-devel] ANTS
Yaroslav Halchenko
debian at onerussian.com
Wed Feb 26 14:44:59 UTC 2014
On Wed, 26 Feb 2014, Gert Wollny wrote:
> >> * is the -fpermissive really needed? Or is this a leftover from 1.9?
> >was originally added in
> >commit 1d6102bbb822b917a891faad58353e8c6911cdb1
> >Author: Yaroslav Halchenko <debian at onerussian.com>
> >Date: Fri May 4 10:31:17 2012 -0400
> > BF: patch from Matthias Klosse for gcc 4.7 (Closes: #667099)
> >not sure if still needed. build would show ;)
> Okay, I will test this.
cool -- thanks in advance
> >indeed itk4 is currently available only for x86, but it might come to other
> >archs eventually. better to get ready IMHO ;)
> Okay. BTW, I've seen that ITK is at version 4.2 in NeuroDebian,
> afaik ANTS will need 4.4 at least. Well, since we need ANTS and ITK
> 4.5 on wheezy I will run builds over the weekend to see how this
> goes.
ANTS 2.0.0 I was packaging should work with ITK 4.4 indeed. I have a
build of ITK 4.4 for wheezy siting around and thought to upload it
whenever it is needed (i.e. for ANTS) after initial checking ;)
FWIW -- it succeeded to build only for wheezy, not any ubuntus
I will now try a blind backport rebuild of 4.5.0-3 -- may be we could
even have that one
> >>* As for the data, can we just add it in the debian/ directory?
> >>Since there are binary files, this may violate Debian policy, but
> >>then again it's data. There seems to be an option to set the test
> >>data root to avoid downloading.
> >could go anywhere but I do not see benefits for under debian/ instead of some
> >directory overlayed over upstream code. It is upstream data after all, and as
> >a data collection might even be copyrightable.
> Well, I always thought everything that is not in the original
> tarball has to be provided as patches or in some other way through
> debian/.
well -- there is no original tarball anyways (besides may be tarball of
tagged release on github)... and 3.0 source package supporting
multiple tarballs came out for a reason ;) Ideally we should just
automate acquisition of such needed data, and that is why I thought it
might be worth a separate source/binary package....
meanwhile -- I see that itk package in Debian carries
InsightToolkit-4.4.0/.ExternalData so might be worth looking where
they get it from
> That's the only reason I choose this approach.
I see
> If you can give me a pointer how to add properly overlay over
> upstream code that doesn't require a patch in debian/ I'll happily
> add the data differently. It seems I figured out how I can point the
> test data download url to where ever I want it :)
cool... pointers -- man dpkg-source:
Format: 3.0 (quilt)
A source package in this format contains at least an original tarball (.orig.tar.ext where ext can be gz, bz2, lzma and xz) and a debian tarball (.debian.tar.ext). It can also contain additional original tarballs (.orig-component.tar.ext). component can only contain alphanumeric char‐
acters and dashes ("-").
Extracting
The main original tarball is extracted first, then all additional original tarballs are extracted in subdirectories named after the component part of their filename (any pre-existing directory is replaced). The debian tarball is extracted on top of the source directory after prior
removal of any pre-existing debian directory. Note that the debian tarball must contain a debian sub-directory but it can also contain binary files outside of that directory (see --include-binaries option).
and also you could apt-get source python-dipy
which has two tarballs... get-orig-source target of debian/rules supposed
to fetch that additional one.
but once again, here it might really be better to have a separate data package
since that data might not change that often if ever.... but it would also
depend on how much data ants would also need to build/test
> I will ask about the copyright of the data.
FWIW: data itself is not copyrighted probably, but the "collection" might be.
upon a quick grep through ITK's copyright -- do not see explicit mention.
there is a good chance it would be the same data btw -- might be worth
checking... may be then ITK package could just "install" it (if it doesn't do it already) and we could jsut use it for ANTS???
--
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate, Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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