[Neurodebian-users] Problem with MIPAV

[Yaroslav Halchenko]

On Fri, 14 Dec 2012, Lorenzo Bandieri wrote:

> > who knows who knows... showing the error could have given a hint

> Ok then :) Here you go:

yeah -- not much of help for me, non-java mortal ;)

> NB.  "find / -type f -name libgcj.so.13" finds nothing on my system.

try -type l since it is a symlink ;-)

> > not so good news:  there is no specific timeline yet for the work
> >   on such a proper package.  We definitely are interested to help and
> >   there is interest "upstream" but no date could be guaranteed/set.
> >   (myself I am not even using MIPAV... more of a Python guy)

> Oh, finally they released the project open source! That's awesome!

yeap -- many similar good news these years, where those beasts come from
underground: freesurfer, NEST and now MIPAV ;)

> Well, if I can help in some way (testing? I'm starting to read
> something about debian packaging, but I don't think I'll be able to
> package anything in the short term) I'd be glad to.

well -- it might be worth building up from the basic package, and
resolving issues along the way, e.g. creating a list of which 3rd party
libraries are used, what versions needed and what are already packaged
in Debian... I think at some point I had such a list somewhere... can't
find

btw -- all our packaging is under
http://git.debian.org/?p=pkg-exppsy/mipav.git
happen you still want to get the sources for that original mipav pkg

so if you care to bite in -- reviewing what is needed could be a good
start ;)

> > since our installer package is pretty much just a 'downloader' for
> > the binary distribution -- indeed you might better off just following
> > stock upstream installation instructions for now
> I'll try this way. I usually try to avoid to install things manually
> because I don't want to risk to bork my system with files unknown to
> apt (happened in the past :) ).

;) same here

> > by default we have deb-src lines in
> > /etc/apt/sources.list.d/neurodebian.sources.list are simply
> > commented out -- uncomment them, and run apt-get update

> Uhm, that's what I did:

> root at linux-laptop:~# cat /etc/apt/sources.list.d/neurodebian.sources.list
> deb http://www.neuro.webdisk.com.ua data main contrib non-free
> deb-src http://www.neuro.webdisk.com.ua data main contrib non-free
> deb http://www.neuro.webdisk.com.ua wheezy main contrib non-free
> deb-src http://www.neuro.webdisk.com.ua wheezy main contrib non-free

exactly -- so you could not even install mipav since itis not avail for
wheezy:

apt-cache policy mipav

would not give you option to get it from http://www.neuro.webdisk.com.ua


you could add a line 

deb-src http://www.neuro.webdisk.com.ua sid main contrib non-free

apt-get update

and then you would be able to fetch sources from sid repo

alternatively -- just use above  GIT repo ;)

> > but once again -- it would be just a downloader package for binary
> > distribution of MIPAV prepared by Bennett (CCed) and there is no newer
> > version seems to be avail on http://www.nitrc.org/frs/?group_id=228

> Indeed, my plan was to modify the package to fetch the binary for the
> latest release leaving the rest unchanged as far as possible (apart
> from the name) :) One of the problem I encountered was that I didn't
> know how to get a url to download the package from...

debian/watch

specifies where to find recent one, but there is no more recent one
there on NITRC, that is why I cc-ed Bennett before


-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
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