[pymvpa] scipy problem at installation

[Yaroslav Halchenko]

On Wed, 10 Feb 2010, patrik andersson wrote:
> I installed the virtual machine and it seems to work fine! However, I
> would like to use the glmnet from R. Whats the best way to get the R,
> rpy etc installation working.
> I managed to compile the R 2.7.2 version. But the Matrix package is
> not in it and I don't know how to get it. And will I have to compile
> the rpy as well?

I guess by virtual machine you mean NeuroDebian one?  If so, then you
are already in the heaven ;) -- you will barely ever need to compile
anything -- you will have simply install them.  Debian is based on
distributing binary  packages of software, and they are readily
available for you, you just need to tell it what to install ;)  See for
instance

http://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html

N.B. just don't forget that you would need to run them from root user or
use sudo like in examples below

Now back to the cows:

* to install R under virtual machine just do

sudo apt-get install r-base

and that is it.  You might like to install additional packages right
away:

sudo apt-get install r-recommended python-rpy python-rpy

* Now lets things become a bit more involved:

 - there is no native package within Debian for glmnet, so you could
   proceed two ways -- standard R way to install libraries (less
   preferable in my taste) or Debian-way -- use additional repository
   (but I've not tested it with stable Debian) ....

 nah... decided to ease yours and our lives a bit: just run

 sudo apt-get update
 sudo apt-get install r-cran-glmnet


 glmnet is interfaced from pymvpa via rpy in 0.4.x branch and via rpy2
 in 0.5.x branch.  rpy2 debian package depends on more recent R release
 (2.10) so I would need to check if it is indeed a strict requirement.
 But you should be all set now to use glmnet from 0.4 branch.

P.S. I am not sure if by "compile the R 2.7.2" you actually meant
"compiled manually and installed manually"... if so, you might get now
two versions of R conflicting, so to go all-Debian way you would need to
remove manually installed R version (or just "reinstall" neurodebian
vm to start from clean)

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