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) -- .-. =------------------------------ /v\ ----------------------------= Keep in touch // \\ (yoh@|www.)onerussian.com Yaroslav Halchenko /( )\ ICQ#: 60653192 Linux User ^^-^^ [175555] _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
