[BioC] Biostrings and A. thaliana genome sequence

[Joern Toedling]

Hello René,

you do not need to have root access to a machine to install your own
versions of R and your favourite packages there. This is how to do it:
1. downloaded the tar.gz of the development version of R from
ftp://ftp.stat.math.ethz.ch/Software/R/
2. uncompress it to a directory you have write access to, say ~/local/R
3. change into the uncompressed directory,  ~/local/R/R-devel
4. run "./configure"
5. run "make"
Afterwards you can start R by executing ~/local/R/R-devel/bin/R; to
simplify that either add the bin directory to your path or create an
alias for R
You do not need to run "make install" to work with R.
For packages, 1. create a directory in which you want the packages
installed, e.g.  ~/local/rpacks  2. create an evironment variable R_LIBS
that holds the path to that directory, e.g.  "setenv
R_LIBS=${HOME}/local/rpacks"  with that directory and a C-shell (use
export with a Bash shell)
This environment variable tells R where to look first for installed
packages and where to install packages when using "install.packages" or
"biocLite". R_LIBS is safe to use, since it only extends the path to
look for packages and does not replace the default R library path.
I would recommend to add the alias for starting R and the R_LIBS
definition to your shell startup file (~/.cshrc  or ~/.bashrc).

Regards,
Joern

Rene Dreos (JIC) wrote:
> Herve, thanks a lot for your reply, but unfortunately R is installed on a machine for which I am not the root and the only user... so I can not easily upload R version without the approval of administrator and other users.
>
> Is it possible for me to build the Arabidopsis genome package by myself and use it with the older R and Biostrings versions?
>
> Cheers
> René
>
>