install R/bioconductor package locally - an example

Here I show an example for installing R/bioconductor package locally.

You need to specify the full path for R you want to install the package to, and the full path for library path the package will be install, and also the folder of the uncompressed files of R/bioconductor package.

In this example,
full path for R:/ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R
package folder: BSgenome/
library path: /ebio/abt6/jmao/bin/R-2.13/Rpacks

jmao@sever:~/bin/R-2.13$ /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD INSTALL BSgenome/ --library=/ebio/abt6/jmao/bin/R-2.13/Rpacks
* installing *source* package ‘BSgenome’ ...
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BSgenome)