I have a recurring problem installing packages, that often looks like this:
Installing package(s) into /usr/local/lib/R/site-library
(as lib is unspecified)
Warning in install.packages("Biobase") :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
to install packages into? (y/n) y
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
package Biobase is not available (for R version 2.15.0)
Sys.info() is as follows:
"#87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012"
Is the error
package Biobase is not available (for R version 2.15.0) due to the fact that I have to install it in a personal library (apparently on the server I work on, the usual library is not writable)? How can I get around this, as I seem to get the same "not available for 2.15" error anytime I try to install a package.
Biobase package is available on Bioconductor, not through CRAN.
This is how you install it:
See Bioconductor for more info.
I am adding the following solution for anyone else that might stumble across this older post.
The root cause of the problem is ownership/permissions for the directory where R is installing the libraries. To quote from a related post:
"the directory is owned by root:staff and of mode 2775, or 'user and group read-write, others read-only'." (Dirk Eddelbuettel)
For more details and how to correct this, please refer to this thread.