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r - problems installing packages on server after update to 2.15

问题描述:

I have a recurring problem installing packages, that often looks like this:

> install.packages("Biobase")

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

~/R/x86_64-pc-linux-gnu-library/2.15

to install packages into? (y/n) y

--- Please select a CRAN mirror for use in this session ---

Loading Tcl/Tk interface ... done

Warning message:

package Biobase is not available (for R version 2.15.0)

My Sys.info() is as follows:

> Sys.info()

sysname

"Linux"

release

"2.6.32-40-server"

version

"#87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012"

nodename

"******"

machine

"x86_64"

login

"**"

user

"**"

effective_user

"**"

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.

网友答案:

The Biobase package is available on Bioconductor, not through CRAN. This is how you install it:

source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")

See Bioconductor for more info.

网友答案:

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.

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