如何将所有R软件包从超级用户重新安装到用户？

Question

I'm using R in Ubuntu. I've realised that I have packages installed in both /usr/local/lib/R/site-library/ and /home/sparhawk/R/x86_64-pc-linux-gnu-library/3.0/ . I'd prefer them all in my user directory.

How can I move all the (non-base) packages to the user directory? I'm happy to reinstall R and/or the packages if necessary.

I've also tried sudo apt-get purge r-base , but this didn't touch the root directory listed above.

Answer 1

Use the destdir option with install.packages to specify the location of the packages to be installed.

install.packages("RCpp,destdir="~/RPackages", CRAN="http://cran.r-project.org")

Answer 2

Uninstall R and packages

First I purged the Ubuntu package

$ sudo apt-get purge r-recommended
$ sudo apt-get --purge autoremove
...
dpkg: warning: while removing r-base-core, directory '/usr/lib/R/library' not empty so not removed

As above, one directory was not removed, so

$ rm -r /usr/lib/R /tmp

The package directories at /usr/local/lib/R/site-library/ and ~/R/x86_64-pc-linux-gnu-library/ were still present, so I removed them.

$ mv /usr/local/lib/R/ /tmp
$ mv ~/R/ /tmp/R-user

Reinstall R and packages

sudo apt-get install r-recommended

Run R from a user account (I used RStudio). Install packages manually.

At one point, I got the warning.

Warning message:
installed directory not writable, cannot update packages 'Matrix' 

So rather than run R as superuser, I attempted to install another version in the user directories. I think I have both versions installed, but R seems to pick the newer version.

> update.packages()
Matrix :
 Version 1.0-14 installed in /usr/lib/R/library 
 Version 1.1-0 available at http://cran.rstudio.com
Update (y/N/c)?  y
Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  'lib = "/usr/lib/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) y
...
> update.packages()
Warning: package 'Matrix' in library '/usr/lib/R/library' will not be updated
> packageVersion('Matrix')
[1] ‘1.1.0’

However, despite R seemingly picking the latest version, I still get warning messages about being unable to upgrade packages.

> biocLite("limma")
Warning message:
installed directory not writable, cannot update packages 'Matrix'