When attempting to run R, I get this error:
Fatal error: cannot mkdir R_TempDir
Your default temporary directory appears to have the wrong permissions. Here I have
$ ls -ld /tmp drwxrwxrwt 22 root root 4096 2011-06-10 09:17 /tmp
The key part is 'everybody' can read or write. You need that too. It certainly can contain subdirectories.
Are you running something like AppArmor or SE Linux?
Edit 2011-07-21: As someone just deemed it necessary to downvote this answer --
help(tempfile) is very clear on what values
tmpdir (the default directory for temporary files or directories) tries:
'tmpdir'will be the directory given by
'tempdir()'. This will be a subdirectory of the temporary directory found by the following rule. The environment variables
'TEMP'are checked in turn and the first found which points to a writable directory is used: if none succeeds
So my money is on checking those three environment variables. But AppArmor and SELinux have shown to be an issue too on some distributions.