Question

When attempting to run R, I get this error:

Fatal error: cannot mkdir R_TempDir

I found two possible fixes for this problem by googling around. The first was to ensure my tmp directory didn’t contain a load of subdirectories – it doesn’t and it’s virtually empty. The second fix was to ensure that TMP, TMPDIR, and R_USER in my environment weren’t set to non-existent paths – I didn’t even have these set. Therefore, I created a tmp directory in my home directory and added it’s path to TMP in my environment. I was able to run R once and then I got the fatal error again. Nothing was in the TMP directory that I set in my environment. Does anyone know what else I can try? Thanks.

Answer 1

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:

By default, '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 'TMPDIR', 'TMP' and 'TEMP'
are checked in turn and the first found which points to a writable
directory is used: if none succeeds '/tmp' is used.

So my money is on checking those three environment variables. But AppArmor and SELinux have shown to be an issue too on some distributions.