Using install.packages with custom temp dir - r

Question

I would like to install a package with a security profile that does not have access to /tmp , but has its own temporary directory, for example /tmp/jeroen. However even though I try to pass the TMPDIR environment variable, it still fails because it tries to use /tmp. Below a toy example using RAppArmor and unixtools (see here for the test profile)
> library(RAppArmor)
> library(unixtools)
> dir.create("/tmp/jeroen")
> set.tempdir("/tmp/jeroen")
> setwd(tempdir());
> aa_change_profile("r-test")
Switching profiles...
> print(tempdir());
[1] "/tmp/jeroen"
> install.packages("plyr", lib="/tmp/jeroen", configure.vars="TMPDIR=/tmp/jeroen")
trying URL 'http://cran.rstudio.com/src/contrib/plyr_1.8.tar.gz'
Content type 'application/x-gzip' length 384462 bytes (375 Kb)
opened URL
==================================================
downloaded 375 Kb
Fatal error: cannot create 'R_TempDir'
The downloaded source packages are in
‘/tmp/jeroen/downloaded_packages’
When looking at the kern.log file (which logs security messages), it turns out that the problem is that R CMD INSTALL still tried to use /tmp which was denied:
Jul 24 19:41:34 Jeroen-Antec kernel: [16270.696805] type=1400 audit(1374687694.097:599):
apparmor="DENIED" operation="mkdir" parent=5798 profile="r-test" name="/tmp/RtmpcUOJuQ/"
pid=5802 comm="R" requested_mask="c" denied_mask="c" fsuid=1000 ouid=1000
Is there any way I can tell R CMD INSTALL to use /tmp/jeroen instead?

Answer 1

The correct answer was given by #hadley in the comments: in order to make sure install.packages uses the custom temporary directory, one needs to do
Sys.setenv(TMPDIR="/tmp/jeroen")
in addition to:
configure.vars="TMPDIR=/tmp/jeroen"
This way both the extraction and the installation of the package avoids the system or user default temporary directory.

Answer 2

The documentation in help(tempdir) pretty clearly states that TMP, TMPDIR, ... are used:
By default, ‘tmpdir’ will be the directory given by ‘tempdir()’.
This will be a subdirectory of the per-session temporary directory
found by the following rule when the R session is started. 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 if setting one alone does not help, maybe you want to set several, and make sure the permissions on your 'replacement directory' are permissive enough etc pp.