read.bismark: option to change tmpdir in fread? about bsseq HOT 4 CLOSED

If you do it this way, all R code you run that uses tempdir() will benefit (not just data.table::fread() and in turn bsseq::read.bismark()). I am unlikely to add a tmpdir argument to bsseq::read.bismar() unless this proposed solution doesn't work (I don't have time to test myself just now, but I seem to recall making use of it in the past).

Changing the TMPDIR environment variable solved this issue. Thanks!

from bsseq.

I think the location of tempdir() can be controlled by environment variables.
From ?tempdir:

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. The path should not contain spaces. Note that setting any of these environment variables in the R session has no effect on tempdir(): the per-session temporary directory is created before the interpreter is started. [emphasis mine]

This means that you need to set this environment variable before starting R.
From memory, this is done using a .Renviron file, which can be at the user or project-level (https://support.posit.co/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf).

from bsseq.

If you do it this way, all R code you run that uses tempdir() will benefit (not just data.table::fread() and in turn bsseq::read.bismark()).
I am unlikely to add a tmpdir argument to bsseq::read.bismar() unless this proposed solution doesn't work (I don't have time to test myself just now, but I seem to recall making use of it in the past).

from bsseq.

Great, happy to help.

from bsseq.