Problem
Running a script or R command results in the error:
Fatal error: cannot create 'R_TempDir'
Error: 18:25: unexpected symbol
17: r <- c(REVO=Revobase::getRevoRepos()
18: LOCAL_3.1
^
Execution halted
Error: 18:25: unexpected symbol
17: r <- c(REVO=Revobase::getRevoRepos()
18: LOCAL_3.1
^
Execution halted
Solution
This is typically due to an inability to write to the current specified temporary directory for the R session either due to permissions or space exhaustion.
By default, the R session on Linux will write its temporary files for each session to a directory of the form '/tmp/RtmpO2MIQ7' where the subdirectory under /tmp is generated randomly for each new session. Within the session, you can determine the current temp directory with the command 'tempdir()'. At the beginning of the session, R will first check, in turn, to see if the environment variables TMPDIR, TMP, and TEMP are set and use the first one that is set as the temp directory. If none are set, it will default to /tmp. If /tmp is inadequate to hold the temporary working files created by some RevoScaleR operations, you may create an alternate temp file system with more space than /tmp and export TMPDIR to point to it in the environment.
For cluster environments, this should be done on all nodes. For LSF clusters, refer to section 7.8.1 of the RRE Installation Guide for Linux as LSF may override this TMPDIR value in some cases and redirect tmp files to /tmp anyway. This can be disabled in the lsf.conf.
