R: Fatal error: creating temporary file for '-e' failed

Question

sessionInfo()

R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.3

library(parallel)
makeCluster(detectCores() - 1)

Output in R:

Fatal error: creating temporary file for '-e' failed

How can I solve this issue? Thank you!

Answer 1

The parallel package appears to save tmp files to /var/tmp/. The error Fatal error: creating temporary file for '-e' failed appears to be related to access issues with this location. I was able to solve the issue by enabling permissions for this folder (in my case by mounting the location in a Docker/Singularity image).

Answer 2

Can you confirm that the code based on the Seurat -included sample data works.

For example, does the following work?

library(Seurat)
res <- ScaleData(object = pbmc_small, vars.to.regress = c("nUMI"))
#Regressing out: nUMI
#  |======================================================================| 100%
#Time Elapsed:  2.64941716194153 secs
#Scaling data matrix
#  |======================================================================| 100%