CODEWITHSUNDEEP
rlinuxtemporary-files
realm
realm

Reputation: 31

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

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!

Upvotes: 3

Views: 1548

Answers (2)

Com
Com

Reputation: 146

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).

Upvotes: 2

Maurits Evers
Maurits Evers

Reputation: 50718

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%

Upvotes: 0

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