Error in makePSOCKcluster(names = spec, ...)

[Tianqi-Ma]

Hi, scMAGIC team

I was playing around this package with the data provided in tutorial (Tasic.Rdata and Campbell_2k.Rdata) in a docker image in Linux. An error occoured says:

[1] "Sum single cell counts matrix:"
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
[1] "Number of overlapped genes:"
[1] 17131
[1] "Start clustering :"
sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied
sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied
sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied
sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied
Error in makePSOCKcluster(names = spec, ...) : 
  Cluster setup failed. 4 of 4 workers failed to connect.
Calls: scMAGIC ... .cluster_increase_speed -> makeCluster -> makePSOCKcluster

It seems come from the parallel thread. Here is the code i used:

# load reference dataset
list.Ref <- readRDS('Tasic.Rdata')
ref.mtx <- list.Ref$mat_exp
ref.labels <-list.Ref$label[, 1]
# load target dataset
list.demo <- readRDS('Campbell_2k.Rdata')
exp_sc_mat <- list.demo$mat_exp
label_sc <-list.demo$label
output.scMAGIC <- scMAGIC(exp_sc_mat, ref.mtx, ref.labels, atlas = 'MCA', num_threads = 4)

Hope get reply from you soon.

[Drizzle-Zhang]

It seems that this error is related to the permission.

[Tianqi-Ma]

It seems that this error is related to the permission.

Yes, you are right. I've figured it out and thanks a lot.