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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Cannot open temporary file error #176

Closed weishwu closed 3 years ago

weishwu commented 3 years ago

Hi,

I got the following errors when running the functions for building and scoring the GRN:

> scenicOptions = runSCENIC_1_coexNetwork2modules(scenicOptions)
08:29   Creating TF modules
Number of links between TFs and targets (weight>=0.001): 3048628
             [,1]
nTFs         1270
nTargets    11775
nGeneSets    7008
nLinks    4365756
Warning message:
In plot.new() :
  Cannot open temporary file '/tmp/RtmpQ9oyVU/pdf4b4d71223a85c' for compression (reason: No such file or directory); compression has been turned off for this device

> scenicOptions = runSCENIC_2_createRegulons(scenicOptions)
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file '/tmp/RtmpQ9oyVU/libloc_198_a387640b811c7977.rds', probable reason 'No such file or directory'

> scenicOptions = runSCENIC_3_scoreCells(scenicOptions, exprMat_log)
Error in .local(object, ...) : 
  It seems the regulons have not been built yet. Please, run runSCENIC_2_createRegulons() first.
File 'int/2.6_regulons_asGeneSet.Rds' does not exist.

Any help? Thanks.

weishwu commented 3 years ago

Fixed.

TapsiS commented 3 years ago

Hi, Could you please post your solution. I am facing the same issue.

Thanks

Portulaca666 commented 3 years ago

Hi, Could you please post your solution. I am facing the same issue.

Thanks