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lima1 / PureCN

Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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PSCBS segmentation failed --> Error in write permission for R directory .cache #367

Closed lmanchon closed 1 month ago

lmanchon commented 2 months ago

--Hi,

PureCN.R used with PSCBS segmentation need write permission to personal .cache directory and sometimes (on HPC cluster) it failed with:

Error in getWritablePathname.Arguments(static, file = "dummy-not-created", : No write permission for directory: /nfs/home/users/.cache/R/R.cache/PSCBS/segmentByCBS/sbdry

I have modified the PureCN.R script at the beginnig to change my .cache directory by using R.cache library, such as:

library("R.cache") setCacheRootPath(path="/tmp/.cache/R/R.cache")

and now it works.

Laurent --