Both workingDir(settings) and settings@workingDir showed the workingDir that I specified. However when I want to check the FraserObject by just running settings, this is the error message that I got
Fri Sep 16 13:17:51 2022: The given working directory '/localhd/125692/Rtmpu2AQgw/FRASER' does not exists. We will create it.
Warning message in dir.create(object@workingDir, recursive = TRUE):
“cannot create dir '/localhd/125692', reason 'Permission denied'”
ERROR while rich displaying an object: Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'scanBamParam': invalid class “FraserDataSet” object: Make sure we can write to the given working directory ' /localhd/125692/Rtmpu2AQgw/FRASER '.
Why the working directory showing here is different from the one that I specified? I am running FRASER on a cluster so I can't change the permission. I am using R 4.0.3 and the FRASER version is FRASER 1.2.1
Update:
Tried to install the package from github/c-mertes/FRASER, which updated the version to 1.9.1. The error disappeared. I don't know why the version I got from bioconductor is 1.2.1
Hi,
I am trying to create the FRASER object using the function
FraserDataSet
and here is the code that I ranBoth
workingDir(settings)
andsettings@workingDir
showed the workingDir that I specified. However when I want to check the FraserObject by just runningsettings
, this is the error message that I gotWhy the working directory showing here is different from the one that I specified? I am running FRASER on a cluster so I can't change the permission. I am using R 4.0.3 and the FRASER version is FRASER 1.2.1
Update: Tried to install the package from github/c-mertes/FRASER, which updated the version to 1.9.1. The error disappeared. I don't know why the version I got from bioconductor is 1.2.1
Thanks for the help! Laur