I have problems to start up my R session with a .Rprofile
on a unix server. When I start an interactive job everything works fine. When I start a batch job, it doesn't (batch jobs are started through TORQUE and distributed across different nodes). I checked ?Startup
but I still don't know what's going on. My .Rprofile
contains a print(...)
line just to make sure and I ran the test-job.r
file below in batch mode. It tells me that I have a .Rprofile
file at the current working directory and at the user directory (they are the same) and that it contains my print(...)
code. So why is R not running the .Rprofile
file on startup?
.Rprofile
print('Hallo World!')
test-job.r
profile1 = paste(getwd(),'/.Rprofile',sep='')
file.exists(profile1)
if(profile1) cat(readChar(profile1, 1e5))
profile2 = '~/.Rprofile'
file.exists(profile2)
if(file.exists(profile2)) cat(readChar(profile2, 1e5))
output
> file.exists(paste(getwd(),'/.Rprofile',sep=''))
[1] TRUE
> if(file.exists(paste(getwd(),'/.Rprofile',sep=''))) cat(readChar(paste(getwd(),'/.Rprofile',sep=''), 1e5))
print('Hallo World!')
>
>
> file.exists('~/.Rprofile')
[1] TRUE
> if(file.exists('~/.Rprofile')) cat(readChar('~/.Rprofile', 1e5))
print('Hallo World!')
From Intro to R :
note that R CMD does not of itself use any R startup files (in particular, neither user nor site Renviron files)
I interpret that as meaning BATCH mode doesn't read the .Profile
file. If you want it, I guess you need to explicitly source
it in test-job.r
.
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