I\'ve heard it said that it is bad practice to use setwd() in a script.
To make things a bit more portable where I work we all put this in a Rprofile
hdrive=
switch(Sys.info()[[1]],
'Linux'="/mnt/hdrive",
'Windows'="H:/",
"Darwin"="/Volumes/hdrive/mnt/hdrive"
)
So i always have that variable to get me to our shared drive. Then in my script we can write
setwd(paste(hdrive,"/relative/path/",sep="/"))
So that gets us around some of the problems that others are talking about.