Hello,
I plan to use a script with R CMD BATCH on different platforms Linux,
Windows and Mac OSX. I use the commandArgs(trailing = FALSE) function
to retrieve the name of the script and the arguments (example below
with output.) The online docs for "Introduction to R" (sections B.1
Invoking R from the command line and B.4 Scripting with R) and
help("commandArgs") leave my head spinning regarding the contents of
the arguments when trailing = FALSE.
(1) What should I expect from commandArgs() when used with R CMD BATCH?
The docs for commandArgs() states, "These arguments are captured
before the standard R command line processing takes place. This means
that they are the unmodified values." However, if I call a script
like this ...
R CMD BATCH --slave --vanilla '--args dogs cats verbose=TRUE' /Users/
Shared/code/R/hbb/pam/script.r my.out
... the actual arguments are as shown in the example output below.
You can see that "--restore --save --no-readline" were picked up which
seems to contradict the documentation. In the online docs
(http://cran.r-project.org/doc/manuals/R-intro.html#Invoking-R
) the --vanilla argument is described as a combination of --no-save, --
no-environ, --no-site-file, --no-init-file and --no-restore. So now I
am wondering if I am confounding the arguments to invoke R with the
arguments to invoke R via CMD BATCH.
(2) Does the name of the script being called always fall in the third
element of the commandArgs() value? If so, does it always include the
full path?
(3) Are "--arg" and the supplied arguments always last in the
commandArgs() value? The docs for commandArgs() states, "This is
especially useful with the --args command-line flag to R, as all of
the command line after that flag is skipped," so I feel pretty
confident that they will be last. But given my confusion in (1)
above ....
Thanks,
Ben
###### script begin
args = commandArgs()
cat("All the arguments...\n\n")
cat(args, sep = "\n")
cat(" \n")
cat(paste("nargs=", length(args)), "\n")
cat(" \n")
cat(paste("source is", basename(args[3]), sep = " "), sep =
"\n")
ix = grep("--arg", args, fixed = TRUE)
if (ix < length(args)){
for (i in (ix+1):length(args)) {
cat(paste("argument #",i-ix,"-->",args[i],
sep=" "), sep = "\n")
}
}
ecode = 0
q(runLast = FALSE, save = "no", status = ecode)
###### script end
###### output file begin
All the arguments...
/Library/Frameworks/R.framework/Resources/bin/exec/i386/R
-f
/Users/Shared/code/R/hbb/pam/script.r
--restore
--save
--no-readline
--slave
--vanilla
--args
dogs
cats
verbose=TRUE
nargs= 12
source is script.r
argument # 1 --> dogs
argument # 2 --> cats
argument # 3 --> verbose=TRUE
#### output file end
##### session info
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.10.1
#######
