From simon.urbanek at r-project.org  Wed May 23 01:50:58 2012
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Tue, 22 May 2012 19:50:58 -0400
Subject: [Rd] Best way to locate R executable from within R?
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On May 22, 2012, at 7:37 PM, Gabor Grothendieck wrote:

> On Tue, May 22, 2012 at 6:04 PM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote:
>> 
>>> On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck
>>> <ggrothendieck at gmail.com> wrote:
>>>> On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>>>>> On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck
>>>>> <ggrothendieck at gmail.com> wrote:
>>>>>> On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I'd like to spawn of a new R process from within R using system(),
>>>>>>> e.g. system("R -f myScript.R").  However, just specifying "R" as in
>>>>>>> that example is not guaranteed to work, because "R" may not be on the
>>>>>>> OS's search path.
>>>>>>> 
>>>>>>>  What is the best way, from within a running R, to infer the command
>>>>>>> (basename or full path) for launching R in way that it works on any
>>>>>>> OS?  I came up with the following alternatives, but I'm not sure if
>>>>>>> they'll work everywhere or not:
>>>>>>> 
>>>>>>> 1. Rbin <- commandArgs()[1];
>>>>>>> 
>>>>>>> 2. Rbin <- file.path(R.home(), "bin", "R");
>>>>>>> 
>>>>>>> Other suggestions that are better?
>>>>>>> 
>>>>>> 
>>>>>> At least on Windows one could run R via R.exe, Rterm.exe or Rgui.exe
>>>>>> amd #2 would not pick up the differences.  On the other hand if I do
>>>>>> this on the Windows command line on my Vista system with R 2.15.0
>>>>>> patched:
>>>>>> 
>>>>>> cd \program files\R\R-2.15.x\bin\i386
>>>>>> Rterm.exe
>>>>>> 
>>>>>> and then enter commandArgs() into R, the output is "Rterm.exe" with no path.
>>>>> 
>>>>> Thanks, I overlooked this need.  For my particular use case, I'm
>>>>> interested in launching R in "batch" mode, so "R" will do (but not
>>>>> "Rgui").
>>>>> 
>>>>>> 
>>>>>> The fact that one can have 32 bit and 64 bit R executables on the same
>>>>>> system complicates things too.
>>>>>> 
>>>>>> Thus, on Windows something like this might work:
>>>>>> 
>>>>>>   file.path(R.home("bin"), R.version$arch, basename(commandArgs()[[1]]))
>>>>>> 
>>>>>> If there are cases that I missed then this might pick up those too:
>>>>>> 
>>>>>>   R <- commandArgs()[[1]]
>>>>>>   if (R == basename(R)) R <- file.path(R.home("bin"), R.version$arch, R)
>>>>> 
>>>>> FYI, R.home("bin") is not the same as file.path(R.home(), "bin"), cf.
>>>>> help("R.home").  R.home("bin") will pick up the current architecture
>>>>> directory (by using .Platform$r_arch), e.g.
>>>>> 
>>>>>> R.home("bin")
>>>>> [1] "C:/PROGRA~1/R/R-2.15.0patched/bin/x64"
>>>>> 
>>>>> /Henrik
>>>>> 
>>>> 
>>>> Then perhaps something like this which is still not 100% foolproof but
>>>> should work most of the time:
>>>> 
>>>> Find(file.exists, c(
>>>>   commandArgs()[[1]],
>>>>   file.path(R.home("bin"), commandArgs()[[1]]),
>>>>   file.path(R.home("bin"), "R")
>>>> ))
>>> 
>>> So that the last one tried works on Windows too it should be:
>>> 
>>> Find(file.exists, c(
>>>   commandArgs()[[1]],
>>>   file.path(R.home("bin"), commandArgs()[[1]]),
>>>   file.path(R.home("bin"), "R"),
>>>   file.path(R.home("bin"), "R.exe")
>>> ))
>>> 
>> 
>> Obviously, you don't want to do that for reasons discussed previously.
>> 
> 
> In most cases with a link the complete path would be passed in which
> case the first arg of Find would be chosen and be correct. If not it
> would fail through to further choices one of which would likely be
> correct and if none of them are then its likely that
> file.path(R.home("bin"), "R")  isn't either since that is already one
> of the choices.  While its not 100% foolproof the cases where it does
> not work are quite pathological whereas the cases where
> file.path(R.home("bin"), "R") fails to use the same executable include
> common cases such as R being called as Rterm or Rscript.
> 

Except that you may not have noticed that no one asked about that since that makes no sense (arguments differ etc.). The question was how to start R and your suggestions make it only worse and unusable - fortunately Henrik asked about better solutions so we can safely close this discussion.

Cheers,
Simon



[Rd] Best way to locate R executable from within R?
Simon Urbanek