From ggrothendieck at gmail.com  Wed May 23 01:37:02 2012
From: ggrothendieck at gmail.com (Gabor Grothendieck)
Date: Tue, 22 May 2012 19:37:02 -0400
Subject: [Rd] Best way to locate R executable from within R?
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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.

-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com



[Rd] Best way to locate R executable from within R?
Gabor Grothendieck