On May 22, 2012, at 3:34 PM, Gabor Grothendieck wrote:
> On Tue, May 22, 2012 at 3:28 PM, Gabor Grothendieck
> <ggrothendi...@gmail.com> wrote:
>> On Tue, May 22, 2012 at 3:05 PM, Henrik Bengtsson <h...@biostat.ucsf.edu>
>> wrote:
>>> On Tue, May 22, 2012 at 11:39 AM, Gabor Grothendieck
>>> <ggrothendi...@gmail.com> wrote:
>>>> On Tue, May 22, 2012 at 1:34 PM, Henrik Bengtsson <h...@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.
>
>
>> --
>> Statistics & Software Consulting
>> GKX Group, GKX Associates Inc.
>> tel: 1-877-GKX-GROUP
>> email: ggrothendieck at gmail.com
>
>
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com
>
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