On May 22, 2012, at 7:37 PM, Gabor Grothendieck wrote:
> On Tue, May 22, 2012 at 6:04 PM, Simon Urbanek
> <simon.urba...@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
>>> <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.
>>
>
> 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
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