[Rd] R CMD BATCH vs R CMD batch
Rainer M Krug
Rainer at krugs.de
Thu Oct 29 10:44:55 CET 2015
Deepayan Sarkar <deepayan.sarkar at gmail.com> writes:
> On Thu, Oct 29, 2015 at 2:09 PM, Rainer M Krug <Rainer at krugs.de> wrote:
>> Dirk Eddelbuettel <edd at debian.org> writes:
>>
>>> On 28 October 2015 at 21:39, Marius Hofert wrote:
>>> | Out of laziness I just used "R CMD batch" instead of "R CMD BATCH". I
>>> | didn't get an error so didn't think about the consequences... One
>>> | consequence is (at least on Mac OS X 10.11 but probably in more
>>> | generality) that R_BATCH_OPTIONS are ignored, which was kind of fatal
>>> | in my case... I am thus wondering whether it makes sense to either a)
>>> | have R_BATCH_OPTIONS also be respected for "R CMD batch" or b) simply
>>> | not allow "R CMD batch" as a valid command (so requiring to use "R CMD
>>> | BATCH"). Both approaches might be delicate... just wanted to point
>>> | this issue out...
>>>
>>> Same reason we have 'R CMD INSTALL' as there often is /usr/bin/install with
>>> different options ...
>>>
>>> In general 'R CMD foo' will run for any 'foo' in the path:
>>>
>>> edd at max:~$ R CMD date
>>> Wed Oct 28 21:05:01 CDT 2015
>>> edd at max:~$
>>
>> So what is R CMD exactly doing in this example? The output is the same if
>> I say only the command (using pwd as otherwise the time has changed...):
>>
>> ,----
>> | 09:35:03 ~$ R CMD pwd
>> | /Users/rainerkrug
>> | 09:35:37 ~$ R CMD pwd
>> | /Users/rainerkrug
>> | 09:37:44 ~$ pwd
>> | /Users/rainerkrug
>> | 09:37:49 ~$
>> `----
>>
>> And this happens, except in cases where the foo is defined as a CMD in R (build, ...):
>>
>> ,----
>> | Commands:
>> | BATCH Run R in batch mode
>> | COMPILE Compile files for use with R
>> | SHLIB Build shared library for dynamic loading
>> | INSTALL Install add-on packages
>> | REMOVE Remove add-on packages
>> | build Build add-on packages
>> | check Check add-on packages
>> | LINK Front-end for creating executable programs
>> | Rprof Post-process R profiling files
>> | Rdconv Convert Rd format to various other formats
>> | Rd2pdf Convert Rd format to PDF
>> | Rd2txt Convert Rd format to pretty text
>> | Stangle Extract S/R code from Sweave documentation
>> | Sweave Process Sweave documentation
>> | Rdiff Diff R output ignoring headers etc
>> | config Obtain configuration information about R
>> | javareconf Update the Java configuration variables
>> | rtags Create Emacs-style tag files from C, R, and Rd files
>> `----
>>
>> Unless I miss something, is this is an inconsistency in R?
>
> One important difference (not sure if the only one) is that R CMD
> defines more environment variables. Compare
>
> env | grep -i tex
> R CMD env | grep -i tex
>
> So for example
>
> R CMD pdflatex
>
> will behave differently from plain pdflatex.
Reading Dirk's email again, I think I get the picture of what ~R CMD foo~ is
doing: running ~foo~ after doing some initial magic.
Out of interest: What is the magic ~R CMD~ is doing? Is it documented
anywhere?
Rainer
>
> -Deepayan
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
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email: Rainer at krugs.de
Skype: RMkrug
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