From Rainer at krugs.de  Thu Oct 29 09:39:34 2015
From: Rainer at krugs.de (Rainer M Krug)
Date: Thu, 29 Oct 2015 09:39:34 +0100
Subject: [Rd] R CMD BATCH vs R CMD batch
In-Reply-To: <22065.32480.203040.942634@max.nulle.part> (Dirk Eddelbuettel's
	message of "Wed, 28 Oct 2015 21:05:20 -0500")
References: <CAM3-Kjagdzcya2ecCm=1Q7roFnNsKH+RR0Ryg3JEWPGU1b=4VA@mail.gmail.com>
	<22065.32480.203040.942634@max.nulle.part>
Message-ID: <m2y4emax15.fsf@krugs.de>

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?

Rainer


>
> Dirk

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

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email:      Rainer at krugs.de

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[Rd] R CMD BATCH vs R CMD batch
Rainer M Krug