R CMD BATCH vs R CMD batch

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.

-Deepayan