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R CMD BATCH vs R CMD batch

7 messages · Marius Hofert, Dirk Eddelbuettel, Deepayan Sarkar +2 more

Original
Marius Hofert
# 
Hi,

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...

Cheers,
M
Dirk Eddelbuettel
#
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:~$ 

Dirk
Rainer M Krug
# 
Dirk Eddelbuettel <edd at debian.org> writes:
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

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Deepayan Sarkar
    

    

      
      #
    

  


  

      
On Thu, Oct 29, 2015 at 2:09 PM, Rainer M Krug <Rainer at krugs.de> wrote:

            

      
      
      
    

        
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

  
  


  


      

    

    

      
      

        


  

        

      Rainer M Krug
    

    

      
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Deepayan Sarkar <deepayan.sarkar at gmail.com> writes:

            

      
      
      
    

        
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

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
      #
    

  


  

      
On 29 Oct 2015, at 10:44 , Rainer M Krug <Rainer at krugs.de> wrote:

        

            

      
      
      
    

        
R is open source.... (and shell scripts are considered self-documenting by some)

On Unix-alikes, R is a shell script which, if called with 1st argument CMD, calls ${R_HOME}/bin/Rcmd, which is another shell script that ends with 

case "${1}" in
## this was a separate command prior to 2.10.0
  Rd2txt)
    cmd="${R_HOME}/bin/Rdconv"
    extra="-t txt"
    ;;
## removed in 2.15.0
  Rd2dvi)
    echo "R CMD Rd2dvi is defunct: use Rd2pdf instead"
    exit 1
    ;;
  *)
    if test -x "${R_HOME}/bin/${1}"; then
      cmd="${R_HOME}/bin/${1}"
    else
      cmd="${1}"
    fi
    ;;
esac
shift

exec "${cmd}" ${extra} "${@}"

I.e., except for setting up variables and such, R CMD ${foo} essentially looks for ${R_HOME}/bin/${foo} and executes it if it exists and is executable, otherwise it just executes ${foo}.

Notice that, somewhat contrary to what Dirk said, this logic works at the mercy of the file system when it comes to case sensitivity. On OSX with the default case-insensitive setup we get

Peters-iMac:IBP pd$ R CMD install
Error: ERROR: no packages specified

which comes from R's package installer, whereas a case-sensitive FS would pick up /usr/bin/install instead. That is just how the "test" shell built-in works: 

Peters-iMac:~ pd$ test -x `R RHOME`/bin/INSTALL ; echo $?
0
Peters-iMac:~ pd$ test -x `R RHOME`/bin/UNSTALL ; echo $?
1
Peters-iMac:~ pd$ test -x `R RHOME`/bin/install ; echo $?
0

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rainer M Krug
    

    

      
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peter dalgaard <pdalgd at gmail.com> writes:

            

      
      
      
    

        
True - should have looked in the sources...

            

      
      
      
    

        
Thanks for that detailed explanation of the mechanism - it is much
clearer now. And as usual, if one knows how something is happening, it's
not "magical" anymore.

            

      
      
      
    

        
Yeah - true. I was already starting to wonder as I always was using ~R
CMD install~ and it always worked on my Mac.

Thanks again,

Rainer