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Declare BASH Array Using R System Function

6 messages · Jeff Newmiller, Peter Dalgaard, Brian Ripley +2 more

Original
Dario Strbenac
# 
Hello,

It is difficult searching for previous posts about this since the keywords are short and ambiguous, so I hope this is not a duplicate question.

I can easily declare an array on the command line.

$ names=(X Y)
$ echo ${names[0]}
X

I am unable to do the same from within R.
sh: Syntax error: "(" unexpected

Reading the documentation for the system function, it appears to only be relevant for executing commands. What can I do instead to declare a BASH array ? Thanks.

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
Jeff Newmiller
# 
You seem confused. You are programming in R, and asking questions about bash on an R mailing list. You seem to need to learn the difference between environment variables and bash variables and how processes acquire and transfer environment variables, which is really an operating system concept and off topic here. Once you do understand this difference, you might be interested in reading the R help file on Sys.setenv().
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Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:
Peter Dalgaard
#
On Jul 29, 2013, at 08:27 , Jeff Newmiller wrote:

            

      
      
      
    

        
Not particularly, but he needs to be aware of _which_ shell R is executing in system() calls. These things work for me:

            

      
      
      
    

        
baz

Dario's issue is suggested by his error message

            

      
      
      
    

        
The shell is (Bourne) "sh", not "bash", so bash extension won't work. 

This is highly system dependent: On OSX Snow Leopard, e.g., /bin/sh really is GNU bash, which is why it works for me. Others have the more sane setup where /bin/sh really is Bourne sh.

Next question is of course how to ensure that bash gets used. I must admit that I have long forgotten...

-Peter D.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On 29/07/2013 08:49, peter dalgaard wrote:

            

      
      
      
    

        
See below: the shell should always be 'sh'.

            

      
      
      
    

        
On recent OS X /bin/sh is *a variant of* bash.  E.g. shopt xpg_echo is 
different if it gets invoked as sh or bash.  Where sh is a link to bash 
the behaviour is usually different depending on how it is invoked.

There are quite a lot of systems for which /bin/sh is not based on 
either bash or Bourne sh.  As I understand it, Debian/Ubuntu nowadays 
use dash by default, and some other Linuxen use ash.  zsh is also seen 
as a system shell.  And in many cases this is configurable

Note too that there is quite a lot of flexibility in how bash is configured.

            

      
      
      
    

        
From ?system

      ?command? is parsed as a command plus arguments separated by
      spaces.  So if the path to the command (or an argument) contains
      spaces, it must be quoted e.g. by ?shQuote?.  Unix-alikes pass the
      command line to a shell (normally ?/bin/sh?, and POSIX requires
      that shell), so ?command? can be anything the shell regards as
      executable, including shell scripts, and it can contain multiple
      commands separated by ?;?.

So you do not have a choice of shell, and the command-line you pass 
needs to invoke a different shell if that is what you want.


But apart from knowing that R's system calls the system(1) OS call (on a 
Unix-alike) there is nothing relevant to R-help here.

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      arun
    

    

      
      #
    

  


  

      
Hi,
?system("names=(X Y); echo ${names[0]}")
#sh: 1: Syntax error: "(" unexpected


#this worked for me:
?system("bash -c 'names=(X Y); echo ${names[0]}'")
#X

A.K.



----- Original Message -----
From: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Sunday, July 28, 2013 10:00 PM
Subject: [R] Declare BASH Array Using R System Function

Hello,

It is difficult searching for previous posts about this since the keywords are short and ambiguous, so I hope this is not a duplicate question.

I can easily declare an array on the command line.

$ names=(X Y)
$ echo ${names[0]}
X

I am unable to do the same from within R.

            

      
      
      
    

        
sh: Syntax error: "(" unexpected

Reading the documentation for the system function, it appears to only be relevant for executing commands. What can I do instead to declare a BASH array ? Thanks.

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia

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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

  
  


  


      

    

    

      
      

        


  

        

      Dario Strbenac
    

    

      
      #
    

  


  

      
Thank you. This answers my question. I am using Linux, too.