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Where to drop a python script?

8 messages · Jonathan Greenberg, Marc Schwartz, Dirk Eddelbuettel +2 more

Original
Marc Schwartz
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On Oct 30, 2013, at 1:54 PM, Jonathan Greenberg <jgrn at illinois.edu> wrote:

            

      
      
      
    

        
See Writing R Extensions Manual, section 1.1.7:

  http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dR-scripts-in-packages

If you want to see a package example, my WriteXLS package uses Perl, but the concepts will be the same:

  https://github.com/marcschwartz/WriteXLS

If you look at WriteXLS.R around line 130, you can see an example of getting the $PATH to the included Perl scripts that I use, which are in the 'inst/Perl' folder. Further down around line 230, is where the script is called via system(). Note the use of shQuote() for some arguments.

Regards,

Marc Schwartz

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 30 October 2013 at 13:54, Jonathan Greenberg wrote:

        
| R-developers:
| 
| I have a small python script that I'd like to include in an R package I'm
| developing, but I'm a bit unclear about which subfolder it should go in.  R
| will be calling the script via a system() call.  Thanks!

Up to you as you control the path. As "Writing R Extensions" explains,
everything below the (source) directory inst/ will get installed.  I like
inst/extScripts/ (or similar) as it denotes that it is an external script.

As an example, the gdata package has Perl code for xls reading/writing below a
directory inst/perl/ -- and I think there are more packages doing this.

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Gilbert
    

    

      
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The old convention was that it went in the exec/ directory, but as you 
can see at 
http://cran.at.r-project.org/doc/manuals/r-devel/R-exts.html#Non_002dR-scripts-in-packages 
  it can be in inst/anyName/. A minor convenience of exec/ is that the 
directory has the same name in source and when installed, whereas 
inst/anyName gets moved to anyName/, so debugging can be a tiny bit 
easier with exec/.

Having just put a package (TSjson) on CRAN with a python script, here 
are a few other pointers for getting it on CRAN:

-SystemRequirements: should indicate if a particular version of python 
is needed, and any non-default modules that are needed. (My package does 
not work with Python 3 because some modules are not available.) Some of 
the libraries have changed, so it could be a bit tricky to make 
something work easily with both 2 and 3.

-You need a README to explain how to install Python. (If you look at or 
use mine, please let me know if you find problems.)

-The Linux and Sun CRAN test machines have Python 2 whereas winbuilder 
has Python 3. Be prepared to explain that the package will not work on 
one or the other.

Another option to system() is pipe()

Paul

        
On 13-10-30 03:15 PM, Dirk Eddelbuettel wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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On 31/10/2013 00:40, Paul Gilbert wrote:

            

      
      
      
    

        
Better to describe exactly what you need: installation instructions go 
stale very easily.

            

      
      
      
    

        
Not true.  Linux and Solaris (sic) have both: the Solaris machines have 
2.6 and 3.3.  Please do not spread misinformation about machines you do 
not have any access to.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Gilbert
    

    

      
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On 13-10-31 03:01 AM, Prof Brian Ripley wrote:

            

      
      
      
    

        
For an R package how does one go about specifying which should be used?

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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On 31/10/2013 15:33, Paul Gilbert wrote:

            

      
      
      
    

        
You ask the user to tell you the path or at least the command name, e.g. 
by an environment variable or R function argument.  Just like any other 
external program such as GhostScript.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Gilbert
    

    

      
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On 13-10-31 01:16 PM, Prof Brian Ripley wrote:

            

      
      
      
    

        
Yes, but since I don't have direct access to the CRAN test machines, 
specifically, on the CRAN test machines, how do I specify to use Python 
2 or Python 3? (That is, I think you are the user when CRAN tests are 
done on Solaris, so I am asking you.)