R help - Feb 2009 - running multiple commands in one system() call

Hi all,

I'm on Mac OS X 10.4...

So I've got a small python script I need to run from R.  However, to get 
the python script working, I need to have the shell that R calls get 
settings from my .bash_profile file, which apparently it doesn't 
currently (the shell R calls uses an older version of python, and also 
this older version of python can't see various python modules I have to 
import to make the python script work).

Basically I need to do this:

===========mytreefile_location <- 
"/bioinformatics/phylocom/_results/beta/ss_newicks/subsamp6_fromea_wnalist.newick"

cmd1 = 'source ~/.bash_profile'
cmd2 = paste('python 
/bioinformatics/phylocom/_scripts/update_newick_root.py ', 
mytreefile_location)

system(cmd1)
system(cmd2)
===========
...but if I do it this way, the sourcing of .bash_profile from the first 
system() call does not carry over to the 2nd system() call.


Any help appreciated!!

Cheers,
Nick



-- 
===================================================Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
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thinking the earth is spherical is just as wrong as thinking the earth 
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14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm

On Sun, 22 Feb 2009, Nick Matzke wrote:
> Hi all,
>
> I'm on Mac OS X 10.4...
For which there is a separate mailing list, R-sig-Mac .
> So I've got a small python script I need to run from R.  However, to
get the
> python script working, I need to have the shell that R calls get settings 
> from my .bash_profile file, which apparently it doesn't currently (the
shell
> R calls uses an older version of python, and also this older version of 
> python can't see various python modules I have to import to make the
python
> script work).
Let me guess: you are in fact using R.app (the GUI, a separate 
project) and not R.  It is most likely not a question of 'the shell 
that R calls' but the 'settitngs that launching a process from the 
desktop uses', and you need to adjust that.  It you are really running 
command-line R, it inherits shell settings (especially the path) from 
the shell which called it.

If you don't know how to set the environment for R.app, ask on the 
R-sig-mac list as it is way off topic here.
> Basically I need to do this:
>
> ===========> mytreefile_location <- 
>
"/bioinformatics/phylocom/_results/beta/ss_newicks/subsamp6_fromea_wnalist.newick"
>
> cmd1 = 'source ~/.bash_profile'
> cmd2 = paste('python
/bioinformatics/phylocom/_scripts/update_newick_root.py
> ', mytreefile_location)
>
> system(cmd1)
> system(cmd2)
> ===========>
> ...but if I do it this way, the sourcing of .bash_profile from the first 
> system() call does not carry over to the 2nd system() call.
Of course: each system() command runs a separate shell.

Your subject line is about something not covered in the body of your 
email: to do that put the commands in an executable bash script and 
call system() on that.


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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