[R] running multiple commands in one system() call

Nick Matzke matzke at berkeley.edu
Mon Feb 23 07:13:09 CET 2009

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 <- 

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


...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!!


Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
Dept. personal page: 
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

"[W]hen people thought the earth was flat, they were wrong. When people 
thought the earth was spherical, they were wrong. But if you think that 
thinking the earth is spherical is just as wrong as thinking the earth 
is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 
14(1), 35-44. Fall 1989.

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