[R] Capturing stderr from system()

From: McGehee, Robert <Robert.McGehee_at_geodecapital.com>
Date: Tue 08 Aug 2006 - 05:00:32 EST

I have a system command that occasionally fails and writes output to standard error, which R will print to the screen when ignore.stderr = FALSE. For example:
> system("BadCommand")

sh: line 1: BadCommand: command not found

I would like to know if the above command fails, and can presumably do this by parsing the stderr message that R prints to the screen. My (hopefully simple) problem is that I can't figure out how to capture this output.

I tried intern = TRUE, capture.output, and sink (with either/both type = "message" and type = "output"). I'm perplexed why sink doesn't get this output (since it's printed to the screen), so wanted to ask the R community how to grab the error message generated by trying to run "BadCommand".

To be clear, below is the sink() syntax I tried. Notice the output of the sink is character(0) rather than the line "sh: line 1: BadCommand: command not found".

> conn <- sink(z <- tempfile())
> sink(conn, type = "message")
> system("BadCommand")

sh: line 1: BadCommand: command not found
> sink(type = "message")
> sink()
> readLines(z)

Thanks in advance,

> R.version

platform       i686-pc-linux-gnu                        
arch           i686                                     
os             linux-gnu                                
system         i686, linux-gnu                          
status         Patched                                  
major          2                                        
minor          3.1                                      
year           2006                                     
month          07                                       
day            27                                       
svn rev        38721                                    
language       R                                        
version.string Version 2.3.1 Patched (2006-07-27 r38721)

Robert McGehee
Quantitative Analyst
Geode Capital Management, LLC
53 State Street, 5th Floor | Boston, MA | 02109 Tel: 617/392-8396 Fax:617/476-6389

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