R help - Jan 2013 - Using system() to dump HDF to text file?

Hi all --

I am working on 64-bit Windows XP.  I'm not a very technical person when it
comes to the command line stuff, so please forgive me if this is a stupid
question.

I have a bunch of HDF files, and I want to dump a single PM25 data layer
from each file to .txt by invoking ncdump.exe from system().  Here's a
sample command string:

"C:/ncdump -v PM25 C:/01aug2010.hdf > C:/01aug2010.txt"

This works perfectly in Python, but does not actually generate the .txt
file in R when:

system(command)

It does show the output on the console, if flagged to do so, and I can
capture the output to an R object with intern = T.  I assume there is some
problem with the way I have specified how to get the output to the text
file (i.e. the ">"), but experimentation with other options has not
gone
well.

Can anyone advise?

Thanks!

Sarah

	[[alternative HTML version deleted]]

Use shell() instead of system().  E.g., I have a bunch of Unix-like
executables in c:\cygwin\bin and I can use pipe and redirection
signs with them using shell():
> tf <- tempfile()
> file.exists(tf)
[1] FALSE
> shell(paste("c:\\cygwin\\bin\\ls | c:\\cygwin\\bin\\head -5
>", shQuote(tf, "cmd")))
> readLines(tf)
[1] "R.dll"       "R.exe"       "RSetReg.exe"
"Rblas.dll"   "Rcmd.exe"   
> getwd()
[1] "C:/Program Files/R/R-2.15.2/bin/x64"
> dir()
 [1] "open.exe"      "R.dll"         "R.exe"      
"Rblas.dll"     "Rcmd.exe"      "Rgraphapp.dll"
"Rgui.exe"      "Riconv.dll"    "Rlapack.dll"  
"Rscript.exe"   "RSetReg.exe"
[12] "Rterm.exe"     "Rzlib.dll"    

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org] On Behalf
> Of Sarah Henderson
> Sent: Tuesday, January 15, 2013 10:28 AM
> To: R List
> Subject: [R] Using system() to dump HDF to text file?
> 
> Hi all --
> 
> I am working on 64-bit Windows XP.  I'm not a very technical person
when it
> comes to the command line stuff, so please forgive me if this is a stupid
> question.
> 
> I have a bunch of HDF files, and I want to dump a single PM25 data layer
> from each file to .txt by invoking ncdump.exe from system().  Here's a
> sample command string:
> 
> "C:/ncdump -v PM25 C:/01aug2010.hdf > C:/01aug2010.txt"
> 
> This works perfectly in Python, but does not actually generate the .txt
> file in R when:
> 
> system(command)
> 
> It does show the output on the console, if flagged to do so, and I can
> capture the output to an R object with intern = T.  I assume there is some
> problem with the way I have specified how to get the output to the text
> file (i.e. the ">"), but experimentation with other options
has not gone
> well.
> 
> Can anyone advise?
> 
> Thanks!
> 
> Sarah
> 
> 	[[alternative HTML version deleted]]
> 
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