[R] Using system() to dump HDF to text file?

William Dunlap wdunlap at tibco.com
Tue Jan 15 20:21:52 CET 2013

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)
> 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]]
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

More information about the R-help mailing list