R help - Aug 2012 - read.table() Issue

Yesterday I changed the headers for a couple of columns in data text files
and removed hyphens from within character strings, too. When I tried to
re-read these data sources using read.table() I encountered an issue I've
not before seen. Both files were read almost instantly until yesterday's
wording changes.

   Now both files seem to cause R to hang. Rather than having the prompt
immediately returned nothing happens. In emacs the 'working' symbol
appears
but the read.table() function does not complete.

   What might cause this?

Rich

On Wed, 1 Aug 2012, Rich Shepard wrote:
>  What might cause this?
   I restored these two files from last Friday and they are read into R with
no problems. So, I'll make one change at a time and see where things break.
Will post results when I have them.

Rich

On Wed, 1 Aug 2012, Rich Shepard wrote:
>  What might cause this?
   Must be computers acting like computers. Restored files from backup, made
changes one at a time, and there are no problems reading them into R data
frames. My apologies for taking up space here.

Rich

An unmatched quote can make read.table run very slowly
when there are lots of lines in the file.  E.g.,
> z <- rep("A B C", 10^6)
> z[2] <- "A \"B C" # unmatched quote on line 2
> tf <- tempfile()
> cat(file=tf, sep="\n", z)
> system.time(z2 <- read.table(tf, skip=2)) # skip bad line
   user  system elapsed
  0.860   0.028   0.887
> str(z2)
'data.frame':   999998 obs. of  3 variables:
 $ V1: Factor w/ 1 level "A": 1 1 1 1 1 1 1 1 1 1 ...
 $ V2: Factor w/ 1 level "B": 1 1 1 1 1 1 1 1 1 1 ...
 $ V3: Factor w/ 1 level "C": 1 1 1 1 1 1 1 1 1 1
...
> system.time(z1 <- read.table(tf, skip=1))
[ no return for several minutes on a 64-bit Linux machine ]

On smaller files it quickly gives the error "line 1 did not have 4
elements",
along with a warning "incomplete final line found by readTableHeader
...".

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 Rich Shepard
> Sent: Wednesday, August 01, 2012 10:52 AM
> To: r-help at r-project.org
> Subject: [R] read.table() Issue
> 
>    Yesterday I changed the headers for a couple of columns in data text
files
> and removed hyphens from within character strings, too. When I tried to
> re-read these data sources using read.table() I encountered an issue
I've
> not before seen. Both files were read almost instantly until
yesterday's
> wording changes.
> 
>    Now both files seem to cause R to hang. Rather than having the prompt
> immediately returned nothing happens. In emacs the 'working' symbol
appears
> but the read.table() function does not complete.
> 
>    What might cause this?
> 
> Rich
> 
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