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Rolf Turner

2008-May-14 01:12 UTC

[R] The try() function with read.delim().

I have written a function which reads data from files using read.delim 
().
The names of these files are complicated and are built using arguments
to the wrapper function.  Since the files in question may or may not
exist, I thought to enclose the read.delim() call in a try():

	file <- <complicated expression>
	temp <- try(read.delim(file))
	if(inherits(temp,"try-error")) {
		(Do something)
	} else {
		(Do something else)
	}

But this doesn't work.  If file doesn't exist, then I get an error,
and the wrapper function terminates, despite the presence of the try().
The object ``temp'' never gets created.

I can of course easily get around the problem by testing with

	file.exists(file)

I just wondered --- why isn't try() working as expected here?  Am I  
being
silly to expect it to work?  If so, what am I not understanding about  
try()?

Thanks for any insights.

	cheers,

		Rolf

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Steven McKinney

2008-May-14 02:23 UTC

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[R] The try() function with read.delim().

> -----Original Message-----
> From: r-help-bounces at r-project.org on behalf of Rolf Turner
> Sent: Tue 5/13/2008 6:12 PM
> To: R help forum
> Subject: [R] The try() function with read.delim().
>  
> 
> I have written a function which reads data from files using read.delim 
> ().
> The names of these files are complicated and are built using arguments
> to the wrapper function.  Since the files in question may or may not
> exist, I thought to enclose the read.delim() call in a try():
> 
> 	file <- <complicated expression>
> 	temp <- try(read.delim(file))
> 	if(inherits(temp,"try-error")) {
> 		(Do something)
> 	} else {
> 		(Do something else)
> 	}
> 
> But this doesn't work.  If file doesn't exist, then I get an error,
> and the wrapper function terminates, despite the presence of the try().
> The object ``temp'' never gets created.
> 
> I can of course easily get around the problem by testing with
> 
> 	file.exists(file)
> 
> I just wondered --- why isn't try() working as expected here?  Am I  
> being
> silly to expect it to work?  If so, what am I not understanding about  
> try()?
It is working for me using R-2.7.0 on a Mac running OS X 10.4
and it also runs pretty much as shown below on my Windoze machine
(R-2.7.0 on Windows XP)

So you may be encountering a bug - not sure what your
sessionInfo() etc. is.

Here's my output of your example
> file <- "foo.bar"
> file.exists(file)
[1] FALSE> temp <- try(read.delim(file))Warning in file(file, "r") :
  cannot open file 'foo.bar': No such file or directory
Error in file(file, "r") : cannot open the
connection> temp[1] "Error in file(file, \"r\") : cannot open the
connection\n"
attr(,"class")
[1] "try-error"> rm("temp")
> temp
Error: object "temp" not found> temp <- try(read.delim(file))Warning in file(file, "r") :
  cannot open file 'foo.bar': No such file or directory
Error in file(file, "r") : cannot open the
connection> temp[1] "Error in file(file, \"r\") : cannot open the
connection\n"
attr(,"class")
[1] "try-error"> class(temp)
[1] "try-error"> sessionInfo()R version 2.7.0 (2008-04-22) 
powerpc-apple-darwin8.10.1 

locale:
en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] tcltk     splines   stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] relimp_0.9-8      abind_1.1-0       rpart_3.1-41      Rcmdr_1.3-14     
[5] car_1.2-8         lme4_0.999375-14  Matrix_0.999375-9 lattice_0.17-6   
[9] survival_2.34-1  

loaded via a namespace (and not attached):
[1] grid_2.7.0  tools_2.7.0> 
Best

Steve McKinney
> 
> Thanks for any insights.
> 
> 	cheers,
> 
> 		Rolf
> 
> ######################################################################
> Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
> 
> ______________________________________________
> 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.
> 
>

Martin Maechler

2008-May-14 08:27 UTC

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[R] The try() function with read.delim().

>>>>> "RT" == Rolf Turner <r.turner at
auckland.ac.nz>
>>>>>     on Wed, 14 May 2008 13:12:02 +1200 writes:
    RT> I have written a function which reads data from files using
read.delim
    RT> ().
    RT> The names of these files are complicated and are built using
arguments
    RT> to the wrapper function.  Since the files in question may or may not
    RT> exist, I thought to enclose the read.delim() call in a try():

    RT> file <- <complicated expression>
    RT> temp <- try(read.delim(file))
    RT> if(inherits(temp,"try-error")) {
    RT>   (Do something)
    RT> } else {
    RT>    (Do something else)
    RT> }

    RT> But this doesn't work.  If file doesn't exist, then I get an
error,

You get an error *message* but not an error, I'd think.

If you don't like the error *message* in this case, use

 try(..., silent=TRUE)

In R,  try() is now using tryCatch(), (type 'try' to see) 
and I would nowadays recommend using tryCatch() inside any function.
Another "advantage" of tryCatch(.) for you is that you can
decide yourself what to do with the error message.

The most simple thing would be something like

	  if(is.null(tryCatch(temp <- read.delim(file),
			      error = function(e) NULL))) {
             ## error reading ...			      	      
	  } else {
	     ## work with the 'temp' data frame
          }

Slightly more sophisticated

 	  temp <- tryCatch(read.delim(file), error = function(e) e)
	  if(inherits(e, "error") {
	     message("Caught error:", e at message, "\n")
             ## error reading ...			      	      
	  } else {
	     ## work with the 'temp' data frame
          }


*However*, there's a small infelicity in the above:

You get an additional warning from file(..)  which you need to
suppress by another  suppressWarnings( ..... ) 
around the call.

Martin

    RT> and the wrapper function terminates, despite the presence of the
try().
    RT> The object ``temp'' never gets created.

    RT> I can of course easily get around the problem by testing with

    RT> file.exists(file)

    RT> I just wondered --- why isn't try() working as expected here?  Am
I
    RT> being
    RT> silly to expect it to work?  If so, what am I not understanding about
    RT> try()?

    RT> Thanks for any insights.

    RT> cheers,

    RT> Rolf

    RT>
######################################################################
    RT> Attention:\ This e-mail message is privileged and
confid...{{dropped:9}}

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

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