Dd Pp Dd Pp - 2 months ago 9
R Question

How to write trycatch in R

I want to write

trycatch
code to deal with error in downloading from web.

url <- c(
"http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html",
"http://en.wikipedia.org/wiki/Xz")
y <- mapply(readLines, con=url)


These two statements run successfully. Below, I create a non-exist web address:

url <- c("xxxxx", "http://en.wikipedia.org/wiki/Xz")


url[1]
does not exist. How does one write a
trycatch
loop (function) so that:


  1. When the url is wrong, the output will be: "web url is wrong, can't get".

  2. When the url is wrong, the code does not stop, but continues to download until the end of list of urls?


Answer

Well then: welcome to the R world ;-)

Here you go

Setting up the code

urls <- c(
    "http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html",
    "http://en.wikipedia.org/wiki/Xz",
    "xxxxx"
)
readUrl <- function(url) {
    out <- tryCatch(
        {
            # Just to highlight: if you want to use more than one 
            # R expression in the "try" part then you'll have to 
            # use curly brackets.
            # 'tryCatch()' will return the last evaluated expression 
            # in case the "try" part was completed successfully

            message("This is the 'try' part")

            readLines(con=url, warn=FALSE) 
            # The return value of `readLines()` is the actual value 
            # that will be returned in case there is no condition 
            # (e.g. warning or error). 
            # You don't need to state the return value via `return()` as code 
            # in the "try" part is not wrapped insided a function (unlike that
            # for the condition handlers for warnings and error below)
        },
        error=function(cond) {
            message(paste("URL does not seem to exist:", url))
            message("Here's the original error message:")
            message(cond)
            # Choose a return value in case of error
            return(NA)
        },
        warning=function(cond) {
            message(paste("URL caused a warning:", url))
            message("Here's the original warning message:")
            message(cond)
            # Choose a return value in case of warning
            return(NULL)
        },
        finally={
        # NOTE:
        # Here goes everything that should be executed at the end,
        # regardless of success or error.
        # If you want more than one expression to be executed, then you 
        # need to wrap them in curly brackets ({...}); otherwise you could
        # just have written 'finally=<expression>' 
            message(paste("Processed URL:", url))
            message("Some other message at the end")
        }
    )    
    return(out)
}

Applying the code

> y <- lapply(urls, readUrl)
Processed URL: http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html
Some other message at the end
Processed URL: http://en.wikipedia.org/wiki/Xz
Some other message at the end
URL does not seem to exist: xxxxx
Here's the original error message:
cannot open the connection
Processed URL: xxxxx
Some other message at the end
Warning message:
In file(con, "r") : cannot open file 'xxxxx': No such file or directory

Investigating the output

> head(y[[1]])
[1] "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">"      
[2] "<html><head><title>R: Functions to Manipulate Connections</title>"      
[3] "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\">"
[4] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"             
[5] "</head><body>"                                                          
[6] ""    

> length(y)
[1] 3

> y[[3]]
[1] NA

Additional remarks

tryCatch

tryCatch returns the value associated to executing expr unless there's an error or a warning. In this case, specific return values (see return(NA) above) can be specified by supplying a respective handler function (see arguments error and warning in ?tryCatch). These can be functions that already exist, but you can also define them within tryCatch() (as I did above).

The implications of choosing specific return values of the handler functions

As we've specified that NA should be returned in case of error, the third element in y is NA. If we'd have chosen NULL to be the return value, the length of y would just have been 2 instead of 3 as lapply() will simply "ignore" return values that are NULL. Also note that if you don't specify an explicit return value via return(), the handler functions will return NULL (i.e. in case of an error or a warning condition).

"Undesired" warning message

As warn=FALSE doesn't seem to have any effect, an alternative way to suppress the warning (which in this case isn't really of interest) is to use

suppressWarnings(readLines(con=url))

instead of

readLines(con=url, warn=FALSE)

Multiple expressions

Note that you can also place multiple expressions in the "actual expressions part" (argument expr of tryCatch()) if you wrap them in curly brackets (just like I illustrated in the finally part).

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