Exception Handling in R

Exception handling in R

Besides Shane's answer pointing you to other StackOverflow discussions, you could try a code search feature. This original answer pointed to Google's Code Search has since been discontinued, but you can try

  • Github search as e.g. in this query for tryCatch in language=R;
  • Ohloh/Blackduck Code search eg this query for tryCatch in R files
  • the Debian code search engine on top of the whole Debian archive

Just for the record, there is also try but tryCatch may be preferable. I tried a quick count at Google Code Search but try gets too many false positives for the verb itself -- yet it seems tryCatch is more widely used.

How to write trycatch in R

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 inside 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).

R Function Doesn't Throw Error As Expected

Two methods:

  1. Preferred: Check for missingness:

    MergePalette <- function(name,name2){
    if (missing(name2)) { stop(...) }
  2. Define a default value of NULL in the formals, and the function works:

    MergePalette <- function(name,name2=NULL){
    if (is.null(name2)) { stop(...) }

    If the user (accidentally) provides an argument to name2 that is itself NULL, the error message will be confusing. As @Moody_Mudskipper noted, by setting the default to NULL, you are implicitly telling the user that this argument is optional and/or that NULL is okay. With that, I suggest that this option is not appropriate for this question/use.

R tryCatch handling one kind of error

You could use try to handle errors:

result <- try(log("a"))

if(class(result) == "try-error"){
error_type <- attr(result,"condition")

print(class(error_type))
print(error_type$message)

if(error_type$message == "non-numeric argument to mathematical function"){
print("Do stuff")
}else{
print("Do other stuff")
}
}

# [1] "simpleError" "error" "condition"
# [1] "non-numeric argument to mathematical function"
# [1] "Do stuff"

R : catching errors in `nls`

I usually use this trick:

params<-... # setup default params.

while(TRUE){

fit<-NULL
try(fit<-nls(...)); # does not stop in the case of error

if(!is.null(fit))break; # if nls works, then quit from the loop

params<-... # change the params for nls

}

Assigning a value in exception handling in R

The problem is the b0 scope of the assignment. However, I find try a little more friendly than tryCatch. This should work:

while(bo!=10){
x = try(getURLContent(Site, verbose = F, curl = handle),silent=TRUE)
if (class(x)=="try-error") {
cat("ERROR1: ", x, "\n")
Sys.sleep(1)
print("reconnecting...")
bo <- bo+1
print(bo)
} else {
break
}
}

The above attempts 10 times to connect to the site. If any of this time succeeds, it exits.



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