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I want to write trycatch code to deal with error in downloading from the 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:
933
The tryCatch() function in R evaluates an expression with the possibility to catch exceptions. The class of the exception thrown by a standard stop() call is try-error. The tryCatch() function allows the users to handle errors. With it, you can do things like: if(error), then(do this).
Throws an exception by calling stop(). Note that throw() can be defined for specific classes, which can then be caught (or not) using tryCatch (). This default function will be overridden by ditto in the R.
The simplest way of handling conditions in R is to simply ignore them: Ignore errors with try() . Ignore warnings with suppressWarnings() .
In R Programming, there are basically two ways in which we can implement an error handling mechanism. Either we can directly call the functions like stop() or warning(), or we can use the error options such as “warn” or “warning. expression”.
Well then: welcome to the R world ;-)
Here you go
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)
}
> 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
> 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
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).
132
tryCatch has a slightly complex syntax structure. However, once we understand the 4 parts which constitute a complete tryCatch call as shown below, it becomes easy to remember:
expr: [Required] R code(s) to be evaluated
error : [Optional] What should run if an error occured while evaluating the codes in expr
warning : [Optional] What should run if a warning occured while evaluating the codes in expr
finally : [Optional] What should run just before quitting the tryCatch call, irrespective of if expr ran successfully, with an error, or with a warning
tryCatch(
expr = {
# Your code...
# goes here...
# ...
},
error = function(e){
# (Optional)
# Do this if an error is caught...
},
warning = function(w){
# (Optional)
# Do this if an warning is caught...
},
finally = {
# (Optional)
# Do this at the end before quitting the tryCatch structure...
}
)
Thus, a toy example, to calculate the log of a value might look like:
log_calculator <- function(x){
tryCatch(
expr = {
message(log(x))
message("Successfully executed the log(x) call.")
},
error = function(e){
message('Caught an error!')
print(e)
},
warning = function(w){
message('Caught an warning!')
print(w)
},
finally = {
message('All done, quitting.')
}
)
}
Now, running three cases:
A valid case
log_calculator(10)
# 2.30258509299405
# Successfully executed the log(x) call.
# All done, quitting.
A "warning" case
log_calculator(-10)
# Caught an warning!
# <simpleWarning in log(x): NaNs produced>
# All done, quitting.
An "error" case
log_calculator("log_me")
# Caught an error!
# <simpleError in log(x): non-numeric argument to mathematical function>
# All done, quitting.
I've written about some useful use-cases which I use regularly. Find more details here: https://rsangole.netlify.com/post/try-catch/
Hope this is helpful.
39
R uses functions for implementing try-catch block:
The syntax somewhat looks like this:
result = tryCatch({
expr
}, warning = function(warning_condition) {
warning-handler-code
}, error = function(error_condition) {
error-handler-code
}, finally={
cleanup-code
})
In tryCatch() there are two ‘conditions’ that can be handled: ‘warnings’ and ‘errors’. The important thing to understand when writing each block of code is the state of execution and the scope. @source
38
Here goes a straightforward example:
# Do something, or tell me why it failed
my_update_function <- function(x){
tryCatch(
# This is what I want to do...
{
y = x * 2
return(y)
},
# ... but if an error occurs, tell me what happened:
error=function(error_message) {
message("This is my custom message.")
message("And below is the error message from R:")
message(error_message)
return(NA)
}
)
}
If you also want to capture a "warning", just add warning= similar to the error= part.
42
Since I just lost two days of my life trying to solve for tryCatch for an irr function, I thought I should share my wisdom (and what is missing). FYI - irr is an actual function from FinCal in this case where got errors in a few cases on a large data set.
Set up tryCatch as part of a function. For example:
irr2 <- function (x) {
out <- tryCatch(irr(x), error = function(e) NULL)
return(out)
}
For the error (or warning) to work, you actually need to create a function. I originally for error part just wrote error = return(NULL) and ALL values came back null.
Remember to create a sub-output (like my "out") and to return(out).
33
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