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).
tryCatch in R execute in case of error
Assign your tryCatch
directly to x
foo <- function() stop("hello")
bar <- function() 'world'
x <- tryCatch(
{
foo()
},
error = function(e){
bar()
}
)
x
# [1] "world"
R tryCatch() - referencing return of expr() in finally?
If the tryCatch
return value is being saved into a variable, such as
x <- tryCatch({ 1; }, finally = { message("value is ", x); })
# Error in message("value is ", x) : object 'x' not found
then the answer is no, since the x
object does not exist when tryCatch
executes finally=
.
However, the code block operates within the parent environment, so you can do this instead:
tryCatch({ x <- 1; }, finally = { message("value is ", x); })
# value is 1
x
# [1] 1
This relies on the return value being set without error. If there's an error somewhere in the execution, then ... obviously there will be no value to retrieve.
tryCatch in R Programming
You can return a string ('error'
) here if error occurs and check it's value to return 1/0.
Error<-function(x){
y <- tryCatch(x,error=function(e) return('error'))
as.integer(y != 'error')
}
Error(sqrt('a'))
#[1] 0
Error(sqrt(64))
#[1] 1
Store errors and warnings with tryCatch() in a list
Here's a version that puts the tryCatch
within the loop, and saves the errors and warnings that were generated:
hospitals_url <- "https://services1.arcgis.com/Hp6G80Pky0om7QvQ/arcgis/rest/services/Hospitals_1/FeatureServer/0/query?where=1%3D1&outFields=*&outSR=4326&f=json"
hospitals_num <- c(0, 2000, 4000, 6000)
hosp_e <- list()
hosp_w <- list()
hosget <- lapply(hospitals_num, function(num) {
tryCatch({
hospitals_url_loop <- paste(hospitals_url, "&resultOffset=", num)
hospitals_json <- fromJSON(hospitals_url_loop)
hospitals_df <- as.data.frame(hospitals_json$features$attributes)},
error = function(e){
hosp_e <<- c(hosp_e, list(e))
print(e)},
warning = function(w){
hosp_w <<- c(hosp_w, list(w))
print(w)}
) })
hospitals_df <- do.call(rbind, hosget)
I didn't adapt your finally
code to this rearrangement; I'll leave that to you. But at the end, hosp_e
will be a list holding all the errors, and hosp_w
will be a list holding all the warnings.
How to write trycatch for this scenario in R
Have you tried wrapping the complete code inside tryCatch
?
tryCatch({
getSymbols(ifelse(
substring(stocksList[i,1],1,1) == "^" | grepl(".BO", stocksList[i,1]),
stocksList[i,1] ,
paste0(stocksList[i,1] , ".NS")
),
from = fromDate,
to = toDate,
periodicity = freqStr ,
return.class = 'zoo',
env = NULL)
},
error = function(e) message('Cannot download the data')
)
How to correctly log warnings and errors using `tryCatch` in R?
Based on Ronak's helpful comment and the following question How do I save warnings and errors as output from a function?, the code can be simplified as follows:
# Storage.
warns = list()
errs = list()
# Example function.
fun <- function(i) {
# Issue warning.
warning(paste("Warn.", i))
# Stop.
if(i == 3) { stop(paste("Err.", i)) }
}
# Evaluate `fun`.
for (i in 1:4) {
tryCatch(withCallingHandlers(
expr = fun(i),
# Handle the warnings.
warning = function(w) {
warns <<- c(warns, list(w))
invokeRestart("muffleWarning")
}),
# Handle the errors.
error = function(e) {
errs <<- c(errs, list(e))
}
)
}
The output then looks like:
warns
# [[1]]
# <simpleWarning in fun(i): Warn. 1>
#
# [[2]]
# <simpleWarning in fun(i): Warn. 2>
#
# [[3]]
# <simpleWarning in fun(i): Warn. 3>
#
# [[4]]
# <simpleWarning in fun(i): Warn. 4>
errs
# [[1]]
# <simpleError in fun(i): Err. 3>
More information and links are provided in the question linked above.
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