I am using tryCatch to catch any errors that occur. However, even though I catch them and return the appropriate error value, it looks like the error is still reported in the logs of my batch system. Is there a way to completely suppress the error and simply proceed with the error handling I provide?
Make sure you're neither (1) returning an error, nor (2) printing to stderr in your error handling code. Note one gotcha here is message sends its output to stderr.
A minimal way to fulfills both conditions is tryCatch(expr, error = function(e) {})
Related
I am running a simulation study in R. Occassionally, my simulation study produces an error message. As I implemented my simulation study in a function, the simulation stops when this error message occurs. I know that it is bad practice to suppress errors, but at this moment to me there is no other option than to suppress the error and then go on with the next simulation until the total number of simulations I like to run. To do this, I have to suppress the error message R produces.
To do this, I tried different things:
library(base64)
suppressWarnings
suppressMessages
options(error = expression(NULL))
In the first two options, only warnings and message are suprressed, so that's no help. If I understand it correctly, in the last case, all error messages should be avoided. However, that does not help, the function still stops with an error message.
Has someone any idea why this does not work the way I expect it to work? I searched the internet for solutions, but could only find the above mentioned ways.
In the function I am running my simulation, a part of the code is analysed by the external program JAGS (Gibbs sampler) and the error message is produced by this analysis. Might this be where it goes wrong?
Note that I do not have to supress a certain/specific error message, as there are no other error messages produced, it is 'good enough' to have an option that supresses just all error messages.
Thanks for your time and help!
As suggested by the previous solution, you can use try or tryCatch functions, which will encapsulate the error (more info in Advanced R). However, they will not suppress the error reporting message to stderr by default.
This can be achieved by setting their parameters. For try, set silent=TRUE. For tryCatch set error=function(e){}.
Examples:
o <- try(1 + "a")
> Error in 1 + "a" : non-numeric argument to binary operator
o <- try(1 + "a", silent=TRUE) # no error printed
o <- tryCatch(1 + "a")
> Error in 1 + "a" : non-numeric argument to binary operator
o <- tryCatch(1 + "a", error=function(e){})
There is a big difference between suppressing a message and suppressing the response to an error. If a function cannot complete its task, it will of necessity return an error (although some functions have a command-line argument to take some other action in case of error). What you need, as Zoonekynd suggested, is to use try or trycatch to "encapsulate" the error so that your main program flow can continue even when the function fails.
Whereas options(warn=2) will prompt an error and hence enable debugging, I'm struggling with doing the same for messages.
For example, somewhere in my codebase, an unknown function seems to use jsonlite-package, which triggers the following message.
So my question is: Is there a convenient way to trace back the origins of messages?
Note: Using browser() doesn't seem to help, since messages are not shown in browser-mode.
You can use wrap your code in a call to withCallingHandlers to turn messages into errors:
withCallingHandlers(
message("example message"),
message = function(m) stop(m)
)
#Error in message("example message") : example message
I have a block of R code that is wrapped in a tryCatch statement. Any of the lines in that block can potentially throw a warning or an error. When caught, I have handlers for both warnings and errors, which perform logging in both cases, and exit handling in the error case.
But in the warning case, I just want the warning to be logged, and the execution to continue as normal. At the moment, when warning is caught, it is logged, but the execution is also stopped. Is there an easy way to allow for this functionality?
Not sure if it's the most idiomatic solution, but using a combination of tryCatch and withCallingHandlers works for me in an almost identical situation.
I wrap the call to my function with withCallingHandlers, providing a function to handle warnings; execution of the function will continue afterwards. I wrap all of that in tryCatch, providing a function to handle errors.
tryCatch(
withCallingHandlers(doSomething(), warning = function(w) logWarning(w)),
error = function(e) logError(e)
)
Thanks to nicola in the comments for the withCallingHandlers tip.
I was wondering how one is able to produce error messages in R, especially from within a function?
Since you don't specify what you really want, all I just can say is take a look at
?message # prints a message but not stop execution
?warning # prints a warning message but not stop execution
?stop # stops execution of the current expression and executes an error action.
Simply include stop() inside your function/script
If you'd like an error message, include it inside stop() like so
stop("This is an error message")
I'm facing a strange issue in R.
Consider the following code (a really simplified version of the real code but still having the problem) :
library(timeSeries)
tryCatch(
{
specificWeekDay <- 2
currTs <- timeSeries(c(1,2),c('2012-01-01','2012-01-02'),
format='%Y-%m-%d',units='A')
# just 2 dates out of range
start <- time(currTs)[2]+100*24*3600
end <- time(currTs)[2]+110*24*3600
# this line returns an empty timeSeries
currTs <- window(currTs,start=start,end=end)
message("Up to now, everything is OK")
# this is the line with the uncatchable error
currTs[!(as.POSIXlt(time(currTs))$wday %in% specificWeekDay),] <- NA
message("I'm after the bugged line !")
},error=function(e){message(e)})
message("End")
When I run that code in RGui, I correctly get the following output:
Up to now, everything is OK
error in evaluating the argument 'i' in
selecting a method for function '[<-': Error in
as.POSIXlt.numeric(time(currTs)) : 'origin' must be supplied
End
Instead, when I run it through RScript (in windows) using the following line:
RScript.exe --vanilla "myscript.R"
I get this output:
Up to now, everything is OK
Execution interrupted
It seems like RScript crashes...
Any idea about the reason?
Is this a timeSeries package bug, or I'm doing something wrong ?
If the latter, what's the right way to be sure to catch all the errors ?
Thanks in advance.
EDIT :
Here's a smaller example reproducing the issue that doesn't use timeSeries package. To test it, just run it as described above:
library(methods)
# define a generic function
setGeneric("foo",
function(x, ...){standardGeneric("foo")})
# set a method for the generic function
setMethod("foo", signature("character"),
function(x) {x})
tryCatch(
{
foo("abc")
foo(notExisting)
},error=function(e)print(e))
It seems something related to generic method dispatching; when an argument of a method causes an error, the dispatcher cannot find the signature of the method and conseguently raises an exception that tryCatch function seems unable to handle when run through RScript.
Strangely, it doesn't happen for example with print(notExisting); in that case the exception is correctly handled.
Any idea about the reason and how to catch this kind of errors ?
Note:
I'm using R-2.14.2 on Windows 7
The issue is in the way the internal C code implementing S4 method dispatch tries to catch and handle some errors and how the non-interactive case is treated in this approach. A work-around should be in place in R-devel and R-patched soon.
Work-around now committed to R-devel and R-patched.
Information about tryCatch() [that the OP already knew and used but I didn't notice]
I think you are missing that your tryCatch() is not doing anything special with the error, hence you are raising an error in the normal fashion. In interactive use the error is thrown and handled in the usual fashion, but an error inside a script run in a non-interactive session (a la Rscript) will abort the running script.
tryCatch() is a complex function that allows the potential to trap and handle all sorts of events in R, not just errors. However by default it is set up to mimic the standard R error handling procedure; basically allow the error to be thrown and reported by R. If you want R to do anything other than the basic behaviour then you need to add a specific handler for the error:
> e <- simpleError("test error")
> tryCatch(foo, error = function(e) e,
+ finally = writeLines("There was a problem!"))
There was a problem!
<simpleError in doTryCatch(return(expr), name, parentenv, handler): object 'foo'
not found>
I suggest you read ?tryCatch in more detail to understand better what it does.
An alternative is to use try(). To modify your script I would just do:
# this is the line with the uncatchable error
tried <- try(currTs[!(as.POSIXlt(time(currTs))$wday %in% specificWeekDay),] <- NA,
silent = TRUE)
if(inherits(tried, "try-error")) {
writeLines("There was an error!")
} else {
writeLines("Everything worked fine!")
}
The key bit is to save the object returned from try() so you can test the class, and to have try() operate silently. Consider the difference:
> bar <- try(foo)
Error in try(foo) : object 'foo' not found
> bar <- try(foo, silent = TRUE)
> class(bar)
[1] "try-error"
Note that in the first call above, the error is caught and reported as a message. In the second, it is not reported. In both cases an object of class "try-error" is returned.
Internally, try() is written as a single call to tryCatch() which sets up a custom function for the error handler which reports the error as a message and sets up the returned object. You might wish to study the R code for try() as another example of using tryCatch().