x = 1
simple <- function(p,q){
return(q)
}
test = simple(x,y)
Error in simple(x, y) : object 'y' not found
Please Note : Even if I don't create a variable "y", I should not get this error. Instead I want a message to be thrown saying "No data".
You can use try() (or the more elaborate tryCatch() to do this. For example,
x = 1
simple <- function(p,q){
q <- try(force(q), silent = TRUE)
if (inherits(q, "try-error")) {
warning("No data")
q <- NULL
}
return(q)
}
test = simple(x,y)
#> Warning in simple(x, y): No data
Created on 2021-01-28 by the reprex package (v0.3.0)
What the force() function does is evaluate the argument. If that fails, it returns an error: but try() catches that. (You don't actually need to call force(q), it would be enough to use try(q), but I think the explicit version is clearer.)
Related
I have a list of file to read. I wrote a loop, like this (it is only a example). However, some of these elements are missing and I got a message error interrupting the loop.I would like to skip the error and finish the loop, with the other elements of the list.
list<- c("ciao",
"miao",
"bau")
for (symbols in list){
a <- symbols
b <- as.Date(symbols)
c <- as.numeric(symbols)
d<- cbind(a,b,c)
write.csv(d)
}
As, far as I know, I could use the function try. I have already read some examples here, but they don't fit my need... or I don't know how to implement it.
Any idea to solve the problem?
Thank you
You can use tryCatch() for this and use the error = part to indicate what you want in the case of an error.
For example, in the below we can continue checking if the symbol == "bau" even after "miao" caused an error:
# error before it checks all args of list
list <- c("ciao", "miao", "bau")
for (symbols in list) {
if (symbols == "miao") stop("Er!")
print(symbols == "bau")
}
#> [1] FALSE
#> Error in eval(expr, envir, enclos): Er!
# now it will check all args even with error
for (symbols in list) {
tryCatch(
expr = {
if (symbols == "miao") stop("Er!")
print(symbols == "bau")
},
error = function(e) NA
)
}
#> [1] FALSE
#> [1] TRUE
Created on 2022-08-03 by the reprex package (v2.0.1)
I have a function that may throw an error. When an error is thrown, I'd like to show the error message, as if the error actually occurred, and further return an object invisibly.
I looked at this thread, which uses withCallingHandlers and logs the error message somewhere. This comes close, but I do not want to log the message as text and then print a text message, the function should show the error message as if it would have exited on error.
The functions workflow looks like the following:
foo <- function(x){
y <- x + 1
if(y == 2) {
stop("oops")
# also return y invisibly when error is thrown,
}
z <- y + 1
z
}
Based on input x an intermediate y is calculated. y is used for the error check. If an error occurs y should be returned invisibly and an normal error message should be thrown. Otherwise z is calculated an returned.
foo(1) should return error message and y invisibly.
I thought about using on.exit but in this case, always y is return invisibly.
Any help is appreciated.
Add: Maybe what I have in mind is not possible. In this case, would it be possible to show a logged error message in a way that comes close to a real error message?
Add2: I thought about issuing a warning, but in my actual use case a warning would be misleading, since the function does not produce desired result z, but just some intermediate result y and I want to return y so that the user can inspect it further, and reason about why it wasn't processed correctly by foo. Thinking about it, other must have encountered the same problem, there should be some kind of solution.
Add3: Maybe it is possible to use on.exit together with a flag which is triggered, so that on.exit will return y invisibly in case of an error and do nothing otherwise.
func <- function(x) { a <- simpleError("quux"); attr(a,"abc") <- 7; stop(a); }
func()
# Error: quux
So far so good, we see an error. If we catch this and look at the contents of the error message we can see the attribute tucked inside:
dput(tryCatch(func(), error=function(e) e))
# structure(list(message = "quux", call = NULL), class = c("simpleError",
# "error", "condition"), abc = 7)
and even extract it easily
dput(tryCatch(func(), error=function(e) attr(e,"abc")))
# 7
Below I post my final solution to my question. Basically it is based on r2evans answer combined with user20650's comment.
As r2evans showed we can use simpleError to create an error and also attach an object in the attributes. The big plus of this approach is that it returns a real error that we can program with. If we would only show the error message and then return a vector invisibly, tryCatch wouldn't recognize it as an error. The downside is that simpleError doesn't look like a normal error to an interactive user when printed in the console. It will show something like <simpleError: x must not be 1>. However, the message is not printed in red like normal errors.
Here user20650's comment shows a nice way out. We can first print the message with message(conditionMessage(e)) and then we can return the simpleError invisibly.
foo <- function(x) {
y <- x + 1
if(y == 2) {
foo_internal <- function(val) {
a <- simpleError("x must not be 1")
attr(a,".data") <- y
stop(a)
}
return(
tryCatch(foo_internal(y),
error = function(e) {
message(conditionMessage(e))
invisible(e)
})
)
}
z <- y + 1
z
}
# this is a special function to inspect the object attached to `simpleError`
inspect <- function(x = NULL) {
if(is.null(x)) {
x <- .Last.value
}
attr(x,".data")
}
# returns error message
foo(1)
#> x must not be 1
# we can get y's value with a special inspect function
inspect()
#> [1] 2
# foo(1) returns a "real" error
class(foo(1))
#> x must not be 1
#> [1] "simpleError" "error" "condition"
Created on 2021-03-13 by the reprex package (v0.3.0)
I have a regression model (lm or glm or lmer ...) and I do fitmodel <- lm(inputs) where inputs changes inside a loop (the formula and the data). Then, if the model function does not produce any warning I want to keep fitmodel, but if I get a warning I want to update the model and I want the warning not printed, so I do fitmodel <- lm(inputs) inside tryCatch. So, if it produces a warning, inside warning = function(w){f(fitmodel)}, f(fitmodel) would be something like
fitmodel <- update(fitmodel, something suitable to do on the model)
In fact, this assignation would be inside an if-else structure in such a way that depending on the warning if(w$message satisfies something) I would adapt the suitable to do on the model inside update.
The problem is that I get Error in ... object 'fitmodel' not found. If I use withCallingHandlers with invokeRestarts, it just finishes the computation of the model with the warning without update it. If I add again fitmodel <- lm(inputs) inside something suitable to do on the model, I get the warning printed; now I think I could try suppresswarnings(fitmodel <- lm(inputs)), but yet I think it is not an elegant solution, since I have to add 2 times the line fitmodel <- lm(inputs), making 2 times all the computation (inside expr and inside warning).
Summarising, what I would like but fails is:
tryCatch(expr = {fitmodel <- lm(inputs)},
warning = function(w) {if (w$message satisfies something) {
fitmodel <- update(fitmodel, something suitable to do on the model)
} else if (w$message satisfies something2){
fitmodel <- update(fitmodel, something2 suitable to do on the model)
}
}
)
What can I do?
The loop part of the question is because I thought it like follows (maybe is another question, but for the moment I leave it here): it can happen that after the update I get another warning, so I would do something like while(get a warning on update){update}; in some way, this update inside warning should be understood also as expr. Is something like this possible?
Thank you very much!
Generic version of the question with minimal example:
Let's say I have a tryCatch(expr = {result <- operations}, warning = function(w){f(...)} and if I get a warning in expr (produced in fact in operations) I want to do something with result, so I would do warning = function(w){f(result)}, but then I get Error in ... object 'result' not found.
A minimal example:
y <- "a"
tryCatch(expr = {x <- as.numeric(y)},
warning = function(w) {print(x)})
Error in ... object 'x' not found
I tried using withCallingHandlers instead of tryCatch without success, and also using invokeRestart but it does the expression part, not what I want to do when I get a warning.
Could you help me?
Thank you!
The problem, fundamentally, is that the handler is called before the assignment happens. And even if that weren’t the case, the handler runs in a different scope than the tryCatch expression, so the handler can’t access the names in the other scope.
We need to separate the handling from the value transformation.
For errors (but not warnings), base R provides the function try, which wraps tryCatch to achieve this effect. However, using try is discouraged, because its return type is unsound.1 As mentioned in the answer by ekoam, ‘purrr’ provides soundly typed functional wrappers (e.g. safely) to achieve a similar effect.
However, we can also build our own, which might be a better fit in this situation:
with_warning = function (expr) {
self = environment()
warning = NULL
result = withCallingHandlers(expr, warning = function (w) {
self$warning = w
tryInvokeRestart('muffleWarning')
})
list(result = result, warning = warning)
}
This gives us a wrapper that distinguishes between the result value and a warning. We can now use it to implement your requirement:
fitmodel = with(with_warning(lm(inputs)), {
if (! is.null(warning)) {
if (conditionMessage(warning) satisfies something) {
update(result, something suitable to do on the model)
} else {
update(result, something2 suitable to do on the model)
}
} else {
result
}
})
1 What this means is that try’s return type doesn’t distinguish between an error and a non-error value of type try-error. This is a real situation that can occur, for example, when nesting multiple try calls.
It seems that you are looking for a functional wrapper that captures both the returned value and side effects of a function call. I think purrr::quietly is a perfect candidate for this kind of task. Consider something like this
quietly <- purrr::quietly
foo <- function(x) {
if (x < 3)
warning(x, " is less than 3")
if (x < 4)
warning(x, " is less than 4")
x
}
update_foo <- function(x, y) {
x <- x + y
foo(x)
}
keep_doing <- function(inputs) {
out <- quietly(foo)(inputs)
repeat {
if (length(out$warnings) < 1L)
return(out$result)
cat(paste0(out$warnings, collapse = ", "), "\n")
# This is for you to see the process. You can delete this line.
if (grepl("less than 3", out$warnings[[1L]])) {
out <- quietly(update_foo)(out$result, 1.5)
} else if (grepl("less than 4", out$warnings[[1L]])) {
out <- quietly(update_foo)(out$result, 1)
}
}
}
Output
> keep_doing(1)
1 is less than 3, 1 is less than 4
2.5 is less than 3, 2.5 is less than 4
[1] 4
> keep_doing(3)
3 is less than 4
[1] 4
Are you looking for something like the following? If it is run with y <- "123", the "OK" message will be printed.
y <- "a"
#y <- "123"
x <- tryCatch(as.numeric(y),
warning = function(w) w
)
if(inherits(x, "warning")){
message(x$message)
} else{
message(paste("OK:", x))
}
It's easier to test several argument values with the code above rewritten as a function.
testWarning <- function(x){
out <- tryCatch(as.numeric(x),
warning = function(w) w
)
if(inherits(out, "warning")){
message(out$message)
} else{
message(paste("OK:", out))
}
invisible(out)
}
testWarning("a")
#NAs introduced by coercion
testWarning("123")
#OK: 123
Maybe you could assign x again in the handling condition?
tryCatch(
warning = function(cnd) {
x <- suppressWarnings(as.numeric(y))
print(x)},
expr = {x <- as.numeric(y)}
)
#> [1] NA
Perhaps not the most elegant answer, but solves your toy example.
Don't put the assignment in the tryCatch call, put it outside. For example,
y <- "a"
x <- tryCatch(expr = {as.numeric(y)},
warning = function(w) {y})
This assigns y to x, but you could put anything in the warning body, and the result will be assigned to x.
Your "what I would like" example is more complicated, because you want access to the expr value, but it hasn't been assigned anywhere at the time the warning is generated. I think you'll have to recalculate it:
fitmodel <- tryCatch(expr = {lm(inputs)},
warning = function(w) {if (w$message satisfies something) {
update(lm(inputs), something suitable to do on the model)
} else if (w$message satisfies something2){
update(lm(inputs), something2 suitable to do on the model)
}
}
)
Edited to add:
To allow the evaluation to proceed to completion before processing the warning, you can't use tryCatch. The evaluate package has a function (also called evaluate) that can do this. For example,
y <- "a"
res <- evaluate::evaluate(quote(x <- as.numeric(y)))
for (i in seq_along(res)) {
if (inherits(res[[i]], "warning") &&
conditionMessage(res[[i]]) == gettext("NAs introduced by coercion",
domain = "R"))
x <- y
}
Some notes: the res list will contain lots of different things, including messages, warnings, errors, etc. My code only looks at the warnings. I used conditionMessage to extract the warning message, but
it will be translated to the local language, so you should use gettext to translate the English version of the message for comparison.
I was looking at the source code for the r function expand.grid and noticed a command I don't understand (the last line):
function (..., KEEP.OUT.ATTRS = TRUE, stringsAsFactors = TRUE)
{
nargs <- length(args <- list(...))
if (!nargs)
I am not familiar with this syntax for an if-statement. What is if(!nargs) testing? I tried testing it with something that did exist, and it worked. But it doesn't work with something that doesn't exist...
x <- list(1, 4, 6)
nargs <- length(x)
if(nargs)
print("Success") #This does print "Success" and nargs exists
if(!nargs)
print("Fail") #Doesn't print, as you'd expect
if(!dogs)
print("Success") #Error: object 'dogs' not found
So my guess (that it was an existence test) is wrong, or I am testing it wrong.
!nargs means you are testing the value of nargs is FALSE (or 0 in your case). nargs must exist before testing its value. In your example it does exist.
!dogs is trying to test a non-existing object, so you cannot test its value, object dogs not found is the correct error message there.
I am using stopifnot and I understand it just returns the first value that was not TRUE. I f that is some freaky dynamic expression someone who is not into the custom function cannot really make something out of that. So I would love to add a custom error message. Any suggestions?
Error: length(unique(nchar(check))) == 1 is not TRUE
Basically states that the elements of the vector check do not have the same length.
Is there a way of saying: Error: Elements of your input vector do not have the same length!?
Use stop and an if statement:
if(length(unique(nchar(check))) != 1)
stop("Error: Elements of your input vector do not have the same length!")
Just remember that stopifnot has the convenience of stating the negative, so your condition in the if needs to be the negation of your stop condition.
This is what the error message looks like:
> check = c("x", "xx", "xxx")
> if(length(unique(nchar(check))) != 1)
+ stop("Error: Elements of your input vector do not have the same length!")
Error in eval(expr, envir, enclos) :
Error: Elements of your input vector do not have the same length!
A custom message can be added as a label to your expression:
stopifnot("Elements of your input vector do not have the same length!" =
length(unique(nchar(check))) == 1)
# Error: Elements of your input vector do not have the same length!
The assertive and assertthat packages have more readable check functions.
library(assertthat)
assert_that(length(unique(nchar(check))) == 1)
## Error: length(unique(nchar(check))) == 1 are not all true.
library(assertive)
assert_is_scalar(unique(nchar(check)))
## Error: unique(nchar(check)) does not have length one.
if(!is_scalar(unique(nchar(check))))
{
stop("Elements of check have different numbers of characters.")
}
## Error: Elements of check have different numbers of characters.
Or you could package it up.
assert <- function (expr, error) {
if (! expr) stop(error, call. = FALSE)
}
So you have:
> check = c("x", "xx", "xxx")
> assert(length(unique(nchar(check))) == 1, "Elements of your input vector do not have the same length!")
Error: Elements of your input vector do not have the same length!
What about embedding the stopifnot into tryCatch and then recasting the exception with stop using customized message?
Something like:
tryCatch(stopifnot(...,error=stop("Your customized error message"))
Unlike some other solutions this does not require additional packages. Compared to using if statement combined with stop you retain the performance advantages of stopifnot, when you use new R versions. Since R version 3.5.0 stopifnot evaluates expressions sequentially and stops on first failure.
I would recommend you check out Hadley's testthat package. It allows for intuitive testing: the names of the functions are great and the way you write them is like a sentence -- "I expect that length(unique(nchar(check))) is [exactly|approximately] 1". The errors produced are informative.
See here:
http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf
In your case,
> library(testthat)
> check = c("x", "xx", "xxx")
> expect_that(length(unique(nchar(check))), equals(1))
Error: length(unique(nchar(check))) not equal to 1
Mean relative difference: 2
Also note that you don't have the problem that #Andrie referenced with sometimes having to think about double negatives with stopifnot. I know it seems simple, but it caused me many headaches!
The answers already provided are quite good, and mine is just an addition to that collection. For some people it could be more convenient to use one-liner in form of the following function:
stopifnotinform <- function(..., message = "err") {
args <- list(...)
if (length(args) == 0) {
return(NULL)
}
for (i in 1:length(args)) {
result <- args[[i]]
if (is.atomic(result) && result == FALSE) {
stop(message)
}
}
}
# throws an error
stopifnotinform(is.integer(1L), is.integer(2), message = "Some number(s) provided is not an integer")
# continues with execution
stopifnotinform(is.integer(1L), is.integer(2L), message = "Some number(s) provided is not an integer")
Bear in mind that this solution provides you with only one (common) error message for all parameters in ....
Try this:
same_length <- FALSE
stopifnot("Elements of your input vector do not have the same length!" = same_length)
#> Error : Elements of your input vector do not have the same length!