Is there any way to stop an R program without error?
For example I have a big source, defining several functions and after it there are some calls to the functions. It happens that I edit some function, and want the function definitions to be updated in R environment, but they are not actually called.
I defined a variable justUpdate and when it is TRUE want to stop the program just after function definitions.
ReadInput <- function(...) ...
Analyze <- function(...) ...
WriteOutput <- function(...) ...
if (justUpdate)
stop()
# main body
x <- ReadInput()
y <- Analyze(x)
WriteOutput(y)
I have called stop() function, but the problem is that it prints an error message.
ctrl+c is another option, but I want to stop the source in specific line.
The problem with q() or quit() is that it terminates R session, but I would like to have the R session still open.
As #JoshuaUlrich proposed browser() can be another option, but still not perfect, because the source terminates in a new environment (i.e. the R prompt will change to Browser[1]> rather than >). Still we can press Q to quit it, but I am looking for the straightforward way.
Another option is to use if (! justUpdate) { main body } but it's clearing the problem, not solving it.
Is there any better option?
I found a rather neat solution here. The trick is to turn off all error messages just before calling stop(). The function on.exit() is used to make sure that error messages are turned on again afterwards. The function looks like this:
stop_quietly <- function() {
opt <- options(show.error.messages = FALSE)
on.exit(options(opt))
stop()
}
The first line turns off error messages and stores the old setting to the variable opt. After this line, any error that occurs will not output a message and therfore, also stop() will not cause any message to be printed.
According to the R help,
on.exit records the expression given as its argument as needing to be executed when the current function exits.
The current function is stop_quietly() and it exits when stop() is called. So the last thing that the program does is call options(opt) which will set show.error.messages to the value it had, before stop_quietly() was called (presumably, but not necessarily, TRUE).
There is a nice solution in a mailing list here that defines a stopQuietly function that basically hides the error shown from the stop function:
stopQuietly <- function(...) {
blankMsg <- sprintf("\r%s\r", paste(rep(" ", getOption("width")-1L), collapse=" "));
stop(simpleError(blankMsg));
} # stopQuietly()
> stopQuietly()
I have a similar problem and, based on #VangelisTasoulas answer, I got a simple solution.
Inside functions, I have to check if DB is updated. If it is not, stop the execution.
r=readline(prompt="Is DB updated?(y/n)")
Is DB updated?(y/n)n
if(r != 'y') stop('\r Update DB')
Update DB
Just putting \r in the beginning of the message, overwrite Error: in the message.
You're looking for the function browser.
You can use the following solution to stop an R program without error:
if (justUpdate)
return(cat(".. Your Message .. "))
Just return something at the line you want to quit the function:
f <- function(x, dry=F) {
message("hi1")
if (dry) return(x)
message("hi2")
x <- 2*x
}
y1 <- f(2) # = 4 hi1 hi2
y2 <- f(2, dry=T) # = 2 hi1
In addition to answer from Stibu on Mar 22 '17 at 7:29, if you want to write a message as a part of stop(), this message is not written.
I perceive strange that following two lines have to be used meaning on.exit(options(options(show....))) doesn't work.
opt <- options(show.error.messages = F)
on.exit(options(opt))
I had forgotten the answer to this and needed to look it up and landed here... You posted the hint to the answer in your question...
ctrl+c is another option, but I want to stop the source in specific line.
Signal an error, warning, or message
rlang::inform("Updated Only")
rlang::interrupt()
I've found it good to write a script and run it with source(). In the script, a write exit statements as a special class of error that a tryCatch() can pick up and send back as just a message:
exit <- function(..., .cl = NULL) {
# Use to capture acceptable stop
cond <- structure(
list(.makeMessage(...), .cl),
class = c("exitError", "error", "condition"),
names = c("message", "call")
)
stop(cond)
}
foo <- function() {
exit("quit here")
1
}
tryCatch(
# rather than foo(), you might use source(filename)
foo(),
exitError = function(e) message(e$message)
)
#> quit here
Created on 2022-01-24 by the reprex package (v2.0.1)
You can use with_options() in the withr package to temporarily disable error messages and then you can call stop() directly.
Here is an example:
weird_math <- function(x, y, z) {
if (x > z) {
withr::with_options(
list(show.error.messages = FALSE),
{
print("You can execute other code here if you want")
stop()
}
)
}
# only runs if x <= z
x + y ^ z
}
weird_math(1, 2, 3)
[1] 9
weird_math(3, 2, 1)
[1] "You can execute other code here if you want"
why not just use an if () {} else {}? It's only a couple of characters...
f1 <- function(){}
f2 <- function(){}
if (justUpdate) {
} else {
# main body
}
or even
f1 <- function(){}
f2 <- function(){}
if (!justUpdate) {
# main body
}
The below code work for me stopped without error messages.
opt <- options(show.error.messages = FALSE)
on.exit(options(opt))
break
Related
For educational purposes we are logging all commands that students type in the rstudio console during labs. In addition we would like to store if call was successful or raised an error, to identify students which struggling to get the syntax right.
The best I can come up with is something like this:
options(error = function(){
timestamp("USER ERROR", quiet = TRUE)
})
This adds an ## ERROR comment on the history log when an exception occurs. Thereby we could analyze history files to see which commands were followed by an ## ERROR comment.
However R's internal history system is not well suited for logging because it is in-memory, limited size and needs to be stored manually with savehistory(). Also I would prefer to store log one-line-per-call, i.e. escape linebreaks for multi-line commands.
Is there perhaps a hook or in the R or RStudio console for logging actual executed commands? That would allow me to insert each evaluated expression (and error) in a database along with a username and timestamp.
A possible solution would be to use addTaskCallback or the taskCallbackManager with a function that writes each top-level command to your database. The callback will only fire on the successful completion of a command, so you would still need to call a logging function on an error.
# error handler
logErr <- function() {
# turn logging callback off while we process errors separately
tcbm$suspend(TRUE)
# turn them back on when we're done
on.exit(tcbm$suspend(FALSE))
sc <- sys.calls()
sclen <- length(sc) # last call is this function call
if(sclen > 1L) {
cat("myError:\n", do.call(paste, c(lapply(sc[-sclen], deparse), sep="\n")), "\n")
} else {
# syntax error, so no call stack
# show the last line entered
# (this won't be helpful if it's a parse error in a function)
file1 <- tempfile("Rrawhist")
savehistory(file1)
rawhist <- readLines(file1)
unlink(file1)
cat("myError:\n", rawhist[length(rawhist)], "\n")
}
}
options(error=logErr)
# top-level callback handler
log <- function(expr, value, ok, visible) {
cat(deparse(expr), "\n")
TRUE
}
tcbm <- taskCallbackManager()
tcbm$add(log, name = "log")
This isn't a complete solution, but I hope it gives you enough to get started. Here's an example of what the output looks like.
> f <- function() stop("error")
f <- function() stop("error")
> hi
Error: object 'hi' not found
myError:
hi
> f()
Error in f() : error
myError:
f()
stop("error")
I have a generic function to catch all exceptions included in my package logR::tryCatch2 defined as:
tryCatch2 <- function(expr){
V=E=W=M=I=NULL
e.handler = function(e){
E <<- e
NULL
}
w.handler = function(w){
W <<- c(W, list(w))
invokeRestart("muffleWarning")
}
m.handler = function(m){
attributes(m$call) <- NULL
M <<- c(M, list(m))
}
i.handler = function(i){
I <<- i
NULL
}
V = suppressMessages(withCallingHandlers(
tryCatch(expr, error = e.handler, interrupt = i.handler),
warning = w.handler,
message = m.handler
))
list(value=V, error=E, warning=W, message=M, interrupt=I)
}
As you can see in the last line it returns a list which is more or less self describing.
It makes the real reaction to the exceptions delayed after the tryCatch2 call by simple !is.null:
f = function(){ warning("warn1"); warning("warn2"); stop("err") }
r = tryCatch2(f())
if(!is.null(r$error)) cat("Error detected\n")
# Error detected
if(!is.null(r$warning)) cat("Warning detected, count", length(r$warning), "\n")
# Warning detected, count 2
It works as expected, I can react with my own code. But in some cases I would like to not stop the interrupt process which is caught too. At the moment it seems I would need to add additional parameter to tryCatch2 which would control if interrupts should be catch or not. So the question asks about some invokeInterrupt function which I could use in the following way:
g = function(){ Sys.sleep(60); f() }
r = tryCatch2(g())
# interrupt by pressing ctrl+c / stop while function is running!
if(!is.null(r$interrupt)) cat("HERE I would like to invoke interrupt\n")
# HERE I would like to invoke interrupt
I think if R is able to catch one it should be also able to invoke one.
How can I achieve invokeInterrupt functionality?
I can propose a partial solution, which relies on the tools package.
invokeInterrupt <- function() {
require(tools)
processId <- Sys.getpid()
pskill(processId, SIGINT)
}
However, be aware that throwing the interrupt signal (SIGINT) with pskill doesn't appear to be very robust. I ran a few tests by sending the exception and catching it with your function, like so:
will_interrupt <- function() {
Sys.sleep(3)
invokeInterrupt()
Sys.sleep(3)
}
r = tryCatch2(will_interrupt())
On linux, this worked well when executed from the R commandline. On windows, the R commandline and R Gui did close when executing this code. There is worse: on both linux and windows, this code crashed Rstudio instantly...
So, if your code is to be executed from the R commandline on Linux, this solution should be OK. Otherwise you might be out of luck...
Late answer but I have found that rlang::interrupt can throw "user interrupts":
interrupt() allows R code to simulate a user interrupt of the kind that is signalled with Ctrl-C.
It is currently not possible to create custom interrupt condition objects.
Source: ?rlang::interrupt
Internally it calls the R API function Rf_onintr which is an alias for the function onintr.
Basically an interrupt is "just" a special condition with these classes:
interrupt and condition (see the R source code).
If you just want to simulate an interrupt to test tryCatching (without the need to interrupt a running R statement) it suffice to throw a condition with these classes via signalCondition:
interrupt_condition <- function() {
structure(list(), class = c("interrupt", "condition"))
}
tryCatch(signalCondition(interrupt_condition()),
interrupt = function(x) print("interrupt detected"))
# [1] "interrupt detected"
Is there a way to have multiple for expections for an expect_that unit test? For instance, for a given expect_that() statement, I'd like to expect that the function f() gives a warning and also returns the number 10.
test_that("f works as expected", {
expect_warning(f())
expect_equal(f(), 10)
}
)
If I understand your context correctly, this should work. The test would fail and report if either or both of the expectations weren't met.
To run the function only once, you could try wrapping the function within the test_that:
test_that("f works as expected", {
a <- tryCatch(f(), warning=function(w) return(list(f(), w)))
expect_equal(a[[2]], "warning text")
expect_equal(a[[1]], 10)
rm(a)
}
)
I haven't tested this so I'm not sure if it'll work in your particular case, but I've used similar approaches with test_that in the past.
context("Checking blah")
test_that("blah works",{
f <- function(){warning("blah"); return(10)}
expect_warning(x <- f())
expect_equal(x, 10)
})
You can save the output while checking for the warning. After that check that the output is what you expect.
Is there any way to stop an R program without error?
For example I have a big source, defining several functions and after it there are some calls to the functions. It happens that I edit some function, and want the function definitions to be updated in R environment, but they are not actually called.
I defined a variable justUpdate and when it is TRUE want to stop the program just after function definitions.
ReadInput <- function(...) ...
Analyze <- function(...) ...
WriteOutput <- function(...) ...
if (justUpdate)
stop()
# main body
x <- ReadInput()
y <- Analyze(x)
WriteOutput(y)
I have called stop() function, but the problem is that it prints an error message.
ctrl+c is another option, but I want to stop the source in specific line.
The problem with q() or quit() is that it terminates R session, but I would like to have the R session still open.
As #JoshuaUlrich proposed browser() can be another option, but still not perfect, because the source terminates in a new environment (i.e. the R prompt will change to Browser[1]> rather than >). Still we can press Q to quit it, but I am looking for the straightforward way.
Another option is to use if (! justUpdate) { main body } but it's clearing the problem, not solving it.
Is there any better option?
I found a rather neat solution here. The trick is to turn off all error messages just before calling stop(). The function on.exit() is used to make sure that error messages are turned on again afterwards. The function looks like this:
stop_quietly <- function() {
opt <- options(show.error.messages = FALSE)
on.exit(options(opt))
stop()
}
The first line turns off error messages and stores the old setting to the variable opt. After this line, any error that occurs will not output a message and therfore, also stop() will not cause any message to be printed.
According to the R help,
on.exit records the expression given as its argument as needing to be executed when the current function exits.
The current function is stop_quietly() and it exits when stop() is called. So the last thing that the program does is call options(opt) which will set show.error.messages to the value it had, before stop_quietly() was called (presumably, but not necessarily, TRUE).
There is a nice solution in a mailing list here that defines a stopQuietly function that basically hides the error shown from the stop function:
stopQuietly <- function(...) {
blankMsg <- sprintf("\r%s\r", paste(rep(" ", getOption("width")-1L), collapse=" "));
stop(simpleError(blankMsg));
} # stopQuietly()
> stopQuietly()
I have a similar problem and, based on #VangelisTasoulas answer, I got a simple solution.
Inside functions, I have to check if DB is updated. If it is not, stop the execution.
r=readline(prompt="Is DB updated?(y/n)")
Is DB updated?(y/n)n
if(r != 'y') stop('\r Update DB')
Update DB
Just putting \r in the beginning of the message, overwrite Error: in the message.
You're looking for the function browser.
You can use the following solution to stop an R program without error:
if (justUpdate)
return(cat(".. Your Message .. "))
Just return something at the line you want to quit the function:
f <- function(x, dry=F) {
message("hi1")
if (dry) return(x)
message("hi2")
x <- 2*x
}
y1 <- f(2) # = 4 hi1 hi2
y2 <- f(2, dry=T) # = 2 hi1
In addition to answer from Stibu on Mar 22 '17 at 7:29, if you want to write a message as a part of stop(), this message is not written.
I perceive strange that following two lines have to be used meaning on.exit(options(options(show....))) doesn't work.
opt <- options(show.error.messages = F)
on.exit(options(opt))
I had forgotten the answer to this and needed to look it up and landed here... You posted the hint to the answer in your question...
ctrl+c is another option, but I want to stop the source in specific line.
Signal an error, warning, or message
rlang::inform("Updated Only")
rlang::interrupt()
I've found it good to write a script and run it with source(). In the script, a write exit statements as a special class of error that a tryCatch() can pick up and send back as just a message:
exit <- function(..., .cl = NULL) {
# Use to capture acceptable stop
cond <- structure(
list(.makeMessage(...), .cl),
class = c("exitError", "error", "condition"),
names = c("message", "call")
)
stop(cond)
}
foo <- function() {
exit("quit here")
1
}
tryCatch(
# rather than foo(), you might use source(filename)
foo(),
exitError = function(e) message(e$message)
)
#> quit here
Created on 2022-01-24 by the reprex package (v2.0.1)
You can use with_options() in the withr package to temporarily disable error messages and then you can call stop() directly.
Here is an example:
weird_math <- function(x, y, z) {
if (x > z) {
withr::with_options(
list(show.error.messages = FALSE),
{
print("You can execute other code here if you want")
stop()
}
)
}
# only runs if x <= z
x + y ^ z
}
weird_math(1, 2, 3)
[1] 9
weird_math(3, 2, 1)
[1] "You can execute other code here if you want"
why not just use an if () {} else {}? It's only a couple of characters...
f1 <- function(){}
f2 <- function(){}
if (justUpdate) {
} else {
# main body
}
or even
f1 <- function(){}
f2 <- function(){}
if (!justUpdate) {
# main body
}
The below code work for me stopped without error messages.
opt <- options(show.error.messages = FALSE)
on.exit(options(opt))
break
When I use tryCatch, I can define an error handler and use conditionCall to determine the call that caused the error. For instance,
tryCatch(
eval(parse(text="prnit('Hello')")),
error=function(e) {
cl <- conditionCall(e)
#...
})
Can I get to the bad call on the R prompt? Until now, I found only this solution:
> err_hdl <- function() {
file1 <- tempfile("Rrawhist")
savehistory(file1)
rawhist <- readLines(file1)
unlink(file1)
cat("Error : ", tail(rawhist,1), "\n")
return(TRUE)
}
> options(error=err_hdl)
> prnit("Hello")
but I believe there must be a more straightforward way..
Any hint appreciated!
I put out a bounty. The first answer that implements the behaviour of the err_hdl function above without file I/O that is platform independent will be accepted.
Edit -- the code above seems only to work on windows. I am looking for the input that raised the error.
It looks like dump.frames can be told not to dump to a file but rather to an object in the .GlobalEnv. However, I haven't tested it on anything but a Mac. Would the following help?
err_hdl2 <- function() {
dump.frames("theErr", to.file = FALSE)
cat("What happened?\n", attr(theErr,"error.message"), "\nOh.\n")
}
options(error = err_hdl2)
> prnit(dt)
Error: could not find function "prnit"
What happened?
Error: could not find function "prnit"
Oh.
There might be a drawback to creating the object theErr in the global environment, I suppose.
> theErr
$`function ()
{
dump.frames("theErr", to.file = FALSE)
cat("What`
<environment: 0x1030fe140>
attr(,"error.message")
[1] "Error: could not find function \"prnit\"\n"
attr(,"class")
[1] "dump.frames"