I have a script that I run from the commandline, like
Rscript example.R
and I'd like to have it tell me some debugging information when it exits. If I don't do anything special, if it hits an error, it exits, right there, and I see the error message. So, I added
options(error=traceback)
and then it gave me not only the error message but the stack at the time of the error, very useful. Great.
But now the script continues on through to the end, tossing up a lot more errors. Why does setting the error change Rscript's behaviour on encountering an error? How do I get it to just exit after the first error, as before?
Ah-ha. The trick is to call q(). In the help for dump.frames:
options(error = quote({dump.frames(to.file = TRUE); q()}))
and to use traceback (and function instead of quote),
options(error = function(){ traceback(); q()} )
would do it.
Related
I'm having an issue where if I execute several lines of code at once and one of them has an error, the lines below don't get executed.
For example if I have:
table(data$AGE)
table(dataREGION)
table(date$SEXE)
I get the table for the first line, and then
Error in table(dataREGION) : object 'dataREGION' not found
>
And the last line does not execute.
Does anyone know why it does that and how to fix it?
(I work with R 4.2.2 and RStudio 2022.12.0+353 "Elsbeth Geranium" Release)
Thanks!
Have a nice day,
Cassandra
Fixed: In Global Options > Console, under "Execution" uncheck the "Discard pending console input on error"
It seems like you want to use try().
try(table(data$AGE), silent = F, outFile = T)
try(table(dataREGION)) # also works without any params
try(table(date$SEXE))
You can also use tryCatch() if you want more control but it doesn't seem necessary for your purpose.
__
As for why your dataREGION doesn't exectue:
Hazarding a guess it might be because you forgot the $ between data and REGION
I have a R script where some of scripts not run sometimes because of data unavailability. I want to ignore this error so that my script can run on cron schedule.
Script:
data1 = data1 %>% mutate(`04_Days`=paste(round(ifelse(`04 Days` %in% c(NA,"NA"),0,`04 Days`)/`Till date attempted1`*100,0)," %"))
where sometimes the variable 04_Daysis not available and I want to ignore this error while running this line.
You can use tryCatch as explained here.
If the code inside tryCatch throws an error, the error function is called. If you want to ignore the error, just leave that function empty.
I have many unattended batch jobs in R running on a server and I have to analyse job failures after they have run.
I am trying to catch errors to log them and recover from the error gracefully but I am not able to get a stack trace (traceback) to log the code file name and line number of the R command that caused the error. A (stupid) reproducible example:
f <- function() {
1 + variable.not.found # stupid error
}
tryCatch( f(), error=function(e) {
# Here I would log the error message and stack trace (traceback)
print(e) # error message is no problem
traceback() # stack trace does NOT work
# Here I would handle the error and recover...
})
Running the code above produces this output:
simpleError in f(): object 'variable.not.found' not found
No traceback available
The traceback is not available and the reason is documented in the R help (?traceback):
Errors which are caught via try or tryCatch do not generate a
traceback, so what is printed is the call sequence for the last
uncaught error, and not necessarily for the last error.
In other words: Catching an error with tryCatch does kill the stack trace!
How can I
handle errors and
log the stack trace (traceback) for further examination
[optionally] without using undocumented or hidden R internal functions that are not guaranteed to work in the future?
THX a lot!
Sorry for the long answer but I wanted to summarize all knowledge and references in one answer!
Main issues to be solved
tryCatch "unrolls" the call stack to the tryCatch call so that traceback and sys.calls do no longer contain the full stack trace to identify the source code line that causes an error or warning.
tryCatch aborts the execution if you catch a warning by passing a handler function for the warning condition. If you just want to log a warning you cannot continue the execution as normal.
dump.frames writes the evaluation environments (frames) of the stack trace to allow post-mortem debugging (= examining the variable values visible within each function call) but dump.frames "forgets" to save the workspace too if you set the parameter to.file = TRUE. Therefore important objects may be missing.
Find a simple logging framework since R does not support decent logging out of the box
Enrich the stack trace with the source code lines.
Solution concept
Use withCallingHandlers instead of tryCatch to get a full stack trace pointing to the source code line that throwed an error or warning.
Catch warnings only within withCallingHandlers (not in tryCatch) since it just calls the handler functions but does not change the program flow.
Surround withCallingHandlers with tryCatch to catch and handle errors as wanted.
Use dump.frames with the parameter to.file = FALSE to write the dump into global variable named last.dump and save it into a file together with the global environment by calling save.image.
Use a logging framework, e. g. the package futile.logger.
R does track source code references when you set options(keep.source = TRUE). You can add this option to your .Rprofile file or use a startup R script that sets this option and source your actual R script then.
To enrich the stack trace with the tracked source code lines you can use the undocumented (but widely used) function limitedLabels.
To filter out R internal function calls from stack trace you can remove all calls that have no source code line reference.
Implementation
Code template
Instead of using tryCatch you should use this code snippet:
library(futile.logger)
tryCatch(
withCallingHandlers(<expression>,
error = function(e) {
call.stack <- sys.calls() # is like a traceback within "withCallingHandlers"
dump.frames()
save.image(file = "last.dump.rda")
flog.error(paste(e$message, limitedLabels(call.stack), sep = "\n"))
}
warning = <similar to error above>
}
error = <catch errors and recover as you would do it normally>
# warning = <...> # never do this here since it stops the normal execution like an error!
finally = <your clean-up code goes here>
}
Reusable implementation via a package (tryCatchLog)
I have implemented a simple package with all the concepts mentioned above.
It provides a function tryCatchLog using the futile.logger package.
Usage:
library(tryCatchLog) # or source("R/tryCatchLog.R")
tryCatchLog(<expression>,
error = function(e) {
<your error handler>
})
You can find the free source code at github:
https://github.com/aryoda/tryCatchLog
You could also source the tryCatchLog function instead of using a full blown package.
Example (demo)
See the demo file that provides a lot of comments to explain how it works.
References
Other tryCatch replacements
Logging of warnings and errors with with a feature to perform multiple attempts (retries) at try catch, e. g. for accessing an unreliable network drive:
Handling errors before warnings in tryCatch
withJavaLogging function without any dependencies to other packages which also enriches the source code references to the call stack using limitedLabels:
Printing stack trace and continuing after error occurs in R
Other helpful links
http://adv-r.had.co.nz/Exceptions-Debugging.html
A Warning About warning() - avoid R's warning feature
In R, why does withCallingHandlers still stops execution?
How to continue function when error is thrown in withCallingHandlers in R
Can you make R print more detailed error messages?
How can I access the name of the function generating an error or warning?
How do I save warnings and errors as output from a function?
options(error=dump.frames) vs. options(error=utils::recover)
General suggestions for debugging in R
Suppress warnings using tryCatch in R
R Logging display name of the script
Background information about the "srcrefs" attribute (Duncan Murdoch)
get stack trace on tryCatch'ed error in R
The traceback function can be used to print/save the current stack trace, but you have to specify an integer argument, which is the number of stack frames to omit from the top (can be 0). This can be done inside a tryCatch block or anywhere else. Say this is the content of file t.r:
f <- function() {
x <- 1
g()
}
g <- function() {
traceback(0)
}
When you source this file into R and run f, you get the stack trace:
3: traceback(0) at t.r#7
2: g() at t.r#3
1: f()
which has file name and line number information for each entry. You will get several stack frames originating from the implementation of tryCatch and you can't skip them by specifying a non-zero argument to traceback, yet indeed this will break in case the implementation of tryCatch changes.
The file name and line number information (source references) will only be available for code that has been parsed to keep source references (by default the source'd code, but not packages). The stack trace will always have call expressions.
The stack trace is printed by traceback (no need to call print on it).
For logging general errors, it is sometimes useful to use options(error=), one then does not need to modify the code that causes the errors.
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) {})
I am running an optimization program I wrote in a multi-language framework. Because I rely on different languages to accomplish the task, everything must be standalone so it can be launched through a batch file. Everything has been going fine for 2-3 months, but I finally ran out of luck when one of the crucial parts of this process, executed through a standalone R script, encountered something new and gave me an error message. This error message makes everything screech to a halt despite my best efforts:
selMEM<-forward.sel(muskfreq, musk.MEM, adjR2thresh=adjR2)
Procedure stopped (adjR2thresh criteria) adjR2cum = 0.000000 with 0 variables (superior to -0.005810)
Error in forward.sel(muskfreq, musk.MEM, adjR2thresh = adjR2) :
No variables selected. Please change your parameters.
I know why I am getting this message: it is warning me that no variables are above the threshold I have programmed to retain during a forward selection. Although this didn't happen in hundreds of runs, it's not that big a deal, I just need to tell R what to do next. This is where I am lost. After an exhaustive search through several posts (such as here), it seams that try() and tryCatch() are the way to go. So I have tried the following:
selMEM<-try(forward.sel(muskfreq, musk.MEM, adjR2thresh=adjR2))
if(inherits(selMEM, "try-error")) {
max<-0
cumR2<-0
adjR2<-0
pvalue<-NA
} else {
max<-dim(selMEM)[1]
cumR2<-selMEM$R2Cum[max]
adjR2<-selMEM$AdjR2Cum[max]
pvalue<-selMEM$pval[max]
}
The code after the problematic line works perfectly if I execute it line by line in R, but when I execute it as a standalone script from the command prompt, I still get the same error message and my whole process screeches to a halt before it executes what follows.
Any suggestions on how to make this work?
Note this in the try help:
try is implemented using tryCatch; for programming, instead of
try(expr, silent = TRUE), something like tryCatch(expr, error =
function(e) e) (or other simple error handler functions) may be more
efficient and flexible.
Look to tryCatch, possibly:
selMEM <- tryCatch({
forward.sel(muskfreq, musk.MEM, adjR2thresh=adjR2)
}, error = function(e) {
message(e)
return(NULL)
})
if(is.null(selMEM)) {
max<-0
cumR2<-0
adjR2<-0
pvalue<-NA
} else {
max<-dim(selMEM)[1]
cumR2<-selMEM$R2Cum[max]
adjR2<-selMEM$AdjR2Cum[max]
pvalue<-selMEM$pval[max]
}
Have you tried setting the silent parameter to true in the Try function?
max<-0
cumR2<-0
adjR2<-0
pvalue<-NA
try({
selMEM <- forward.sel(muskfreq, musk.MEM, adjR2thresh=adjR2)
max<-dim(selMEM)[1]
cumR2<-selMEM$R2Cum[max]
adjR2<-selMEM$AdjR2Cum[max]
pvalue<-selMEM$pval[max]
}, silent=T)