R: Catch errors and continue execution after logging the stacktrace (no traceback available with tryCatch)

Question

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 recove

Answer 1

Sorry for the long answer but I wanted to summarize all knowledge and references in one answer!

Main issues to be solved

1. 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.

2. 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.

3. 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.

4. Find a simple logging framework since R does not support decent logging out of the box

5. Enrich the stack trace with the source code lines.

Solution concept

1. Use withCallingHandlers instead of tryCatch to get a full stack trace pointing to the source code line that throwed an error or warning.

2. Catch warnings only within withCallingHandlers (not in tryCatch) since it just calls the handler functions but does not change the program flow.

3. Surround withCallingHandlers with tryCatch to catch and handle errors as wanted.

4. 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.

5. Use a logging framework, e. g. the package futile.logger.

6. 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.

7. To enrich the stack trace with the tracked source code lines you can use the undocumented (but widely used) function limitedLabels.

8. 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(,
    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 = 
  }
  error = 
  # warning = <...> # never do this here since it stops the normal execution like an error!
  finally = 
}

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(,
            error = function(e) {
              
            })

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