[R] on abort error, always show call stack?
Dear R Wizards---is it possible to get R to show its current call stack (sys.calls()) upon an error abort? I don't use ESS for execution, and it is often not obvious how to locate how I triggered an error in an R internal function. Seeing the call stack would make this easier. (right now, I sprinkle cat statements everywhere, just to locate the line where the error appears.) Of course, I would really love to see the line in my program that triggered this, but I have asked this before, and I understand this is too difficult to get into the R language. regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] on abort error, always show call stack?
On Sun, 2010-08-22 at 11:41 -0400, ivo welch wrote: Dear R Wizards---is it possible to get R to show its current call stack (sys.calls()) upon an error abort? I don't use ESS for execution, and it is often not obvious how to locate how I triggered an error in an R internal function. Seeing the call stack would make this easier. (right now, I sprinkle cat statements everywhere, just to locate the line where the error appears.) Of course, I would really love to see the line in my program that triggered this, but I have asked this before, and I understand this is too difficult to get into the R language. The traceback() function will print out the call stack after an error. However, you may find the debug() family of functions more useful for debugging. Also see the browser() function. -Matt regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] on abort error, always show call stack?
On Sun, 22 Aug 2010, Matt Shotwell wrote: On Sun, 2010-08-22 at 11:41 -0400, ivo welch wrote: Dear R Wizards---is it possible to get R to show its current call stack (sys.calls()) upon an error abort? I don't use ESS for execution, and it is often not obvious how to locate how I triggered an error in an R internal function. Seeing the call stack would make this easier. (right now, I sprinkle cat statements everywhere, just to locate the line where the error appears.) Of course, I would really love to see the line in my program that triggered this, but I have asked this before, and I understand this is too difficult to get into the R language. The traceback() function will print out the call stack after an error. However, you may find the debug() family of functions more useful for debugging. Also see the browser() function. Further, you might set options( error = recover ) which prints the list of current calls, and prompts the user to select one of them. And then allows browser()-ing. Chuck -Matt regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] on abort error, always show call stack?
yes, thank you. is it possible to have it invoked to STDERR automatically on a program abort? /iaw On Sun, Aug 22, 2010 at 11:50 AM, Matt Shotwell shotw...@musc.edu wrote: On Sun, 2010-08-22 at 11:41 -0400, ivo welch wrote: Dear R Wizards---is it possible to get R to show its current call stack (sys.calls()) upon an error abort? I don't use ESS for execution, and it is often not obvious how to locate how I triggered an error in an R internal function. Seeing the call stack would make this easier. (right now, I sprinkle cat statements everywhere, just to locate the line where the error appears.) Of course, I would really love to see the line in my program that triggered this, but I have asked this before, and I understand this is too difficult to get into the R language. The traceback() function will print out the call stack after an error. However, you may find the debug() family of functions more useful for debugging. Also see the browser() function. -Matt regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] on abort error, always show call stack?
How about this:
test - function(x) log(x)
tryCatch({
#Code that will error
test(a)
}, finally = {
sink(stderr())
traceback()
sink()
})
If you are running non-interactively, invoke R with the --interactive
flag to force it. Saving the code above to test.R, you can see the
effect with
$ R --interactive test.R 1 test.out 2 test.err
This seems reasonable, but maybe others will say if I'm missing
something more automagic.
-Matt
On Sun, 2010-08-22 at 11:58 -0400, ivo welch wrote:
yes, thank you. is it possible to have it invoked to STDERR
automatically on a program abort?
/iaw
On Sun, Aug 22, 2010 at 11:50 AM, Matt Shotwell shotw...@musc.edu wrote:
On Sun, 2010-08-22 at 11:41 -0400, ivo welch wrote:
Dear R Wizards---is it possible to get R to show its current call
stack (sys.calls()) upon an error abort? I don't use ESS for
execution, and it is often not obvious how to locate how I triggered
an error in an R internal function. Seeing the call stack would make
this easier. (right now, I sprinkle cat statements everywhere, just
to locate the line where the error appears.) Of course, I would
really love to see the line in my program that triggered this, but I
have asked this before, and I understand this is too difficult to get
into the R language.
The traceback() function will print out the call stack after an error.
However, you may find the debug() family of functions more useful for
debugging. Also see the browser() function.
-Matt
regards,
/iaw
Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Matthew S. Shotwell
Graduate Student
Division of Biostatistics and Epidemiology
Medical University of South Carolina
--
Matthew S. Shotwell
Graduate Student
Division of Biostatistics and Epidemiology
Medical University of South Carolina
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] on abort error, always show call stack?
For what's it worth, the Exception class of R.oo extends the simpleError class. When an Exception object is instantiated it also records the stack trace (traceback()). Then when the exception is thrown it will behave just as stop(). For the convenience, throw(message) does all this in one go, cf. stop(). You can use throw() wherever you use stop(). Then, when an Exception object is print():ed, it also displays the traceback. Example: library(R.oo); Loading required package: R.methodsS3 R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3 for help. R.oo v1.7.3 (2010-06-04) successfully loaded. See ?R.oo for help. bar - function() throw(Woops!) foo - function() bar() foo() Error in list(`foo()` = environment, `bar()` = environment, `throw(Woops!) ` = environment, : [2010-08-22 11:05:09] Exception: Woops! at throw(Exception(...)) at throw.default(Woops!) at throw(Woops!) at bar() at foo() The neat thing with always getting the traceback is that almost always people will cut'n'paste it when report errors/asking questions, which avoids standard replied asking for Please rerun and when you get the error write traceback() and report back.. I haven't done it yet, but you imagine adding an global option() where the sessionInfo() is also printed, an additional message referring to webpage etc. /Henrik On Sun, Aug 22, 2010 at 8:41 AM, ivo welch ivo.we...@gmail.com wrote: Dear R Wizards---is it possible to get R to show its current call stack (sys.calls()) upon an error abort? I don't use ESS for execution, and it is often not obvious how to locate how I triggered an error in an R internal function. Seeing the call stack would make this easier. (right now, I sprinkle cat statements everywhere, just to locate the line where the error appears.) Of course, I would really love to see the line in my program that triggered this, but I have asked this before, and I understand this is too difficult to get into the R language. regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
