[R] Line numbers with errors and warnings?
Steve Lianoglou
mailinglist.honeypot at gmail.com
Sun Dec 2 23:46:52 CET 2012
Similar to Duncan's example, if you have a script "test.R" which looks like so:
==== start script =====
a1 <- 1:10
a2 <- 101:122
plot(a1, a1)
plot(a1, a2)
==== end script ======
You can source it one way:
R> source('test.R', keep.source=TRUE)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
R> traceback()
8: stop("'x' and 'y' lengths differ")
7: xy.coords(x, y, xlabel, ylabel, log)
6: plot.default(a1, a2)
5: plot(a1, a2) at test.R#4 ### <- Error is on line 4
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("test.R", keep.source = TRUE)
If you `source("test.R", keep.source=FALSE)`, you will see that the
line number is not reported.
Also:
R> library(devtools)
R> options(keep.source=TRUE)
R> install_github("BadPackage", "lianos")
R> plot.me(1:10)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
R> traceback()
5: stop("'x' and 'y' lengths differ")
4: xy.coords(x, y, xlabel, ylabel, log)
3: plot.default(x, c(x, 0), pch = 16)
2: plot(x, c(x, 0), pch = 16) at test.R#4 #### <- BAM
1: plot.me(1:10)
HTH,
-steve
On Sun, Dec 2, 2012 at 5:08 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 12-12-02 5:02 PM, John Sorkin wrote:
>>
>> Gentleman,
>> This thread has been of great interest. Perhaps I missed part of it, but
>> do far I have not seen an example of code that has line numbers that
>> demonstrates how one can (in some instances) recover the line number of
>> an error. Can I impose upon the people who contributed to this thread to
>> post example code? The question if very important, and the discussion
>> about solutions has been somewhat abstract to this point.
>
>
> From my post this morning:
>
>
>> For example, in Windows, if I put this code into the clipboard:
>>
>> f <- function() {
>> stop("this is the error")
>> }
>>
>> g <- function() {
>> f()
>> }
>>
>> g()
>>
>> then run source("clipboard") followed by traceback(), this is what I see:
>>
>> > source("clipboard")
>> Error in f() (from clipboard#2) : this is the error
>> > traceback()
>> 7: stop("this is the error") at clipboard#2
>> 6: f() at clipboard#6
>> 5: g() at clipboard#9
>> 4: eval(expr, envir, enclos)
>> 3: eval(ei, envir)
>> 2: withVisible(eval(ei, envir))
>> 1: source("clipboard")
>>
>> You can ignore entries 1 to 4; they are part of source(). Entries 5, 6,
>> and 7 each tell the line of the script where they were parsed.
>>
>> Duncan Murdoch
>
>
>
>> Thank you,
>> John
>>
>> John David Sorkin M.D., Ph.D.
>> Chief, Biostatistics and Informatics
>> University of Maryland School of Medicine Division of Gerontology
>> Baltimore VA Medical Center
>> 10 North Greene Street
>> GRECC (BT/18/GR)
>> Baltimore, MD 21201-1524
>> (Phone) 410-605-7119
>> (Fax) 410-605-7913 (Please call phone number above prior to faxing)>>>
>> Milan Bouchet-Valat <nalimilan at club.fr> 12/2/2012 4:00 PM >>>
>> Le dimanche 02 décembre 2012 à 14:21 -0500, Duncan Murdoch a écrit :
>> > On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote:
>> > > Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit :
>> > >> On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote:
>> > >>> Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit
>> :
>> > >>>> Hi,
>> > >>>>
>> > >>>> On Sun, Dec 2, 2012 at 12:31 AM, Worik R <worikr at gmail.com> wrote:
>> > >>>>> What I mean is how do I get the R compilation or execution
>> process to spit
>> > >>>>> out a line number with errors and warnings?
>> > >>> Indeed, I often suffer from the same problem when debugging R
>> code too.
>> > >>> This is a real issue for me.
>> > >>>
>> > >>>> As Duncan mentioned already, you can't *always* get a line
>> number. You
>> > >>>> can, however, usually get enough context around the failing call
>> for
>> > >>>> you to be able to smoke the problem out.
>> > >>> What are the cases where you cannot get line numbers? Duncan said
>> > >>> source()ed code comes with line numbers, but what's the more
>> general
>> > >>> rule?
>> > >>
>> > >> The general rule is that parse() needs to be called with the
>> "srcfile"
>> > >> argument set to a srcfile object. source() does that by default.
>> > > OK. But isn't it technically possible to compute a line number even
>> when
>> > > no source file is present?
>> >
>> > Yes, you don't really need to have a file present, you just need a
>> > srcfile object. For example, on Windows when you use
>> > source("clipboard"), there's no file, just the system clipboard.
>> >
>> > If you call fix() on any function, you will
>> > > get something like a source file even if srcfile was not set.
>> >
>> > Yes, and then you can call source on that object, and you'll get line
>> > number information attached, relative to whatever you sourced.
>> >
>> >
>> > So it
>> > > could make sense to have a line number referring to what you would
>> see
>> > > in fix(). Or at least, the last executed line when calling browser()
>> or
>> > > when using options(error=recover), like gdb does.
>> >
>> > The thing is that if you didn't attach the line number information to
>> > the code, then it's not there. R can't figure out after the fact where
>> > the code came from. It needs to have the debug info in place when it
>> > runs it. How could R figure out where some expression came from that
>> it
>> > happens to be executing? Using eval() on a constructed expression in a
>> > function is not all that uncommon, but to the evaluator, it looks just
>> > like any other evaluation.
>> OK.
>>
>> > > This could be especially useful for packages that were not installed
>> > > with keep.source=TRUE. It could even help getting more useful error
>> > > messages on R-help...
>> >
>> > If you're debugging a package, then why not install it with
>> > keep.source=TRUE?
>> Of course. I just wondered whether this step could possibly be avoided.
>> It can be useful to have debugging details when casual users report a
>> bug, without reinstalling the package. Not a big deal, though.
>>
>>
>> Regards
>>
>> ______________________________________________
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>> http://www.R-project.org/posting-guide.html
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>>
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>
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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