[R] Debugging R's code: boxplot.stats

[Matthew Walker]

On Sun, 2006-10-29 at 18:47 -0500, Duncan Murdoch wrote:
[snip]
> > Hi Duncan,
> > 
> > Thanks for your reply.
> > 
> > How do you know that (i) boxplot.stats lives in the grDevices namespace?
> 
> getAnywhere(boxplot.stats) starts out as
> 
>  > getAnywhere(boxplot.stats)
> A single object matching 'boxplot.stats' was found
> It was found in the following places
>    package:grDevices
>    registered S3 method for boxplot from namespace grDevices
>    namespace:grDevices
> 
> > and (ii) how do you know/change that boxplot will look in grDevices
> > before it uses the local copy?
> 
> That was actually a guess.  But checking now:
> 
>  > getAnywhere(boxplot)
> A single object matching 'boxplot' was found
> It was found in the following places
>    package:graphics
>    namespace:graphics
> with value
> 
> function (x, ...)
> UseMethod("boxplot")
> <environment: namespace:graphics>
> 
> so boxplot() is in the graphics package, and works in that namespace. 
> The graphics namespace file starts out
> 
> import(grDevices)
> 
> so functions in that package will look in grDevices before they look 
> elsewhere.  I thought that meant that S3 methods would be found there 
> before they're found anywhere else, but I didn't actually check this. 
> So let's check:
> 
>  > boxplot.stats <- function(x, ...) stop("mine")
>  > x <- 1
>  > class(x) <- "stats"
>  > boxplot(x)
> Error in boxplot.stats(x) : mine

> Whoops!  Looks as though my local copy does get found first.  Not sure 
> if this is a bug...

That's an interesting way to check.  If I enter
boxplot.stats <- function(x, ...) stop("mine")
boxplot(1)

I get a graph (i.e. no error) and so I concluded that the original
boxplot is calling the original boxplot.stats.  In other words, the
original is ignoring my local copy.

> 
> > I tried to do as you suggested and create a local copy of boxplot.  I
> > used the following commands:
> > boxplot.stats <- edit(boxplot.stats)  # Made changes to line 14
> > boxplot <- edit(boxplot)              
> > boxplot.default <- edit(boxplot.default)  # Added a call to "cat()"
> > 
> > When I called boxplot() the local copy was executed (as I could see the
> > output of my "cat" commands), however it appears that the local copy of
> > boxplot.stats isn't the one being called from my version of "boxplot".
> > How do I fix this?
> 
> That's very strange.  Which R version are you using?  Are you sure the 
> wrong version was being called?  I was doing my tests in 2.4.0.

I'm using 2.4.0 too (on Linux; sessionInfo() copied below)

If I execute the following:
boxplot.stats <- function(x, ...) stop("mine")

boxplot <- edit(boxplot) 
  # Added cat("local boxplot\n")

boxplot.default <- edit(boxplot.default) 
  # Added cat("local boxplot.default\n")

boxplot(1) 

I get a graph with the text
"local boxplot
local boxplot.default"

Had boxplot.default called the local version of boxplot.stats, I would
have expected the error "mine".

Is there a way I can avoid all this?  Perhaps I can somehow edit the
file that R loads when it reads the original "boxplot.stats"?


Cheers,

Matthew

*** Output of sessionInfo(): ***
R version 2.4.0 (2006-10-03)
i686-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"