[BioC] IRanges causes bug in complete.cases

[Kasper Daniel Hansen]

After loading IRanges, complete.cases ceases to work (see below).  Test via example("complete.cases", package = "stats")

To avoid stuff like this in the future, perhaps it would make sense to think of some kind of testing for packages making an S4 generic out of a "base" function.

Kasper

compute-0-5:~/> R-devel

R version 2.11.0 Under development (unstable) (2009-12-08 r50689)
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ISBN 3-900051-07-0

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> example(complete.cases)

cmplt.> x <- airquality[, -1] # x is a regression design matrix

cmplt.> y <- airquality[,  1] # y is the corresponding response

cmplt.> stopifnot(complete.cases(y) != is.na(y))

cmplt.> ok <- complete.cases(x,y)

cmplt.> sum(!ok) # how many are not "ok" ?
[1] 42

cmplt.> x <- x[ok,]

cmplt.> y <- y[ok]
> library(IRanges)

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 Map,
	 mapply,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table 

> example(complete.cases, package = "stats") 

cmplt.> x <- airquality[, -1] # x is a regression design matrix

cmplt.> y <- airquality[,  1] # y is the corresponding response

cmplt.> stopifnot(complete.cases(y) != is.na(y))
Error: '...' used in an incorrect context
Error in complete.cases(y) : 
  error in evaluating the argument '...' in selecting a method for function 'complete.cases'
> sessionInfo()
R version 2.11.0 Under development (unstable) (2009-12-08 r50689) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
 [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915   
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C                     
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           

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

other attached packages:
[1] IRanges_1.5.16

loaded via a namespace (and not attached):
[1] tools_2.11.0