[BioC] IRanges: interaction with model fitting

[Kasper Daniel Hansen]

locfit is a package from CRAN for doing local regression (think
loess).  It does not have a NAMESPACE, and it uses what to my casual
eyes look like a pretty standard model setup.  But there is a strange
thing happening when IRanges is loaded.  An example is best:

First get some data and define two functions that essentially does the same:

library(locfit)
utils::data(anorexia, package = "MASS")
myData <- anorexia
tmp <- function(dat) {
    anorex.1 <- glm(Postwt ~ lp(Prewt),
                           family = "gaussian", data = dat)
}
tmp1 <- function(dat1) {
    tmp2 <- function(dat2) {
        anorex.1 <- locfit(Postwt ~ lp(Prewt),
                           family = gaussian, data = dat2)

    }
    tmp2(dat2 = dat1)
}

tmp(myData)
tmp1(myData)

This works great.  Now load IRanges and do the same

library(IRanges)
> tmp(myData)
Error in terms.formula(formula, data = data) :
  'data' argument is of the wrong type

Enter a frame number, or 0 to exit

1: tmp(myData)
2: locfit(Postwt ~ lp(Prewt), family = "gaussian", data = dat)
3: eval(m, sys.frame(sys.parent()))
4: eval(m, sys.frame(sys.parent()))
5: eval(expr, envir, enclos)
6: model.frame(formula = Postwt ~ lp(Prewt), data = dat)
7: model.frame.default(formula = Postwt ~ lp(Prewt), data = dat)
8: terms(formula, data = data)
9: terms.formula(formula, data = data)

Selection: 0
> tmp1(myData)
Error in inherits(x, "data.frame") : object 'dat2' not found

Enter a frame number, or 0 to exit

 1: tmp1(myData)
 2: tmp2(dat2 = dat1)
 3: locfit(Postwt ~ lp(Prewt), family = gaussian, data = dat2)
 4: eval(m, sys.frame(sys.parent()))
 5: eval(m, sys.frame(sys.parent()))
 6: eval(expr, envir, enclos)
 7: model.frame(formula = Postwt ~ lp(Prewt), data = dat2)
 8: model.frame.default(formula = Postwt ~ lp(Prewt), data = dat2)
 9: is.data.frame(data)
10: inherits(x, "data.frame")

Selection: 0

Clearly something seems wrong.  The error messages for tmp and tmp1
are different.  Perhaps the lacking NAMESPACE for locfit makes a
difference.  And locfit sets up the design matrix using a slightly
different set of commands, that to my eye mostly look like an older
paradigm.

Any idea on what happens and why this is affected by IRanges?

Kasper