From rkoenker at uiuc.edu  Wed Nov  4 17:32:36 2009
From: rkoenker at uiuc.edu (Roger Koenker)
Date: Wed, 4 Nov 2009 10:32:36 -0600
Subject: [Rd] s4 generic issue
Message-ID: <DBFFDE16-6480-498F-912A-F326E6930A30@uiuc.edu>

I'm hoping that someone with deeper insight into S4 than I,
that is to say virtually everyone reading this list, could help
resolve the following problem in SparseM.  We have

setGeneric("backsolve",
         function(r, x, k = NULL, upper.tri = NULL, transpose = NULL,   
twice = TRUE, ...)
                 standardGeneric("backsolve"),
         useAsDefault= function(r, x,  k = ncol(r), upper.tri = TRUE,
                 transpose = FALSE, twice = TRUE, ...)
                 base::backsolve(r, x, k = ncol(r), upper.tri = TRUE,
                         transpose = FALSE, ...))

and then proceed to use setMethod for a class matrix.csr.chol.   
However, this seems
to cause problems in the following instance:  if one does the following

require(lars)
require(SparseM)
example(lars)
....[snip]
lars> object3 <- lars(x,y,type="for") # Can use abbreviations
Error in base::backsolve(r, x, k = ncol(r), upper.tri = TRUE,  
transpose = FALSE,  :
   NA/NaN/Inf in foreign function call (arg 4)
 > traceback()
10: .C("bakslv", t = r, ldt = nrow(r), n = k, b = x, ldb = k, nb = nb,
         x = matrix(0, k, nb), job = job, info = integer(1L), DUP =  
FALSE,
         PACKAGE = "base")
9: base::backsolve(r, x, k = ncol(r), upper.tri = TRUE, transpose =  
FALSE,
        ...)
8: backsolve(R, backsolvet(R, Sign[positive]))
7: backsolve(R, backsolvet(R, Sign[positive]))
6: nnls.lars(active, Sign, R, directions, Gram[active, active],
        trace = trace, use.Gram = TRUE, eps = eps)
5: lars(x, y, type = "for")
4: eval.with.vis(expr, envir, enclos)
3: eval.with.vis(ei, envir)
2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix,
        getOption("prompt"), sep = ""), continue.echo = paste 
(prompt.prefix,
        getOption("continue"), sep = ""), verbose = verbose,  
max.deparse.length = Inf,
        encoding = encoding, skip.echo = skips, keep.source = TRUE)
1: example(lars)

So clearly base::backsolve is getting called as would be desired in  
this case,
but something is rotten in the way arguments are being passed.

I'm aware that the R-extensions manual suggests another strategy than
setGeneric for making generics, but I would like to understand what is  
going
wrong here.

Roger


url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    rkoenker at uiuc.edu            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Urbana, IL 61801



[Rd] s4 generic issue
Roger Koenker