From rmcgehee at walleyetrading.net  Fri Jan 27 23:41:10 2017
From: rmcgehee at walleyetrading.net (Robert McGehee)
Date: Fri, 27 Jan 2017 22:41:10 +0000
Subject: [Rd] Matrix package breaks as.matrix method
Message-ID: <30D28A63376088428E8318DD67FD407F705B2E@ny-mailstore1.walleyetrading.net>

Hi,
The Matrix package and the as.matrix method do not seem to be compatible inside of a package.

Here's an example. I've created a simple package "mat" that defines an eponymous class and as.matrix method on that class. All is well, unless that package has the Matrix package in its Depends or Imports (and imports, e.g. the "Diagonal" function). Then my as.matrix method stops working, even if I'm not using any part of the Matrix package.

Here's an example on R 3.3.2:

First, create an empty package "mat" (e.g. with package.skeleton) with one file in mat/R/mat.R with the following contents:

setClass("mat", representation(H="matrix"))
mat <- function(H) new("mat", H=H)
setMethod("as.matrix", signature("mat"), function(x, ...) crossprod(x at H))
testmat <- function() {
    H <- matrix(1:3, 1, 3)
    M <- mat(H)
    as.matrix(M)
}

Then install the mat package :
> require(mat)
> testmat()
     [,1] [,2] [,3]
[1,]    1    2    3
[2,]    2    4    6
[3,]    3    6    9

All works fine!

Now add "Depends: Matrix" into the package's DESCRIPTION file (alternatively add "Imports: Matrix" and 'importFrom("Matrix","Diagonal")' in the NAMESPACE).

Try again:
> require(mat)
> testmat()
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector

Bug? If not, can anyone provide a work around? In my case, I'd like to mix matrix and Matrix functions in my package, but am obviously having difficulty.

I've come across a somewhat similar report on stackoverflow http://stackoverflow.com/questions/13812373/overloading-operator-in-r-s4-classes-and-matrix-package regarding defining the "+" operator with the Matrix package, but I don't think the solution or the problem quite applies.

Thanks in advance, Robert

> R.version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          3.2                         
year           2016                        
month          10                          
day            31                          
svn rev        71607                       
language       R                           
version.string R version 3.3.2 (2016-10-31)
nickname       Sincere Pumpkin Patch       



[Rd] Matrix package breaks as.matrix method
Robert McGehee