[R] building a package that contains S4 classes and methods

[Marie Pierre Sylvestre]

Hello R users,

I am trying to make a my first package and I get an error that I can
understand. The package is build out of three files (one for functions, 1
for s4 classes and 1 for s4 methods).

Once I source them I run 

package.skeleton( name="TDC" )

within a R session and I get 

Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './TDC/Read-and-delete-me'.
Warning messages:
1: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R",  :
  deparse of an S4 object will not be source()able
2: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R",  :
  deparse of an S4 object will not be source()able
3: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R",  :
  deparse of an S4 object will not be source()able
4: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R",  :
  deparse may be incomplete


I keep going in spite of the warnings with 
R CMD check --no-examples TDC

and I get 
* checking for working pdflatex ... OK
* using log directory
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: UTF-8
* checking for file 'TDC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDC' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'TDC' can be installed ... ERROR
Installation failed.

The error file says:
 
* Installing *source* package 'TDC' ...
** R
** preparing package for lazy loading
Error in parse(n = -1, file = file) : unexpected '<' at
102: `.__C__BindArgs` <-
103: <
Calls: <Anonymous> -> code2LazyLoadDB -> sys.source -> parse
Execution halted
ERROR: lazy loading failed for package 'TDC'
** Removing
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck/TDC'

The problem is with my classes and methods. The respective files contain:

setClass("BindArgs",  signature( "function" ))
setClass("BindArgs2", signature( "function" )) 

and

setMethod("initialize", "BindArgs", function( .Object, f, ... )
      callNextMethod( .Object, function( x ) f( x, ... ) )) 

setMethod("initialize", "BindArgs2", function( .Object, f, ...)
      callNextMethod( .Object, function( x, y ) f( x, y, ... ) )) 

Everything works well within a R session but I can build the package.

If I look at the internal R file that this created I get

`.__C__BindArgs` <-
<S4 object of class structure("classRepresentation", package = "methods")>
`.__C__BindArgs2` <-
<S4 object of class structure("classRepresentation", package = "methods")>
`.__M__initialize:methods` <-
<S4 object of class structure("MethodsList", package = "methods")>
`.__T__initialize:methods` <-
<environment>

Well, let just say that I am new to classes so this confuses me greatly. I
have checked the documentation and tried a few things but I reached my
personal limits!

I am using R 2.7.1 on Linux Fedora 8.

Any comments on what is happening and/or help would be greatly appreciated.

MP