R devel - Aug 2009 - R CMD check does not recognize S4 functions inside other functions?

I am developing a new R package and am now checking it for submission to
CRAN.

The some functions in the package make use of the sparse matrix routines
in the package 'Matrix'.

When these are loaded in R, they create no problems.

However, when running R CMD check, I run into the following error in 
executing the examples in a .rd file:

 >   DD = Matrix(diag(1,200),sparse=TRUE)
 >   tDD = t(DD)
 >
 > fres = FitMatchOpt(coefs=coefs,which=2,pars=pars,proc)
Error in t.default(DD) : argument is not a matrix
Calls: FitMatchOpt -> t -> t.default
Execution halted

The first two lines of the function FitMatchOpt are

   DD = Matrix(diag(1,200),sparse=TRUE)
   tDD = t(DD)

These were fine when given in the examples section of the .rd file 
directly. However, when defined within a function in the package, the 
lines cause an error.

Sparse matrices improve the computational efficiency of the routines I 
am developing and I would like to use them. But I'm not sure how I can 
get around this error.

Many thanks,

Giles Hooker

It looks as if it is very related to the message I posted just some day  
ago ("Problem with standard generic methods in Matrix package").

Sylvain

On Fri, 28 Aug 2009 03:12:48 +0200, Giles Hooker <gjh27 at cornell.edu>
wrote:
> I am developing a new R package and am now checking it for submission to
> CRAN.
>
> The some functions in the package make use of the sparse matrix routines
> in the package 'Matrix'.
>
> When these are loaded in R, they create no problems.
>
> However, when running R CMD check, I run into the following error in  
> executing the examples in a .rd file:
>
>  >   DD = Matrix(diag(1,200),sparse=TRUE)
>  >   tDD = t(DD)
>  >
>  > fres = FitMatchOpt(coefs=coefs,which=2,pars=pars,proc)
> Error in t.default(DD) : argument is not a matrix
> Calls: FitMatchOpt -> t -> t.default
> Execution halted
>
> The first two lines of the function FitMatchOpt are
>
>    DD = Matrix(diag(1,200),sparse=TRUE)
>    tDD = t(DD)
>
> These were fine when given in the examples section of the .rd file  
> directly. However, when defined within a function in the package, the  
> lines cause an error.
>
> Sparse matrices improve the computational efficiency of the routines I  
> am developing and I would like to use them. But I'm not sure how I can
> get around this error.
>
> Many thanks,
>
> Giles Hooker
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> "GH" == Giles Hooker <gjh27 at cornell.edu>
>>>>>     on Thu, 27 Aug 2009 21:12:48 -0400 writes:
    GH> I am developing a new R package and am now checking it for submission
to
    GH> CRAN.

    GH> The some functions in the package make use of the sparse matrix
routines
    GH> in the package 'Matrix'.

    GH> When these are loaded in R, they create no problems.

    GH> However, when running R CMD check, I run into the following error in 
    GH> executing the examples in a .rd file:

    >> DD = Matrix(diag(1,200),sparse=TRUE)
    >> tDD = t(DD)

{{well, the transpose of a diagonal matrix, really ??}}

Just a remark:   For larger values of n=200,
it would be more efficient (and elegant) to directly use

   DD <- Diagonal(200)

See   ?Diagonal,  and e.g.,

  > Diagonal(4)
  4 x 4 diagonal matrix of class "ddiMatrix"
       [,1] [,2] [,3] [,4]
  [1,]    1    .    .    .
  [2,]    .    1    .    .
  [3,]    .    .    1    .
  [4,]    .    .    .    1
  > .symDiagonal(4)
  4 x 4 sparse Matrix of class "dsCMatrix"

  [1,] 1 . . .
  [2,] . 1 . .
  [3,] . . 1 .
  [4,] . . . 1





    >> 
    >> fres = FitMatchOpt(coefs=coefs,which=2,pars=pars,proc)
    GH> Error in t.default(DD) : argument is not a matrix
    GH> Calls: FitMatchOpt -> t -> t.default
    GH> Execution halted

    GH> The first two lines of the function FitMatchOpt are

    GH> DD = Matrix(diag(1,200),sparse=TRUE)
    GH> tDD = t(DD)

    GH> These were fine when given in the examples section of the .rd file 
    GH> directly. However, when defined within a function in the package, the
    GH> lines cause an error.

How does your package "get Matrix"?

I'm sure there's some problem in requiring Matrix, in either
your DESCRIPTION or your NAMESPACE  (or a .First.library or ...)

Your DESCRIPTION should have

Depends: ...., Matrix
Imports: ...., Matrix

and your NAMESPACE  

either
   importFrom("Matrix", .....)# the things you need

or (if you use many things from the Matrix package, and/or
    in some way just *extend* it ...)

   import("Matrix")



Does that help?

Best regards,
Martin Maechler


    GH> Sparse matrices improve the computational efficiency of the routines
I
    GH> am developing and I would like to use them. But I'm not sure how
I can
    GH> get around this error.

    GH> Many thanks,

    GH> Giles Hooker

    GH> ______________________________________________
    GH> R-devel at r-project.org mailing list
    GH> https://stat.ethz.ch/mailman/listinfo/r-devel