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Laurence Kell FM CEFAS

2003-Jun-23 14:18 UTC

[R] FW: S4 classes, creating in C

I am using C code to create an S4 object based on Douglas Bates's example
in his lecture notes on
<http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Tutorials/RExtensions/slide
s.pdf>
http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Tutorials/RExtensions/slides
.pdf

e.g.

SEXP La_DGE_dc(SEXP A)
        {
        SEXP aa = PROTECT(duplicate(A));
        SEXP adims, pivot, val;
        int m, n, info;
       
        if (!isMatrix(aa) || !isReal(aa)) {
                error("A must be a double precision matrix");
                }

        adims = GET_DIM(aa); m = INTEGER(adims)[0]; n = INTEGER(adims)[1];
        pivot = PROTECT(NEW_INTEGER(m < n ? m : n));

        F77_CALL(dgetrf)(&m, &n, REAL(aa), &m, INTEGER(pivot),
&info);
       
        check_Lapack_error(info, "dtrtrf");
       
        val = PROTECT(NEW_OBJECT(MAKE_CLASS("LUdecomposition")));

        SET_SLOT(val, install("a"), aa);
        SET_SLOT(val, install("pivot"), pivot);
       
        UNPROTECT(3);
        return val;
        }

LUdecomposition is an S4 class defined as

setClass("LUdecomposition", representation(a="matrix", pivot
= "integer"))

This works in R 1.7.0 and R 1.7.1 but if I initialise any of the slots

setClass("LUdecomposition", representation(a="matrix", pivot
= "integer"),
                            prototype=list(pivot = NA)                    )

then I get the following error message in R 1.7.1 but not R 1.7.0

Error in makePrototypeFromClassDef(properties, ClassDef, immediate) :
        In making the prototype for class "LUdecomposition" elements
of the
prototype
        failed to match the corresponding slot class: pivot (class "
integer
")

Why  can I no longer use the prototype to set the default values?
Laurence Kell
CEFAS Lowestoft Laboratory
Pakefield Road
Lowestoft, NR33 0HT
UK
Tel +44 1502 52 42 57
Fax +44 1502 52 45 11
e-mail l.t.kell@cefas.co.uk

 

 


	[[alternative HTML version deleted]]

Douglas Bates

2003-Jun-23 15:38 UTC

head link

[R] FW: S4 classes, creating in C

Laurence Kell FM CEFAS <L.T.Kell at cefas.co.uk> writes:
>  
>  I am using C code to create an S4 object based on Douglas Bates's
example
> in his lecture notes on
>
<http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Tutorials/RExtensions/slide
> s.pdf>
>
http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Tutorials/RExtensions/slides
> .pdf
> 
> e.g.
> 
> SEXP La_DGE_dc(SEXP A)
>         {
>         SEXP aa = PROTECT(duplicate(A));
>         SEXP adims, pivot, val;
>         int m, n, info;
>        
>         if (!isMatrix(aa) || !isReal(aa)) {
>                 error("A must be a double precision matrix");
>                 }
> 
>         adims = GET_DIM(aa); m = INTEGER(adims)[0]; n = INTEGER(adims)[1];
>         pivot = PROTECT(NEW_INTEGER(m < n ? m : n));
> 
>         F77_CALL(dgetrf)(&m, &n, REAL(aa), &m, INTEGER(pivot),
&info);
>        
>         check_Lapack_error(info, "dtrtrf");
>        
>         val = PROTECT(NEW_OBJECT(MAKE_CLASS("LUdecomposition")));
> 
>         SET_SLOT(val, install("a"), aa);
>         SET_SLOT(val, install("pivot"), pivot);
>        
>         UNPROTECT(3);
>         return val;
>         }
> 
> LUdecomposition is an S4 class defined as
> 
> setClass("LUdecomposition", representation(a="matrix",
pivot = "integer"))
> 
> This works in R 1.7.0 and R 1.7.1 but if I initialise any of the slots
> 
> setClass("LUdecomposition", representation(a="matrix",
pivot = "integer"),
>                             prototype=list(pivot = NA)                    )
> 
> then I get the following error message in R 1.7.1 but not R 1.7.0
> 
> Error in makePrototypeFromClassDef(properties, ClassDef, immediate) :
>         In making the prototype for class "LUdecomposition"
elements of the
> prototype
>         failed to match the corresponding slot class: pivot (class "
integer
> ")
> 
> Why  can I no longer use the prototype to set the default values?
I'm not sure.  This may be the type of question that requires John
Chambers' attention and I think he is away from his email this week.

Matthias Burger

2003-Jun-23 17:38 UTC

head link

[R] FW: S4 classes, creating in C

Hi Laurence,




Laurence Kell FM CEFAS wrote:>  
[...]> LUdecomposition is an S4 class defined as
> 
> setClass("LUdecomposition", representation(a="matrix",
pivot = "integer"))
> 
> This works in R 1.7.0 and R 1.7.1 but if I initialise any of the slots
> 
> setClass("LUdecomposition", representation(a="matrix",
pivot = "integer"),
>                             prototype=list(pivot = NA)                    )
> 
> then I get the following error message in R 1.7.1 but not R 1.7.0
> 
> Error in makePrototypeFromClassDef(properties, ClassDef, immediate) :
>         In making the prototype for class "LUdecomposition"
elements of the
> prototype
>         failed to match the corresponding slot class: pivot (class "
integer
> ")
> 
> Why  can I no longer use the prototype to set the default values?
just tried your example in R 1.6.2 and it worked. And as you say for R 1.7.1 it 
won't.

So take a look at (R 1.7.1)

 > setClass("LUdecompositio", representation(a="matrix",
pivot = "integer"),
prototype(pivot=NA))
[1] "LUdecompositio"

 > lu<-new("LUdecompositio")
Error in makePrototypeFromClassDef(properties, ClassDef, immediate) :
         In making the prototype for class "LUdecompositio" elements
of the
prototype failed to match the corresponding slot class: pivot (class "
integer ")

 > setClass("LUdecompositi", representation(a="matrix",
pivot = "integer"),
prototype(pivot=as.integer(NA))
+
+ )
[1] "LUdecompositi"

 > lu3<-new("LUdecompositi")
 > lu3
An object of class "LUdecompositi"
Slot "a":
<0 x 0 matrix>

Slot "pivot":
[1] NA

 > is(lu3 at pivot)
[1] "integer" "vector"  "numeric"

So providing an explicit cast in the prototype cures the problem.

HTH,

   Matthias


> Laurence Kell
> CEFAS Lowestoft Laboratory
> Pakefield Road
> Lowestoft, NR33 0HT
> UK
> Tel +44 1502 52 42 57
> Fax +44 1502 52 45 11
> e-mail l.t.kell at cefas.co.uk
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 

-- 
Matthias Burger

Bioinformatics R&D
Epigenomics AG                      www.epigenomics.com
Kleine Pr?sidentenstra?e 1          fax:   +49-30-24345-555
10178 Berlin Germany                phone: +49-30-24345-0

Richard A. O'Keefe

2003-Jun-24 02:44 UTC

head link

[R] FW: S4 classes, creating in C

Laurence Kell FM CEFAS <L.T.Kell at cefas.co.uk> asked about
	> setClass("LUdecomposition", representation(a="matrix",
pivot = "integer"),
	>                             prototype=list(pivot = NA)                   
)
	> 
	> then I get the following error message in R 1.7.1 but not R 1.7.0
	> 
	> Error in makePrototypeFromClassDef(properties, ClassDef, immediate) :
	>         In making the prototype for class "LUdecomposition"
elements of the
	> prototype
	>         failed to match the corresponding slot class: pivot (class "
integer
	> ")
	> 
	> Why  can I no longer use the prototype to set the default values?
	
The prototype says 'pivot = "integer"'.
Had you noticed in the R language PDf file that typeof(NA) =
"logical"?
What happens when you try

    prototype=list(pivot=as.integer(NA))

instead?

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