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]]
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.
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
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?