Re: [Rd] SEXPs and slots

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Mon, 15 Nov 2010 10:01:47 -0800

On 11/15/2010 07:45 AM, Patrick Leyshock wrote:
> Very helpful, thank you.
>
> A couple other questions, please:
>
> 1. I've got a function written in C, named "my_c_function". In my R
> code I call this function, passing to it an INTSXP and a STRSXP,
> respectively:
>
> result <- .Call("my_c_function", int_vector, str_vector)
>
> The prototype of "my_c_function" is:
>
> SEXP my_c_function(SEXP int_vec, SEXP str_vec);
>
> Within my_c_function I am able to extract the values within the integer
> vector, e.g. I can grab the first value with these lines of code:
>
> int extracted_value;
> extracted_value = *INTEGER(int_vec);
>
> What I cannot figure out how to do is extract the value from the
> STRSXP. I'm assuming that I can create a pointer to a character array,
> then malloc enough memory to hold the value. Is there an analogous
> operation on "INTEGER" for STRSXPs?

STRING_ELT(str_vec, 0)

gets the 0th component of str_vec, which is a CHARSXP, i.e., an SEXP for a character string. The char* can be retrieved with CHAR, so the usual paradigm is

  const char *x = CHAR(STRING_ELT(str_vec, 0));

note the const-ness of the char* -- it's not mutable, because R is managing char * memory.

The converse action, of assigning to an element, is

  SET_STRING_ELT(str_vec, 0, mkChar("foo"));

mkChar() is creating a copy (if necessary) of "foo", managing it, and returning a CHARSXP. Working through protection (which will likely be your next obstacle ;) in this last example is a good exercise.

There is a parallel operation VECTOR_ELT / SET_VECTOR_ELT for lists.

> 2. Any good references/resources for developing R? Nearly all the
> documents I've found are for programming R as a user, not as a
> developer. I have copies of the documentation, which are very helpful,
> but it'd be helpful to have additional resources to fill in their gaps.

Chambers, 2008, Software for Data Analysis: Programming with R chapters 11 & 12,

Gentleman, 2008, R Programming for Bioinformatics chapter 6

might be helpful, but by the time they arrive you might find that you're most of the way through the material covered...

I guess my opinion is that Rcpp would not be useful for understanding R's C layer, whatever its merits for 'getting the job done'.

Martin

>
> Thank you,
>
> Patrick
>
>
> On Fri, Nov 12, 2010 at 4:36 PM, Martin Morgan <mtmorgan_at_fhcrc.org
> <mailto:mtmorgan_at_fhcrc.org>> wrote:
>
> On 11/12/2010 02:31 PM, Patrick Leyshock wrote:
> > Hello,
> >
> > I've created this class:
> >
> > setClass("example",
> > representation (
> > size = "numeric",
> > id = "character"
> > )
> > )
> >
> > Suppose I create a new instance of this class:
> >
> >> x <- new("example", 4, "id_value")
> >
> > This creates an S4 object with two slots. Am I correct in
> thinking that
> > slots are "filled" by SEXPs?
>
> Hi Patrick --
>
> If I
>
> > eg = new("example", size=4, id="id_value")
>
> (note the named arguments) and take a peak at the str'ucture of eg,
> I see
>
> > str(eg)
> Formal class 'example' [package ".GlobalEnv"] with 2 slots
> ..@ size: num 4
> ..@ id : chr "id_value"
>
> so the @size slot is a numeric vector of length 1 containing the value
> 4. One doesn't really have to know the detailed representation, but one
> can find out from
>
> > .Internal(inspect(eg))
> @df70e48 25 S4SXP g0c0 [OBJ,NAM(2),gp=0x10,ATT]
> ATTRIB:
> @df70ef0 02 LISTSXP g0c0 []
> TAG: @769258 01 SYMSXP g1c0 [MARK] "size"
> @c0f6db8 14 REALSXP g0c1 [NAM(2)] (len=1, tl=0) 4
> TAG: @15b0228 01 SYMSXP g1c0 [MARK,NAM(2)] "id"
> @c0f6178 16 STRSXP g0c1 [NAM(2)] (len=1, tl=0)
> @12341c80 09 CHARSXP g0c2 [gp=0x20] "id_value"
> TAG: @607ce8 01 SYMSXP g1c0 [MARK,NAM(2),gp=0x4000] "class"
> @c0f6d58 16 STRSXP g0c1 [NAM(2),ATT] (len=1, tl=0)
> @96ed08 09 CHARSXP g1c1 [MARK,gp=0x21] "example"
> ATTRIB:
> @df70fd0 02 LISTSXP g0c0 []
> TAG: @624f70 01 SYMSXP g1c0 [MARK,NAM(2)] "package"
> @c0f6d88 16 STRSXP g0c1 [NAM(2)] (len=1, tl=0)
> @67f5e0 09 CHARSXP g1c2 [MARK,gp=0x21,ATT] ".GlobalEnv"
>
> that the 'eg' object is an S4SXP with an attribute that is a LISTSXP.
> The LISTSXP has elements that are tagged with SYMSXP representing the
> slot name, and values that are REALSXP (for 'size') or STRSXP (for
> 'id'). The LISTSXP attribute itself has an attribute, which contains
> information about the package where the class is defined. With these
> hints one can see through the S4 interface to the underlying
> implementation
>
> > attributes(eg)
> $size
> [1] 4
>
> $id
> [1] "id_value"
>
> $class
> [1] "example"
> attr(,"package")
> [1] ".GlobalEnv"
>
> But probably you have a specific goal in mind, and this is too much
> information...
>
> Martin
>
> >
> > Thanks, Patrick
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel_at_r-project.org <mailto:R-devel_at_r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
>

-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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