[Rd] SEXPs and slots

Mon Nov 15 19:01:47 CET 2010

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]]
>     >
>     > ______________________________________________
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> 
> 
>     --
>     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