Re: [Rd] SEXPs and slots

From: Patrick Leyshock <ngkbr8es_at_gmail.com>
Date: Mon, 15 Nov 2010 12:20:19 -0800

Thanks Martin and Hadley, this is very helpful.

I should also add that I'm constantly reading the source code, but sometimes a response like this one can eliminate many, many hours of puzzlement. Much appreciated.

Patrick

On Mon, Nov 15, 2010 at 12:07 PM, Patrick Leyshock <pleyshock_at_gmail.com>wrote:

> Thanks Martin and Hadley, this is very helpful.
>
> I should also add that I'm constantly reading the source code, but
> sometimes a response like this one can eliminate many, many hours of
> puzzlement. Much appreciated.
>
> Patrick
>
>
> On Mon, Nov 15, 2010 at 10:01 AM, Martin Morgan <mtmorgan_at_fhcrc.org>wrote:
>
>> 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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