Re: [Rd] Dealing with R list objects in C/C++
Many thanks for the quick reply Martin, your code works as expected. Next I'd like to retrieve heterogeneous data from an SEXP object (let's just pretend it's the same type as the one what I'm constructing). I'm sure the relevant APIs are defined in Rinternals.h, do we have API documentations for this header file somewhere? @Dirk: thanks for your help too. I'm doing something very simple at the moment, so I prefer not to bring in Rinside/Rcpp if possible. Thanks again, Wayne -Original Message- From: Martin Morgan [mailto:mtmor...@fhcrc.org] Sent: Wednesday, January 26, 2011 10:04 PM To: Zhang, Wayne: IT (NYK) Cc: r-devel@r-project.org Subject: Re: [Rd] Dealing with R list objects in C/C++ On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote: Hi, I'd like to construct an R list object in C++, fill it with relevant data, and pass it to an R function which will return a different list object back. I have browsed through all the R manuals, and examples under tests/Embedding, but can't figure out the correct way. Below is my code snippet: #include Rinternals.h // Rf_initEmbeddedR and other setups already performed SEXP arg, ret; // this actually creates a pairlist. I can't find any API that creates a list PROTECT(arg = allocList(3)); Allocate a list of length 3 via SEXPTYPE VECSXP PROTECT(arg = allocVector(VECSXP, 3)); // I want the first element to be type integer, second double, and third a vector. INTEGER(arg)[0] = 1;// - runtime exception: INTEGER() can only be applied to a 'integer', not a 'pairlist' set the first element of the list to an integer vector of length 1, and assign a value SET_VECTOR_ELT(arg, 0, allocVector(INTSXP, 1)); INTEGER(VECTOR_ELT(arg, 0))[0] = 1 or more succinctly SET_VECTOR_ELT(arg, 0, ScalarInteger(1)); REAL(arg)[1] = 2.5; // control never reached here and the second element SET_VECTOR_ELT(arg, 1, ScalarReal(2.5)); VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4); and for the third allocate a REALSXP and then fill SET_VECTOR_ELT(arg, 2, allocVector(REALSXP, 4)); next lines should be ok as REAL(VECTOR_ELT(arg, 2))[0] = 10.0; or with less typing as double *x = REAL(VECTOR_ETL(arg, 2)); x[0] = 10.0; x[1] = 11.0; x[2] = 12.0; x[3] = 13.0; REAL(VECTOR_PTR(arg)[2])[0] = 10.0; REAL(VECTOR_PTR(arg)[2])[1] = 11.0; REAL(VECTOR_PTR(arg)[2])[2] = 12.0; REAL(VECTOR_PTR(arg)[2])[3] = 13.0; PROTECT(call = lang2(install(entryPoint.c_str()), arg)); not sure where entryPoint.c_str() is coming from, but PROTECT(call = lang2(install(fun), arg)); with some debate about whether install(fun) should be PROTECT'ed. ret = R_tryEval(call, R_GlobalEnv, errorOccurred); likely PROTECT(ret = ...) while checking errorOccurred, etc. Hope that helps, Martin I'll be grateful if you can point me to any online docs/samples. Thanks in advance, Wayne ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered off i! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Dealing with R list objects in C/C++
On 1/27/2011 1:03 PM, wayne.zh...@barclayscapital.com wrote: Many thanks for the quick reply Martin, your code works as expected. Next I'd like to retrieve heterogeneous data from an SEXP object (let's just pretend it's the same type as the one what I'm constructing). I'm sure the relevant APIs are defined in Rinternals.h, do we have API documentations for this header file somewhere? Hi Wayne -- Your best bet might be sections 5 and 6 of RShowDoc(R-exts) or the books Dirk mentioned; see also Rdefines.h. Martin @Dirk: thanks for your help too. I'm doing something very simple at the moment, so I prefer not to bring in Rinside/Rcpp if possible. Thanks again, Wayne -Original Message- From: Martin Morgan [mailto:mtmor...@fhcrc.org] Sent: Wednesday, January 26, 2011 10:04 PM To: Zhang, Wayne: IT (NYK) Cc: r-devel@r-project.org Subject: Re: [Rd] Dealing with R list objects in C/C++ On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote: Hi, I'd like to construct an R list object in C++, fill it with relevant data, and pass it to an R function which will return a different list object back. I have browsed through all the R manuals, and examples under tests/Embedding, but can't figure out the correct way. Below is my code snippet: #includeRinternals.h // Rf_initEmbeddedR and other setups already performed SEXP arg, ret; // this actually creates a pairlist. I can't find any API that creates a list PROTECT(arg = allocList(3)); Allocate a list of length 3 via SEXPTYPE VECSXP PROTECT(arg = allocVector(VECSXP, 3)); // I want the first element to be type integer, second double, and third a vector. INTEGER(arg)[0] = 1;//- runtime exception: INTEGER() can only be applied to a 'integer', not a 'pairlist' set the first element of the list to an integer vector of length 1, and assign a value SET_VECTOR_ELT(arg, 0, allocVector(INTSXP, 1)); INTEGER(VECTOR_ELT(arg, 0))[0] = 1 or more succinctly SET_VECTOR_ELT(arg, 0, ScalarInteger(1)); REAL(arg)[1] = 2.5; // control never reached here and the second element SET_VECTOR_ELT(arg, 1, ScalarReal(2.5)); VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4); and for the third allocate a REALSXP and then fill SET_VECTOR_ELT(arg, 2, allocVector(REALSXP, 4)); next lines should be ok as REAL(VECTOR_ELT(arg, 2))[0] = 10.0; or with less typing as double *x = REAL(VECTOR_ETL(arg, 2)); x[0] = 10.0; x[1] = 11.0; x[2] = 12.0; x[3] = 13.0; REAL(VECTOR_PTR(arg)[2])[0] = 10.0; REAL(VECTOR_PTR(arg)[2])[1] = 11.0; REAL(VECTOR_PTR(arg)[2])[2] = 12.0; REAL(VECTOR_PTR(arg)[2])[3] = 13.0; PROTECT(call = lang2(install(entryPoint.c_str()), arg)); not sure where entryPoint.c_str() is coming from, but PROTECT(call = lang2(install(fun), arg)); with some debate about whether install(fun) should be PROTECT'ed. ret = R_tryEval(call, R_GlobalEnv,errorOccurred); likely PROTECT(ret = ...) while checking errorOccurred, etc. Hope that helps, Martin I'll be grateful if you can point me to any online docs/samples. Thanks in advance, Wayne ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered o! ff i! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Dealing with R list objects in C/C++
Hi, I'd like to construct an R list object in C++, fill it with relevant data, and pass it to an R function which will return a different list object back. I have browsed through all the R manuals, and examples under tests/Embedding, but can't figure out the correct way. Below is my code snippet: #include Rinternals.h // Rf_initEmbeddedR and other setups already performed SEXP arg, ret; // this actually creates a pairlist. I can't find any API that creates a list PROTECT(arg = allocList(3)); // I want the first element to be type integer, second double, and third a vector. INTEGER(arg)[0] = 1;// - runtime exception: INTEGER() can only be applied to a 'integer', not a 'pairlist' REAL(arg)[1] = 2.5; // control never reached here VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4); REAL(VECTOR_PTR(arg)[2])[0] = 10.0; REAL(VECTOR_PTR(arg)[2])[1] = 11.0; REAL(VECTOR_PTR(arg)[2])[2] = 12.0; REAL(VECTOR_PTR(arg)[2])[3] = 13.0; PROTECT(call = lang2(install(entryPoint.c_str()), arg)); ret = R_tryEval(call, R_GlobalEnv, errorOccurred); I'll be grateful if you can point me to any online docs/samples. Thanks in advance, Wayne ___ This e-mail may contain information that is confidential, privileged or otherwise protected from disclosure. If you are not an intended recipient of this e-mail, do not duplicate or redistribute it by any means. Please delete it and any attachments and notify the sender that you have received it in error. Unless specifically indicated, this e-mail is not an offer to buy or sell or a solicitation to buy or sell any securities, investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Barclays. Any views or opinions presented are solely those of the author and do not necessarily represent those of Barclays. This e-mail is subject to terms available at the following link: www.barcap.com/emaildisclaimer. By messaging with Barclays you consent to the foregoing. Barclays Capital is the investment banking division of Barclays Bank PLC, a company registered in England (number 1026167) with its registered offi! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Dealing with R list objects in C/C++
Hi Wayne,
On 26 January 2011 at 17:56, wayne.zh...@barclayscapital.com wrote:
| Hi,
|
| I'd like to construct an R list object in C++, fill it with relevant data,
and pass it to an R function which will return a different list object back. I
have browsed through all the R manuals, and examples under tests/Embedding, but
can't figure out the correct way. Below is my code snippet:
|
| #include Rinternals.h
| // Rf_initEmbeddedR and other setups already performed
|
| SEXP arg, ret;
|
| // this actually creates a pairlist. I can't find any API that creates a
list
| PROTECT(arg = allocList(3));
|
| // I want the first element to be type integer, second double, and third a
vector.
| INTEGER(arg)[0] = 1;// - runtime exception: INTEGER() can
only be applied to a 'integer', not a 'pairlist'
| REAL(arg)[1] = 2.5; // control never reached here
|
| VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4);
| REAL(VECTOR_PTR(arg)[2])[0] = 10.0;
| REAL(VECTOR_PTR(arg)[2])[1] = 11.0;
| REAL(VECTOR_PTR(arg)[2])[2] = 12.0;
| REAL(VECTOR_PTR(arg)[2])[3] = 13.0;
|
| PROTECT(call = lang2(install(entryPoint.c_str()), arg));
|
| ret = R_tryEval(call, R_GlobalEnv, errorOccurred);
|
|
| I'll be grateful if you can point me to any online docs/samples.
This is a non-trivial problem when the use the C API provided by R. It is all
documented, but you need to study the 'Writing R Extensions' in some detail,
as well as maybe 'R Programming' by Gentleman and/or 'Software for Data
Analysis' by Chambers.
But there is another API you can use. It is provided by RInside (to embed R
inside C++) which uses Rcpp (for R and C++ integration). Install those two
packages from CRAN, and then drop the few lines below as a file, say,
wayne.cpp in the examples/standard/ directory of RInside. Saying 'make wayne'
will build an executable, using proper flags and linker options, and you can
run that:
edd@max:~/svn/rinside/pkg/inst/examples/standard$ make wayne
g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
-I/usr/local/lib/R/site-library/RInside/include -O3 -pipe -g -Wall
wayne.cpp -L/usr/lib64/R/lib -lR -lblas -llapack
-L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp
-Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib
-L/usr/local/lib/R/site-library/RInside/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib -o wayne
edd@max:~/svn/rinside/pkg/inst/examples/standard$ ./wayne
Showing list content:
L[0] 1
L[1] 2.5
L[2][0] 10
L[2][1] 11
Showing list content:
L[0] 42
L[1] 42
L[2][0] 10
L[2][1] 42
edd@max:~/svn/rinside/pkg/inst/examples/standard$
The code a list as you spec'ed with int, double and vector. The list is shown
on stdout, then passed to R, transformed by R and shown again at the C++ level.
Questions on RInside and Rcpp are welcome on the rcpp-devel list.
Hope this helps, Dirk
-
#include RInside.h// for the embedded R via RInside
void show(const Rcpp::List L) {
// this function is cumbersome as we haven't defined operators
std::cout Showing list content:\n;
std::cout L[0] Rcpp::asint(L[0]) std::endl;
std::cout L[1] Rcpp::asdouble(L[1]) std::endl;
Rcpp::IntegerVector v = Rcpp::asRcpp::IntegerVector(L[2]);
std::cout L[2][0] v[0] std::endl;
std::cout L[2][1] v[1] std::endl;
}
int main(int argc, char *argv[]) {
// create an embedded R instance
RInside R(argc, argv);
Rcpp::List mylist(3);
mylist[0] = 1;
mylist[1] = 2.5;
Rcpp::IntegerVector v(2); v[0] = 10; v[1] = 11; // with C++0x we could
assign directly
mylist[2] = v;
show(mylist);
R[myRlist] = mylist;
std::string r_code = myRlist[[1]] = 42; myRlist[[2]] = 42.0;
myRlist[[3]][2] = 42; myRlist;
Rcpp::List reslist = R.parseEval(r_code);
show(reslist);
exit(0);
}
-
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Dealing with R list objects in C/C++
On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote: Hi, I'd like to construct an R list object in C++, fill it with relevant data, and pass it to an R function which will return a different list object back. I have browsed through all the R manuals, and examples under tests/Embedding, but can't figure out the correct way. Below is my code snippet: #include Rinternals.h // Rf_initEmbeddedR and other setups already performed SEXP arg, ret; // this actually creates a pairlist. I can't find any API that creates a list PROTECT(arg = allocList(3)); Allocate a list of length 3 via SEXPTYPE VECSXP PROTECT(arg = allocVector(VECSXP, 3)); // I want the first element to be type integer, second double, and third a vector. INTEGER(arg)[0] = 1;// - runtime exception: INTEGER() can only be applied to a 'integer', not a 'pairlist' set the first element of the list to an integer vector of length 1, and assign a value SET_VECTOR_ELT(arg, 0, allocVector(INTSXP, 1)); INTEGER(VECTOR_ELT(arg, 0))[0] = 1 or more succinctly SET_VECTOR_ELT(arg, 0, ScalarInteger(1)); REAL(arg)[1] = 2.5; // control never reached here and the second element SET_VECTOR_ELT(arg, 1, ScalarReal(2.5)); VECTOR_PTR(arg)[2] = allocVector(REALSXP, 4); and for the third allocate a REALSXP and then fill SET_VECTOR_ELT(arg, 2, allocVector(REALSXP, 4)); next lines should be ok as REAL(VECTOR_ELT(arg, 2))[0] = 10.0; or with less typing as double *x = REAL(VECTOR_ETL(arg, 2)); x[0] = 10.0; x[1] = 11.0; x[2] = 12.0; x[3] = 13.0; REAL(VECTOR_PTR(arg)[2])[0] = 10.0; REAL(VECTOR_PTR(arg)[2])[1] = 11.0; REAL(VECTOR_PTR(arg)[2])[2] = 12.0; REAL(VECTOR_PTR(arg)[2])[3] = 13.0; PROTECT(call = lang2(install(entryPoint.c_str()), arg)); not sure where entryPoint.c_str() is coming from, but PROTECT(call = lang2(install(fun), arg)); with some debate about whether install(fun) should be PROTECT'ed. ret = R_tryEval(call, R_GlobalEnv, errorOccurred); likely PROTECT(ret = ...) while checking errorOccurred, etc. Hope that helps, Martin I'll be grateful if you can point me to any online docs/samples. Thanks in advance, Wayne ___ i! ce at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ [[alternative HTML version deleted]] __ R-devel@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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
