How to use a user-defined data C structure into an R package - r

Question

This minimal example compiles when I "source" the file:
/*
read_header.c
*/
#include <stdio.h>
#include <stdlib.h>
#include <RcppCommon.h>
typedef struct {
int my_data;
} MY_HEADER_INFO;
namespace Rcpp {
template <> SEXP wrap(const MY_HEADER_INFO& x);
}
#include <Rcpp.h>
namespace Rcpp {
template <>
SEXP wrap(const MY_HEADER_INFO& x) {
std::vector<std::string> names;
std::vector<SEXP> elements(1);
// do something with the elements and names
names.push_back("my_data");
elements[0] = Rcpp::wrap( x.my_data );
};
}
//' #export
// [[Rcpp::export]]
MY_HEADER_INFO read_header() {
MY_HEADER_INFO *header;
header = (MY_HEADER_INFO*)malloc(sizeof(MY_HEADER_INFO));
memset(header, 0, sizeof(MY_HEADER_INFO));
return *header;
}
When I try to build it in RStudio into a package (CMD + SHIFT + B), I get the following, long, error message, that clearly lists the problem is my user-defined return structure, MY_HEADER_INFO:
DESCRIPTION
Package: myPackage
Type: Package
Title: What the Package Does (Title Case)
Version: 0.1.0
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
Imports:
Rcpp
Suggests:
knitr,
rmarkdown,
testthat
VignetteBuilder: knitr
LinkingTo:
Rcpp
NAMESPACE
# Generated by roxygen2: do not edit by hand
export(read_header)
I receive the following error:
==> Rcpp::compileAttributes()
* Updated src/RcppExports.cpp
* Updated R/RcppExports.R
==> devtools::document(roclets = c('rd', 'collate', 'namespace'))
Updating myPackage documentation
Loading myPackage
Re-compiling myPackage
─ installing *source* package ‘myPackage’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:9:1: error: unknown type name 'MY_HEADER_INFO'
MY_HEADER_INFO read_header();
^
1 error generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘myPackage’
─ removing ‘/private/var/folders/gl/jvj9b0xn34lgq6_h9370p8q80000gn/T/RtmpLKsw0o/devtools_install_1f333d54be59/myPackage’
Error: System command 'R' failed, exit status: 1, stdout + stderr:
E> * installing *source* package ‘myPackage’ ...
E> ** using staged installation
E> ** libs
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
E> RcppExports.cpp:9:1: error: unknown type name 'MY_HEADER_INFO'
E> MY_HEADER_INFO read_header();
E> ^
E> 1 error generated.
E> make: *** [RcppExports.o] Error 1
E> ERROR: compilation failed for package ‘myPackage’
E> * removing ‘/private/var/folders/gl/jvj9b0xn34lgq6_h9370p8q80000gn/T/RtmpLKsw0o/devtools_install_1f333d54be59/myPackage’
Stack trace:
1. base:::suppressPackageStartupMessages({ ...
2. base:::withCallingHandlers(expr, packageStartupMessage = function(c) tryInv ...
3. devtools::document(roclets = c("rd", "collate", "namespace"))
4. withr::with_envvar(r_env_vars(), roxygen2::roxygenise(pkg$path, ...
5. base:::force(code)
6. roxygen2::roxygenise(pkg$path, roclets, load_code = load_code)
7. roxygen2:::load_code(base_path)
8. pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
9. pkgbuild::compile_dll(path, quiet = quiet)
10. withr::with_makevars(compiler_flags(TRUE), assignment = "+=", ...
11. withr:::with_envvar(c(R_MAKEVARS_USER = makevars_file), { ...
12. base:::force(code)
13. base:::force(code)
14. pkgbuild:::install_min(path, dest = install_dir, components = "libs", ...
15. pkgbuild:::rcmd_build_tools("INSTALL", c(path, paste("--library=", ...
16. pkgbuild:::with_build_tools(callr::rcmd_safe(..., env = env, ...
17. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...
18. callr:::run_r(options)
19. base:::with(options, with_envvar(env, do.call(processx::run, ...
20. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
21. base:::eval(substitute(expr), data, enclos = parent.frame())
22. base:::eval(substitute(expr), data, enclos = parent.frame())
23. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
24. base:::force(code)
25. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
26. (function (command = NULL, args = character(), error_on_status = TRUE, ...
27. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'R' failed, exit status: 1, stdout + stderr:
E> * installing *source* package ‘myPackage’ ...
E> ** using staged installation
E> ** libs
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
E> RcppExports.cpp:9:1: error: unknown type name 'MY_HEADER_INFO'
E> MY_HEADER_INFO read_header();
E> ^
E> 1 error generated.
E> make: *** [RcppExports.o] Error 1
E> ERROR: compilation failed for package ‘myPackage’
E> * removing ‘/private/var/folders/gl/jvj9b0xn34lgq6_h9370p8q80000gn/T/RtmpLKsw0o/devtools_install_1f333d54be59/myPackage’
Execution halted
Exited with status 1.
The following is written to Rcpp_exports:
// Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <Rcpp.h>
using namespace Rcpp;
// read_header
MY_HEADER_INFO read_header();
RcppExport SEXP _myPackage_read_header() {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
rcpp_result_gen = Rcpp::wrap(read_header());
return rcpp_result_gen;
END_RCPP
}
static const R_CallMethodDef CallEntries[] = {
{"_myPackage_read_header", (DL_FUNC) &_myPackage_read_header, 0},
{NULL, NULL, 0}
};
RcppExport void R_init_myPackage(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
If I try to modify this file, however, it all gets written over when I call CMD+SHIFT+B.
Other C programs I've written for this same package that return standard data types (e.g., "std::vector") compile without a problem, both when I "source" the code in the Console and when I build them into a package.
I have read through the Rcpp documentation and related vignettes (and even bought Dirk's book!), but I cannot find how to tell the package builder where the definition of MY_HEADER_INFO is located. How do I tell the package compiler where the definition of this file is located?
Thanks!

Answer 1

That look like another instance of a not-entirely-uncommon problem for which we do have a wonderfully simple answer that is somewho less known than it should be.
In short, for a package <pkg> (where <pkg> is an alias for your package name, with lower or undercase as you please. and obviously no < or >) please such struct (or in the C++ case class) or typedef or ... definitions into a file inst/include/<pkg>_types.h (replacing <pkg> with your package name).
If such a file exists, it is automagically included by RcppExports.cpp and you are good to go.
Details are in the Rcpp Attributes vignette, and a few related forms are allowed as well:
src/<pkg>_types.h
src/<pkg>_types.hpp
inst/include/<pkg>_types.h
inst/include/<pkg>_types.hpp
inst/include/<pkg>.h
but inst/include/<pkg>_types.h may be the most commonly used one. One example of using it via src/ is src/RSQLite_types.h. On the other hand, an example of using it in inst/include/ is inst/include/RcppQuantuccia_types.h and another, much larger one in inst/include/RcppGSL_types.h.