Rcpp functions undefined when used alongside Stan - r

Question

I have an R package that uses Rcpp for some internal functions. These functions are not exported for the user to access directly (see minimally reproducible example in the rcpptest repository).
I am now attempting to add Stan code to the src/ directory to be compiled when the package is installed (reproducible example in the rcppstan repository). However, when I modify the package to work with Stan, I get the following error in R CMD CHECK:
#> ❯ checking R code for possible problems ... NOTE
#> meanC: no visible binding for global variable ‘_rcppstan_meanC’
#> Undefined global functions or variables:
#> _rcppstan_meanC
And indeed, when I try to call the R function that uses the meanC function, I get an error saying Error in meanC(x) : object '_rcppstan_meanC' not found.
From what I can tell, here is what is changing when I modify the package to work with rstan, and thus the likely cause.
When only using Rcpp, the following is in the src/RcppExports.cpp:
static const R_CallMethodDef CallEntries[] = {
{"_rcpptest_timesTwo", (DL_FUNC) &_rcpptest_timesTwo, 1},
{NULL, NULL, 0}
};
RcppExport void R_init_rcpptest(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
When Stan is incorporated, that code is no longer generated in the src/RcppExports.cpp file. Instead, it appears that this is being handles by the src/init.cpp file created by the rstantools package. The relevant chunk from that file is here:
static const R_CallMethodDef CallEntries[] = {
{NULL, NULL, 0}
};
void attribute_visible R_init_rcppstan(DllInfo *dll) {
// next line is necessary to avoid a NOTE from R CMD check
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, TRUE); // necessary for .onLoad() to work
}
Why does the code in src/init.cpp make the Rcpp functions undefined? Conversely, is there a way to edit src/init.cpp so that the Stan models are able to compile and be accessed correctly, while still allowing the Rcpp functions to be defined?

Answer 1

The init.cpp takes of registering methods and Makevars inhibits compilation of the cpp files. With the following changes in Makevars (and Makevars.win) I got it to compile:
diff --git a/src/Makevars b/src/Makevars
index 7aedc5b..3ea312e 100644
--- a/src/Makevars
+++ b/src/Makevars
## -1,8 +1,9 ##
STANHEADERS_SRC = `"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`
PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error
-SOURCES = $(wildcard stan_files/*.stan)
-OBJECTS = $(SOURCES:.stan=.o) init.o
+CPP_SOURCES = $(wildcard *.cpp)
+STAN_SOURCES = $(wildcard stan_files/*.stan)
+OBJECTS = $(STAN_SOURCES:.stan=.o) $(CPP_SOURCES:.cpp=.o)
all: $(SHLIB)
#if test -e "/usr/bin/install_name_tool" && test -e "/usr/local/clang4/lib/libc++.1.dylib" && test -e "/usr/lib/libc++.1.dylib"; then /usr/bin/install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib $(SHLIB); fi
After calling Rcpp::compileAttributes() the method registration was again present in RcppExports.cpp. When I tried R CMD INSTALL, I got an error from .onLoad(), c.f. https://github.com/stan-dev/rstanarm/issues/190. Using the workaround from there, i.e. R CMD INSTALL --preclean solved the issue first, but was not reliable. What solved the issue for me was to change
R_useDynamicSymbols(dll, FALSE);
into
R_useDynamicSymbols(dll, TRUE);
in RcppExports.cpp. That is of course problematic, since that file might be overwritten, in particular when RStudio/devtools is used. A rather hacky solution would be to add
RcppExports.o: patch
patch:
sed -i 's/R_useDynamicSymbols(dll, FALSE)/R_useDynamicSymbols(dll, TRUE)/' RcppExports.cpp
.phony: all clean patch
in the Makevars(.win). But in the end the problem seems to be that C++ code for Rcpp modules is generated during package installation in a subdirectory of src. Therefore Rcpp::compileAttributes() cannot include the corresponding methofs in the list of registered methods. I do not see a good solution for that.
Now the package builds, checks and installs with two NOTEs:
N checking installed package size
installed size is 7.8Mb
sub-directories of 1Mb or more:
libs 7.7Mb
N checking for GNU extensions in Makefiles
GNU make is a SystemRequirements.