I’m migrating this from a StackOverflow discussion , because I think it will be easier to have a discussion of what’s happening here. The issue is a package that has compiled code from both representations of Stan models and Rcpp functions. A minimally reproducible example can be found in my rcppstan …

I think I should have said to change OBJECTS = $(SOURCES:.stan=.o) init.o to OBJECTS = $(SOURCES:.stan=.o) RcppExports.o.

This introduces a new installation error: installing to /Users/jakethompson/R/rcppstan/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(dllfile) : …

That undefined symbol is meanC(Rcpp::Vector<14, Rcpp::PreserveStorage>), which I think is coming from the Rcpp stuff rather than the Stan stuff. Can you successfully compile and load just the Rcpp stuff?

Yes, this was my mistake. I needed to regenerate src/rcppstan.so. Now the package builds correctly. I’ve now reached what I think is the last hurdle. The package builds and installs fine, but when attached with library(rcppstan) throws this error: Error: package or namespace load failed for ‘rcppst…

[image] wjakethompson: Do you know how stop the automatic over ride of src/RcppExports.cpp ? Or is this a better question for the Rcpp devs? Yeah. Those Stan things are Rcpp modules. So the question for the Rcpp devs is how to have Rcpp modules and Rcpp non-modules in the same package?

It appears I was mistaken earlier. src/rcppstan.so was generating correctly originally. In an effort to compile only the Rcpp functions, I removed all of the Stan infrastructure, and built the package. This worked fine, with no errors as expected. Then I added back in the Stan files. When rebuilding…

Those Makevars files tell R what needs to get compiled and how. It seems that the procedures for making Stan packages and Rcpp packages are interfering with each other.

Yeah, I think the easiest and probably best solution for now anyway is to split off the Stan functionality into a separate package. This way those processes won’t interfere with each other. Thanks for all of you help!

Compiled code from Stan and Rcpp

General

bgoodri June 5, 2018, 6:16pm 7

It is possible that you can take the module loading line out of .onLoad() in zzz.R and not load it until right before you call rstan::sampling.

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Compiled code from Stan and Rcpp

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