[R-pkg-devel] moving from C to C++ with Rcpp in R package

[THIOULOUSE JEAN]

Thank you Ivan and Dirk for your messages. I tried to follow your advice (modifying the src/init.c file by hand to add the things from the C++ function), but the function R_init_ade4 cannot be defined in both init.c and RcppExports.cpp. So I still have the same problem ("object '_ade4_RVrandtestCpp' not found").

As suggested by Ivan Krylov, I have created a new branch of the ade4 package (called ade4-Rcpp on github: https://github.com/sdray/ade4/tree/ade4-Rcpp) with the modifications listed here.

I am also cc-ing this message to rcpp-devel that may be more suitable for followups.

Thank you again for your help,
Jean


> Le 1 juin 2022 à 22:18, Dirk Eddelbuettel <edd using debian.org> a écrit :
> 
> 
> On 1 June 2022 at 11:03, THIOULOUSE JEAN wrote:
> | Hello
> | 
> | I need some help to add C++ functions using Rcpp to the ade4 package.
> | 
> | The ade4 package (on CRAN) already contains many C functions, mainly to perform randomization tests, and we would like to replace some of these functions by C++ ones using Rcpp, as well as add more new C++ functions, using also Rcpp.
> | 
> | To start with, I have only one C++ function and one R wrapper function, named respectively RV.randtest and RVrandtestCpp. Both functions work fine, using sourceCpp("RVrandtestCpp.cpp") and calling it with RV.randtest in R from the command line, and I also checked that the RcppExamples package compiles without problem with my configuration. Everything is available in https://github.com/thioulouse/RVrandtest
> | 
> | Now, I want to integrate these two functions in the ade4 package, so I have done the following things:
> | 
> | - added Rcpp and RcppArmadillo to the Imports field in the DESCRIPTION file
> | - added the LinkingTo field, with Rcpp and RcppArmadillo in the DESCRIPTION file
> | - added importFrom("Rcpp", "sourceCpp") in the NAMESPACE file
> | - added export("RV.randtest") and export("RVrandtestCpp") in the NAMESPACE file
> | - added RV.randtest.Rd in the man directory and \alias{RVrandtestCpp} in ade4-internal.Rd
> | - added RV.randtest.R in the R directory
> | - added RVrandtestCpp.cpp in the src directory
> | 
> | Then I used the Rcpp compileAttributes() function to add:
> | 
> | - RcppExports.cpp in the src directory
> | - RcppExports.R in the R directory
> | 
> | But when I check the modified ade4 package (with R CMD BUILD / R CMD CHECK), I get the following notes:
> | 
> | * checking R code for possible problems ... NOTE
> | RVrandtestCpp: no visible binding for global variable
> |   ‘_ade4_RVrandtestCpp’
> | Undefined global functions or variables:
> |   _ade4_RVrandtestCpp
> | 
> | And when running the examples I get the following error:
> | 
> | > rv1 <- RV.randtest(pca1$tab, pca2$tab, 99)
> | Error in RVrandtestCpp(X, Y, nrepet) : 
> |   object '_ade4_RVrandtestCpp' not found
> | Calls: RV.randtest -> RVrandtestCpp
> | Execution halted
> | 
> | So I am probably missing something, and I have the following questions:
> | 
> | Do I have to modify the init.c file in the src directory ? It contains the reference to all the C functions called in the ade4 package, but not the C++ function from Rcpp. Should I add it here ? I tried to do it, with no luck.
> | 
> | The NAMESPACE file contains this first line: 
> | useDynLib(ade4, .registration = TRUE, .fixes = "C_")
> | The .fixes argument is related to C function calls. Can this raise a problem for calling C++ functions ?
> | 
> | Why is the _ade4_RVrandtestCpp function (defined by compileAttributes() in RcppExports.cpp) not visible in RVrandtestCpp and not found at runtime ?
> 
> You most likely have an issue with the code commonly placed in src/init.c
> which registers entry points.
> 
> Rcpp is rather good at autogenerating it for more standard packages
> containing only C++ code.  Mixing C and C++ code is not something the package
> is that well set up for.  I think I fought the same issue in the past on
> packages that transitioned, or just added a C++ file or two. I don't think
> there is a great solution.  I would suggest you
> - use the init.c you have from the existing package
> - create a new one-off package with the C++ functions you want to use 
> - manually carry this over to your existing init.c
> 
> I would generally recommend starting with Rcpp.package.skeleton("testpackage")
> (or a similar name) and try to move your package to a similar structure. The
> 'all files in one directory' you have in https://github.com/thioulouse/RVrandtest
> is not what R prefers.
> 
> Follow-up may be more suitable for the rcpp-devel list.  This list here is
> general interest, your question is a bit more specific to ins and outs of
> just one package.
> 
> Best, Dirk
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org