How to build a package with RcppArmadillo? - r

Question

I wish to build a package, but I write part of it using RcppArmadillo and now I am suffering the consequences. I am using roxygen2 and devtools to help me with DESCRIPTION and NAMESPACE. I am coding in R / Ubuntu. In the DESCRIPTION I include two lines to load the packages:
Depends: R (>= 3.4.4), MASS (>= 7.3-49), Rcpp (>= 1.0.5), RcppArmadillo (>= 0.9.900.2.0)
LinkingTo: Rcpp, RcppArmadillo
and in the folder /src I write a script name loss_function.cpp, inside it there is:
> // [[Rcpp::depends(RcppArmadillo)]]
>
> #include <RcppArmadillo.h>
>
> using namespace Rcpp;
>
> //' Check function.
> //'
> //' #param x vector
> //' #param tau percentile
> //' #return y new vector
> // [[Rcpp::export(rho_koenker)]]
> arma::vec rho_koenker(arma::vec x, double tau){
> int n = x.n_elem;
> arma::vec y(n);
> for(int i = 0; i < n; ++i){
> if(x(i)<0){
> y(i) = x(i)*(tau-1);
> } else {
> y(i) = x(i)*tau;
> }
> }
> return(y);
> }
>
> //' Quantile regression loss function
> //'
> //' #param beta parameter
> //' #param x matrix
> //' #param y vector
> //' #param tau percentile
> //' #param N total number of observations
> //' #param d beta's length
> //' #return eta numeric
> // [[Rcpp::export(loss_qr)]]
> double loss_qr(arma::vec beta, arma::mat x, arma::vec y, double tau, int N, int d){
> double eta = 0;
> arma::vec res(N);
> arma::vec rho(N);
> res = y - (x * beta);
> rho = rho_koenker(res,tau);
> eta = accu(rho);
> return(eta);
> }
When I check the package (build -> check package) there comes an error msg:
Error in .Call("_pqfe_loss_qr", PACKAGE = "pqfe", beta, x, y, tau, N, :
"_pqfe_loss_qr" not available for .Call() for package "pqfe"
Calls: qr ... optim_qr -> <Anonymous> -> <Anonymous> -> fn -> .Call
Execution halted
Warning message:
Can't find generic `sew` in package knitr to register S3 method.
This message is only shown to developers using devtools.
Do you need to update knitr to the latest version?

Answer 1

As alluded in the comment above, it is not clear where you error would lie here with RcppArmadillo. So I
invoked RcppArmadillo.package.skeleton() (via the helper command kitten.r from littler relying on pkgKitten but those are details)
added in src/loss_function.cpp based on what you had
added one missing #export tag to you doxygen/roxygen to also have the R documentation created
called Rcpp::compileAttributes() (via helper compAttr.r from `littler) to have the interal glue code generated / updated
called roxygenize() (via helper roxy.r from littler) to have help files created
called R CMD build (directly, or via helper build.r from littler)
ran R CMD check (directly, or via helper rcc.r from littler)
and it all works:
edd#rob:~/git/stackoverflow/73405262(master)$ R CMD build soDemo
* checking for file ‘soDemo/DESCRIPTION’ ... OK
* preparing ‘soDemo’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘soDemo_1.0.tar.gz’
edd#rob:~/git/stackoverflow/73405262(master)$
and checks nicely too
edd#rob:~/git/stackoverflow/73405262(master)$ R CMD check soDemo_1.0.tar.gz
* using log directory ‘/home/edd/git/stackoverflow/73405262/soDemo.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘soDemo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soDemo’ version ‘1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘soDemo’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: OK
edd#rob:~/git/stackoverflow/73405262(master)$
I put the tarball here if you want to take it from there.