debug

.github/workflows/R-CMD-check.yaml

@@ -11,9 +11,7 @@ name: R-CMD-check
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
-
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
     strategy:
       fail-fast: false
       matrix:
@@ -44,14 +42,27 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - name: Regenerate Rcpp exports
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libarmadillo-dev
+
+      - name: Install RcppArmadillo
+        run: |
+          install.packages("RcppArmadillo")
+        shell: Rscript {0}
+
+      - name: Check C++ compilation
         run: |
-          Rscript -e "Rcpp::compileAttributes()"
-          Rscript -e "devtools::document()"
+          Rcpp::compileAttributes()
+          devtools::document()
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          args: 'c("--no-build-vignettes", "--no-manual")'
 
       - name: Show testthat output
         if: always()

DESCRIPTION

@@ -10,13 +10,12 @@ Maintainer: Rafael Daníel Vias <[email protected]>
 Description: Fits a discharge rating curve based on the power-law and the generalized power-law from data on paired stage and discharge measurements in a given river using a Bayesian hierarchical model as described in Hrafnkelsson et al. (2020) <arXiv:2010.04769>.
 Depends: R (>= 3.5.0)
 License: MIT + file LICENSE
-LazyData: true
 RoxygenNote: 7.3.2
 Imports:
     ggplot2,
     grid,
     gridExtra,
-    Rcpp,
+    Rcpp (>= 0.11.0),
     rlang,
     scales
 Suggests:
@@ -30,5 +29,7 @@ URL: https://sor16.github.io/bdrc
 BugReports: https://github.com/sor16/bdrc/issues
 Encoding: UTF-8
 LinkingTo: 
-    Rcpp,
-    RcppArmadillo
+    Rcpp (>= 0.11.0),
+    RcppArmadillo (>= 0.2.35)
+LazyData: yes
+ByteCompile: TRUE

NAMESPACE

@@ -43,7 +43,7 @@ export(plm)
 export(plm0)
 export(spread_draws)
 export(tournament)
-importFrom(Rcpp,sourceCpp)
+exportPattern("^[[:alpha:]]+")
 importFrom(ggplot2,"%+replace%")
 importFrom(ggplot2,aes)
 importFrom(ggplot2,autoplot)

R/bdrc-package.R

@@ -1,5 +1,4 @@
 ## usethis namespace: start
-#' @importFrom Rcpp sourceCpp
 #' @useDynLib bdrc, .registration = TRUE
 ## usethis namespace: end
 NULL

src/Makevars

@@ -1,3 +1,2 @@
-CXX_STD = CXX11
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DR_NO_REMAP
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,4 +1,2 @@
-CXX_STD = CXX11
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DR_NO_REMAP
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
-USE_CXX14 = yes

src/cppFunctions.h

@@ -2,8 +2,9 @@
 #define CPP_FUNCTIONS_H
 
 #define _USE_MATH_DEFINES
-#include <cmath>
+
 #include <RcppArmadillo.h>
+#include <cmath>
 
 // Help function declarations
 arma::mat matMult(const arma::mat& A, const arma::mat& B);

src/gplm.cpp

@@ -5,14 +5,8 @@
 
 #include "cppFunctions.h"
 
-// [[Rcpp::depends(RcppArmadillo)]]
-#include <RcppArmadillo.h>
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
 using namespace Rcpp;
-using namespace arma;
+
 
 
 

src/gplm0.cpp

@@ -5,14 +5,8 @@
 
 #include "cppFunctions.h"
 
-// [[Rcpp::depends(RcppArmadillo)]]
-#include <RcppArmadillo.h>
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
 using namespace Rcpp;
-using namespace arma;
+
 
 
 

src/help_functions.cpp

@@ -5,14 +5,8 @@
 
 #include "cppFunctions.h"
 
-// [[Rcpp::depends(RcppArmadillo)]]
-#include <RcppArmadillo.h>
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
 using namespace Rcpp;
-using namespace arma;
+
 
 
 // [[Rcpp::export]]
@@ -59,9 +53,9 @@ arma::vec compute_w(const arma::mat& L, const arma::vec& y, const arma::mat& X,
 // [[Rcpp::export]]
 DataFrame get_MCMC_summary_cpp(const arma::mat& X, const Nullable<NumericVector>& h ) {
     int n = X.n_rows;
-    mat summary_dat(n, 3);
+    arma::mat summary_dat(n, 3);
     for(int i = 0; i < n; ++i) {
-        rowvec row = X.row(i);
+        arma::rowvec row = X.row(i);
         row = sort(row);
         int size = row.n_elem;
         summary_dat(i, 0) = row(std::floor(0.025 * (size - 1)));

src/plm.cpp

@@ -5,14 +5,8 @@
 
 #include "cppFunctions.h"
 
-// [[Rcpp::depends(RcppArmadillo)]]
-#include <RcppArmadillo.h>
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
 using namespace Rcpp;
-using namespace arma;
+
 
 
 

src/plm0.cpp

@@ -5,14 +5,8 @@
 
 #include "cppFunctions.h"
 
-// [[Rcpp::depends(RcppArmadillo)]]
-#include <RcppArmadillo.h>
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
 using namespace Rcpp;
-using namespace arma;
+