attempt to fix R CMD CHECK (#59)

vandenman · web-flow · commit 1f13285f3492 · 2025-09-24T14:15:15.000+02:00
* attempt to fix R CMD CHECK

* try again

* add cleanup

* bugfix for &gt;2 groups
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,4 @@
 ^vignettes/introduction_cache
 ^doc$
 ^Meta$
+^\.vscode$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -21,7 +21,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       BUILD_VIGNETTE: "true"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -18,7 +18,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,5 @@ src/*.dll
 .DS_Store
 /doc/
 /Meta/
+src/Makevars
+src/Makevars.win
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,12 +30,11 @@ Imports:
 RdMacros: Rdpack
 LinkingTo: 
     Rcpp, 
-    RcppProgress, 
     RcppArmadillo, 
     RcppParallel, 
     dqrng, 
     BH
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends: 
     R (>= 3.5)
 LazyData: true
diff --git a/R/datasets.R b/R/datasets.R
@@ -38,7 +38,7 @@
 #'   \item{startle}{Feeling jumpy or easily startled?}
 #' }
 #'
-#' @source \url{http://psychosystems.org/wp-content/uploads/2014/10/Wenchuan.csv}
+#' @source \url{https://psychosystems.org/wp-content/uploads/2014/10/Wenchuan.csv}
 #'
 #' @docType data
 #' @keywords datasets
@@ -93,7 +93,7 @@ NULL
 #' }
 #'
 #' @source \insertCite{Silk_2019_ADHD;textual}{bgms}.
-#' Data retrieved from \url{https://doi.org/10.1371/journal.pone.0211053.s004}.
+#' Data retrieved from \doi{doi:10.1371/journal.pone.0211053.s004}.
 #' Licensed under the CC-BY 4.0: https://creativecommons.org/licenses/by/4.0/
 #'
 #' @docType data
diff --git a/cleanup b/cleanup
@@ -0,0 +1,4 @@
+#!/bin/sh
+# Remove generated Makevars files
+rm -f src/Makevars
+rm -f src/Makevars.win
diff --git a/configure b/configure
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+# Get flags from RcppParallel
+RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::CxxFlags())"`
+RCPP_PARALLEL_LIBS=`"${R_HOME}/bin/Rscript" -e "cat(RcppParallel::LdFlags())"`
+
+# Substitute into Makevars
+sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
+    -e "s|@RCPP_PARALLEL_LIBS@|${RCPP_PARALLEL_LIBS}|" \
+src/Makevars.in > src/Makevars
diff --git a/configure.win b/configure.win
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+RCPP_PARALLEL_CPPFLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppParallel::CxxFlags())"`
+RCPP_PARALLEL_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "cat(RcppParallel::LdFlags())"`
+
+# Substitute into Makevars.win
+sed -e "s|@RCPP_PARALLEL_CPPFLAGS@|${RCPP_PARALLEL_CPPFLAGS}|" \
+    -e "s|@RCPP_PARALLEL_LIBS@|${RCPP_PARALLEL_LIBS}|" \
+    src/Makevars.in > src/Makevars.win
diff --git a/man/ADHD.Rd b/man/ADHD.Rd
diff --git a/man/Wenchuan.Rd b/man/Wenchuan.Rd
diff --git a/src/Makevars b/src/Makevars
diff --git a/src/Makevars.in b/src/Makevars.in
@@ -0,0 +1,5 @@
+CXX_STD = CXX20
+
+PKG_CPPFLAGS = @RCPP_PARALLEL_CPPFLAGS@
+
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @RCPP_PARALLEL_LIBS@
diff --git a/src/Makevars.win b/src/Makevars.win
diff --git a/src/bgmCompare_helper.h b/src/bgmCompare_helper.h
@@ -86,7 +86,7 @@ inline void initialise_graph_bgmcompare(
       indicator(i,j) = indicator(j,i) = draw;
       if (!draw) {
         int row = pairwise_indices(i, j);
-        pairwise.row(row).cols(1, G-1) = 0.0;
+        pairwise(row, arma::span(1, G-1)).zeros();
       }
     }
   }
@@ -97,9 +97,7 @@ inline void initialise_graph_bgmcompare(
     if(!draw) {
       int start = main_indices(i,0);
       int end = main_indices(i,1);
-      for(int row = start; row < end; row++) {
-        main.row(row).cols(1, G-1) = 0.0;
-      }
+      main(arma::span(start, end), arma::span(1, G - 1)).zeros();
     }
   }
-};
+};
diff --git a/src/bgm_helper.cpp b/src/bgm_helper.cpp
@@ -33,7 +33,7 @@ arma::vec vectorize_main_effects_bgm (
   arma::vec main_effect_vector (num_parameters);
   int offset = 0;
 
-  for (int variable = 0; variable < main_effects.n_rows; variable++) {
+  for (int variable = 0; variable < static_cast<int>(main_effects.n_rows); variable++) {
     const int num_pars = is_ordinal_variable (variable) ? num_categories(variable) : 2;
     main_effect_vector.subvec (offset, offset + num_pars - 1) =
       main_effects.row (variable).cols (0, num_pars - 1).t ();
diff --git a/src/mcmc_adaptation.h b/src/mcmc_adaptation.h
@@ -174,7 +174,7 @@ struct WarmupSchedule {
   int current_window(int i) const {
     for (size_t k = 0; k < window_ends.size(); ++k)
       if (i < window_ends[k]) return static_cast<int>(k);
-      return -1;
+    return -1;
   }
 };
 
diff --git a/src/progress_manager.cpp b/src/progress_manager.cpp
diff --git a/src/progress_manager.h b/src/progress_manager.h
