Fix CRAN check issues. Update version number. Re-generate documentati…

…on. Added cran-check github action to test for various configurations

.Rbuildignore

@@ -12,4 +12,5 @@
 ^\.github$
 ^\.log$
 ^CHANGELOG\.md$
-^cran-comments\.md$
+^cran-comments\.md$
+^llvm/

.github/workflows/cran-check.yml

@@ -8,31 +8,102 @@ permissions:
   contents: read
 
 jobs:
-  cran-check: 
-    runs-on: ubuntu-latest
-    env:
-      _R_CHECK_DONTTEST_EXAMPLES_: false
+  cran-check:
+    strategy:
+      fail-fast: false 
+      matrix:
+        include: [
+          {os: "ubuntu-latest", r: "release", compiler_version: 15},
+          {os: "ubuntu-latest", r: "devel", compiler_version: 15},
+          {os: "windows-latest", r: "release", compiler_version: 15},
+          {os: "windows-latest", r: "devel", compiler_version: 15},
+          {os: "macos-latest", r: "release", compiler_version: 15},
+          {os: "macos-latest", r: "devel", compiler_version: 15},
+          {os: "macos-latest", r: "release", compiler_version: 14},
+        ]
+        # os: [ubuntu-latest]
+        # r: ['release']
+        # compiler: ['clang']
+        # compiler_version: [14, 17]
+    runs-on: ${{matrix.os}}
+    name: ${{ matrix.os }}_${{ matrix.r}}
     steps:
       - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
+        with:
+            r-version: ${{matrix.r}}
       - uses: awalsh128/cache-apt-pkgs-action@latest
+        if: runner.os == 'Linux'
         with:
-          packages: cmake cmake-data dh-elpa-helper libcmark-gfm-extensions0.29.0.gfm.3 libcmark-gfm0.29.0.gfm.3 libcurl4-openssl-dev libjsoncpp25 librhash0 pandoc pandoc-data
+          packages: | 
+            cmake cmake-data gsl dh-elpa-helper libcmark-gfm-extensions0.29.0.gfm.3 
+            libcmark-gfm0.29.0.gfm.3 libcurl4-openssl-dev libjsoncpp25 librhash0 
+            pandoc pandoc-data texlive-latex-base texlive-latex-recommended 
+            texlive-fonts-recommended
           version: 1.0
-      - name: Restore R package cache
+      - name: Restore R package cache (Linux)
+        if: runner.os == 'Linux'
         id: cache-packages
         uses: actions/cache@v4
         with:
           key: r-${{ hashFiles('DESCRIPTION') }}
           path: ${{ env.R_LIBS_USER }}
+      - name: Install GSL (macOS)
+        if: runner.os == 'macOs'
+        run: |
+          brew install gsl openssl
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck, any::roxygen2
           needs: check
-      - name: Document
-        run: roxygen2::roxygenise()
-        shell: Rscript {0}
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Setup compiler
+        if: runner.os == 'macOs'
+        uses: KyleMayes/install-llvm-action@v2
+        with:
+          version: ${{matrix.compiler_version}}
+          env: true
+          directory: ".."
+      - name: Setup Xcode
+        if: runner.os == 'macOs'
+        uses: maxim-lobanov/setup-xcode@v1
         with:
-          args: 'c("--no-manual", "--as-cran")'
-          error-on: '"error"'
+          xcode-version: latest
+      - name: Build and Check ToxicR
+        if: runner.os != 'Windows'
+        run: |
+          R CMD build .
+          file config.log
+          cat config.log
+          r_output=$(R CMD build .)
+          echo "$r_output"
+          package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p") 
+          echo "$package_name"
+          R CMD check --as-cran --no-manual $package_name
+          file ToxicR.Rcheck/00install.log
+          file ToxicR/ToxicR.Rcheck/00install.log
+          cat ToxicR.Rcheck/00install.log
+          cat ToxicR.Rcheck/00check.log
+        shell: bash
+        working-directory: "."
+      - name: Build and Check ToxicR
+        if: runner.os == 'Windows'
+        run: |
+          r_output=$(R CMD build .)
+          echo "$r_output"
+          package_name=$(echo "$r_output" | sed -n "s/.*building '\([^']*\.tar\.gz\)'.*/\1/p")
+          echo "$package_name"
+          R CMD check --as-cran --no-manual $package_name
+          file ToxicR.Rcheck/00install.log
+          file ToxicR/ToxicR.Rcheck/00install.log
+          cat ToxicR.Rcheck/00install.log
+          cat ToxicR.Rcheck/00check.log
+        shell: bash
+        working-directory: "."
+      # - name: Show testthat output
+      #   if: always()
+      #   run: |
+      #     echo ::group::Show testthat output
+      #     find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+      #     echo ::endgroup::
+      #   shell: bash
+      #   working-directory: "."

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ToxicR
 Type: Package
 Title: Analyzing Toxicology Dose-Response Data
-Version: 23.10.1.1.3
-Date: 2024-04-12
+Version: 23.10.1.2.0
+Date: 2024-05-17
 Authors@R: 
     c(
     person(given = "Matt",
@@ -18,8 +18,7 @@ Authors@R:
            role = "ctb"),
     person(given = "Shail",
            family = "Choksi",
-	   role = "ctb",
-	   comment = "Setup github actions for automated tests and builds."),
+	   role = "ctb"),
     person(given = "Brian",
            family = "Kidd",
 	   role = "ctb"),
@@ -89,6 +88,8 @@ Packaged: 2024-04-12 20:00:54 UTC; shail.choksi
 Author: Matt Wheeler [aut, cre] (<https://orcid.org/0000-0002-8242-2391>),
   Sooyeong Lim [aut],
   Eric Wimberly [ctb],
+  Shail Choksi [ctb],
+  Brian Kidd [ctb],
   Keith Shockley [com],
   Jennifer Fostel [com],
   Lonlong Yang [ctb] (Modfied Cochran-Armitage test.),

R/MAdensity_plot.R

@@ -15,7 +15,7 @@
 #' model <- ma_continuous_fit(doses, y,
 #'   fit_type = "mcmc", BMR_TYPE = "sd", BMR = 1
 #' )
-#' MAdensity_plot(model)
+#' try(MAdensity_plot(model))
 #' }
 #' @export
 MAdensity_plot <- function(A) {

R/opening_messages.R

@@ -25,7 +25,7 @@
     | |/ _ \\ \\/ / |/ __|  _  /
     | | (_) >  <| | (__| | \\ \\
     |_|\\___/_/\\_\\_|\\___|_|  \\_\\
-                           23.10.1.1.3
+                           23.10.1.2.0
     ___
     | |
     / \\                   ____()()

R/update_ToxicR.R

@@ -142,6 +142,10 @@ update_ToxicR <- function(force = TRUE, upgrade_other_pkg = FALSE, confirm = TRU
 #' @return there will be no output from this function. Rather, packages
 #' given as inputs to the function will be installed, loaded, and attached.
 #'
+#' @examples
+#' \dontrun{
+#' try(prep("data.table"))
+#' }
 prep <- function(..., pkg_names_as_object = FALSE, silent_if_successful = FALSE, silent_load_pkgs = FALSE) {
     arg_list <- as.list(match.call(expand.dots = FALSE))[["..."]]
     if ("..." %in% names(arg_list)) {

src/Makevars.in

@@ -1,8 +1,6 @@
-PKG_CXXFLAGS=  -I./code_base -I./include @OPENMP@ @NLOPT_CPPFLAGS@ @GSL_CPPFLAGS@ -DR_COMPILATION -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -DEIGEN_WARNINGS_DISABLED
+PKG_CXXFLAGS=  -I./code_base -I./include @OPENMP@ @NLOPT_CPPFLAGS@ @GSL_CPPFLAGS@ -DR_COMPILATION
 PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @NLOPT_LIBS@  @GSL_LIBS@ @OPENMP@
-CXX14FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
-CXX11FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
-
+# CXXFLAGS+=-Wno-ignored-attributes -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
 # Include all C++ files in src/ and its subdirectories
 SOURCES=@SRC_SOURCES@ @SUBDIR_SOURCES@
 

src/Makevars.ucrt

@@ -1,7 +1,7 @@
-PKG_CXXFLAGS=  -I./code_base -I./include $(SHLIB_OPENMP_CXXFLAGS) -I$(R_TOOLS_SOFT)/include/nlopt -I$(R_TOOLS_SOFT)/include/gsl -DR_COMPILATION -ftree-vectorize -Os -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -DEIGEN_WARNINGS_DISABLED
-PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -lgsl -lgslcblas -lnlopt
-# CXX14FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
-# CXX11FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
+PKG_CXXFLAGS+=-I./code_base -I./include $(SHLIB_OPENMP_CXXFLAGS) -I$(R_TOOLS_SOFT)/include/nlopt -I$(R_TOOLS_SOFT)/include/gsl -DR_COMPILATION -ftree-vectorize -Os
+PKG_LIBS+=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -lgsl -lgslcblas -lnlopt
+# CXXFLAGS+=-Wno-ignored-attributes -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+
 
 POLYK        = $(wildcard polyK/*.cpp)
 MAIN         = $(wildcard *.cpp)

src/Makevars.win

@@ -1,8 +1,8 @@
-PKG_CPPFLAGS= -I../windows/gsl-2.7/include -I../windows/nlopt-2.7.1/include  -I./ -I./code_base  -I./include -DR_COMPILATION -ftree-vectorize -Os -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -DEIGEN_WARNINGS_DISABLED
-PKG_LIBS= -L../windows/nlopt-2.7.1/lib${R_ARCH}${CRT}  -L../windows/gsl-2.7/lib${R_ARCH}${CRT} -lgsl -lgslcblas -lnlopt
+PKG_CPPFLAGS+=-I../windows/gsl-2.7/include -I../windows/nlopt-2.7.1/include  -I./ -I./code_base  -I./include -DR_COMPILATION -ftree-vectorize -Os 
+PKG_LIBS+=-L../windows/nlopt-2.7.1/lib${R_ARCH}${CRT}  -L../windows/gsl-2.7/lib${R_ARCH}${CRT} -lgsl -lgslcblas -lnlopt
+
+# CXXFLAGS+=-Wno-ignored-attributes -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
 
-# CXX14FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
-# CXX11FLAGS= -Wno-ignored-attributes -Wno-sign-compare -Wno-unused -Wno-builtin-macro-redefined
 
 POLYK        = $(wildcard polyK/*.cpp)
 MAIN         = $(wildcard *.cpp)

src/code_base/DichGammaBMD_NC.cpp

@@ -2,57 +2,62 @@
 
 #ifdef R_COMPILATION
 // necessary things to run in R
-#include <RcppGSL.h>
+#ifdef ToxicR_DEBUG
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-attributes"
+#include <RcppEigen.h>
+#pragma GCC diagnostic pop
+#else
 #include <RcppEigen.h>
+#endif
+#include <RcppGSL.h>
 #else
 #include <Eigen/Dense>
 #endif
 
+#include <gsl/gsl_blas.h>
+#include <gsl/gsl_cdf.h>
+#include <gsl/gsl_ieee_utils.h>
+#include <gsl/gsl_integration.h>
+#include <gsl/gsl_linalg.h>
 #include <gsl/gsl_math.h>
+#include <gsl/gsl_matrix.h>
 #include <gsl/gsl_randist.h>
 #include <gsl/gsl_rng.h>
 #include <gsl/gsl_test.h>
-#include <gsl/gsl_ieee_utils.h>
-#include <gsl/gsl_integration.h>
 #include <gsl/gsl_vector.h>
-#include <gsl/gsl_matrix.h>
-#include <gsl/gsl_blas.h>
-#include <gsl/gsl_linalg.h>
-#include <gsl/gsl_cdf.h>
 
-double GAMMA_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void *data)
-{
-	log_gamma_inequality *M = (log_gamma_inequality *)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool geq = M->geq;
-
-	double g = GAMMA_G(theta(0, 0));
-	double a = GAMMA_A(theta(1, 0));
-	double Z = GAMMA_EXTRA_Z(g, a, BMR); // note BMD is a placeholder
-	Z = Z / BMD;
-	double rV = 0.0;
-	rV = (geq) ? inequality - Z : Z - inequality;
-	return rV;
+double GAMMA_BMD_EXTRA_NC_INEQUALITY(Eigen::MatrixXd theta, void *data) {
+  log_gamma_inequality *M = (log_gamma_inequality *)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
+
+  double g = GAMMA_G(theta(0, 0));
+  double a = GAMMA_A(theta(1, 0));
+  double Z = GAMMA_EXTRA_Z(g, a, BMR); // note BMD is a placeholder
+  Z = Z / BMD;
+  double rV = 0.0;
+  rV = (geq) ? inequality - Z : Z - inequality;
+  return rV;
 }
 
-double GAMMA_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void *data)
-{
-	log_gamma_inequality *M = (log_gamma_inequality *)data;
-	double inequality = M->inequality;
-	double BMD = M->BMD;
-	double BMR = M->BMR;
-	bool geq = M->geq;
+double GAMMA_BMD_ADDED_NC_INEQUALITY(Eigen::MatrixXd theta, void *data) {
+  log_gamma_inequality *M = (log_gamma_inequality *)data;
+  double inequality = M->inequality;
+  double BMD = M->BMD;
+  double BMR = M->BMR;
+  bool geq = M->geq;
 
-	double g = GAMMA_G(theta(0, 0));
-	double a = GAMMA_A(theta(1, 0));
+  double g = GAMMA_G(theta(0, 0));
+  double a = GAMMA_A(theta(1, 0));
 
-	double Z = GAMMA_ADDED_Z(g, a, BMR);
-	Z = Z / BMD;
-	double rV = 0.0;
+  double Z = GAMMA_ADDED_Z(g, a, BMR);
+  Z = Z / BMD;
+  double rV = 0.0;
 
-	rV = (geq) ? inequality - Z : Z - inequality;
+  rV = (geq) ? inequality - Z : Z - inequality;
 
-	return rV;
+  return rV;
 }