Add OpenMP guards for MacOS. Add github workflow for mac testing and …

…fix issues with pipeline. Bump version number

.github/workflows/cran-check.yml

@@ -9,6 +9,8 @@ permissions:
 
 jobs:
   cran-check:
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:
       fail-fast: false 
       matrix:
@@ -18,13 +20,9 @@ jobs:
           {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: "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:
@@ -56,18 +54,13 @@ jobs:
         with:
           extra-packages: any::rcmdcheck, any::roxygen2
           needs: check
-      - name: Setup compiler
+      - name: Install mac-r-tools
         if: runner.os == 'macOs'
-        uses: KyleMayes/install-llvm-action@v2
-        with:
-          version: ${{matrix.compiler_version}}
-          env: true
-          directory: ".."
-      - name: Setup Xcode
-        if: runner.os == 'macOs'
-        uses: maxim-lobanov/setup-xcode@v1
-        with:
-          xcode-version: latest
+        run: |
+          install.packages("remotes")
+          remotes::install_github("coatless-mac/macrtools")
+          macrtools::macos_rtools_install()
+        shell: Rscript {0}
       - name: Build and Check ToxicR
         if: runner.os != 'Windows'
         run: |
@@ -79,10 +72,6 @@ jobs:
           package_name=$(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
@@ -98,12 +87,4 @@ jobs:
           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: "."
+        working-directory: "."

.github/workflows/mac-check.yml

@@ -0,0 +1,81 @@
+name: MacOS check
+
+on:
+  push:
+    branches: [ "bk_omp" ]
+  workflow_dispatch:
+
+permissions: 
+  contents: read
+
+jobs:
+  cran-check:
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    strategy:
+      fail-fast: false 
+      matrix:
+        include: [
+          {os: "macos-latest", r: "release", compiler_version: 15},
+          {os: "macos-latest", r: "release", compiler_version: 14},
+        ]
+    runs-on: ${{matrix.os}}
+    name: ${{ matrix.os }}_${{ matrix.r}}_${{matrix.compiler_version}}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
+        with:
+            r-version: ${{matrix.r}}
+      - uses: awalsh128/cache-apt-pkgs-action@latest
+        if: runner.os == 'Linux'
+        with:
+          packages: | 
+            cmake cmake-data gsl dh-elpa-helper libcmark-gfm-extensions0.29.0.gfm.3 
+            libcmark-gfm0.29.0.gfm.3 libcurl4-openssl-dev libjsoncpp25 librhash0 
+            pandoc pandoc-data texlive-latex-base texlive-latex-recommended 
+            texlive-fonts-recommended
+          version: 1.0
+      - name: Restore R package cache (Linux)
+        if: runner.os == 'Linux'
+        id: cache-packages
+        uses: actions/cache@v4
+        with:
+          key: r-${{ hashFiles('DESCRIPTION') }}
+          path: ${{ env.R_LIBS_USER }}
+      - name: Install GSL (macOS)
+        if: runner.os == 'macOs'
+        run: |
+          brew install gsl openssl
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::roxygen2
+          needs: check
+      - name: Install mac-r-tools
+        if: runner.os == 'macOs'
+        run: |
+          install.packages("remotes")
+          remotes::install_github("coatless-mac/macrtools")
+          macrtools::macos_rtools_install()
+        shell: Rscript {0}
+      - name: Build and Check ToxicR
+        if: runner.os == 'Linux'
+        run: |
+          R CMD build .
+          r_output=$(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 $package_name
+        shell: bash
+        working-directory: "."
+      - name: Build and Check ToxicR (MacOs)
+        if: runner.os == 'macOs'
+        run: |
+          R CMD build .
+          r_output=$(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
+        shell: bash
+        working-directory: "."

CHANGELOG.md

@@ -1,7 +1,8 @@
 # Changes
-## Version 23.10.1.2.0 
-## The following cumulative fixes are in version 23.10.1.2.0
+## Version 23.10.1.2.3 
+## The following cumulative fixes are in version 23.10.1.2.3
 - Add the ability to set a seed for nlopt and GSL to allow for consistent results
+- Set additional checks and guards for openMP
 ## New Features 
 - Added setseedGSL function with a default seed value of 12331
 ## Version 23.10.1.1.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ToxicR
 Type: Package
 Title: Analyzing Toxicology Dose-Response Data
-Version: 24.1.1.2.2
-Date: 2024-07-17
+Version: 24.1.1.2.3
+Date: 2024-07-31
 Authors@R: 
     c(
     person(given = "Matt",

R/opening_messages.R

@@ -25,7 +25,7 @@
     | |/ _ \\ \\/ / |/ __|  _  /
     | | (_) >  <| | (__| | \\ \\
     |_|\\___/_/\\_\\_|\\___|_|  \\_\\
-                           24.1.1.2.2
+                           24.1.1.2.3
     ___
     | |
     / \\                   ____()()

src/include/seeder.h

@@ -3,7 +3,9 @@
 #ifndef SEEDER
 #define SEEDER
 
-#include "omp.h"
+#ifndef NO_OMP
+#include <omp.h>
+#endif
 #include <Rcpp.h>
 #include <gsl/gsl_randist.h>
 #include <gsl/gsl_rng.h>
@@ -30,7 +32,11 @@ class Seeder {
     std::lock_guard<std::mutex> lock(instanceMutex);
     if (!instance) {
       instance = new Seeder();
+      #ifndef NO_OMP
       instance->max_threads = omp_get_num_threads();
+      #else 
+      instance->max_threads = 1;
+      #endif
       instance->T = gsl_rng_mt19937;
       instance->currentSeed = 0;
       instance->rngs.reserve(instance->max_threads);
@@ -40,6 +46,7 @@ class Seeder {
   }
 
   void reset_max_threads(int threads) {
+  #ifndef NO_OMP
     if(max_threads < threads) {
       int num_prev_threads = max_threads;
       max_threads = threads;
@@ -56,6 +63,7 @@ class Seeder {
         rngs[thread_num] = r_local;
       }
     }
+  #endif
   }
 
   ~Seeder() {
@@ -68,6 +76,8 @@ class Seeder {
     if (seed < 0) {
       Rcpp::stop("Error: Seed must be a positive integer.");
     }
+
+    #ifndef NO_OMP
     if(rngs.empty()) {
       #pragma omp parallel for
       for (int i = 0; i < max_threads; i++) {
@@ -87,25 +97,44 @@ class Seeder {
         rngs[thread_num] = r_local;
       }
     }
+    #else // MacOs or non-OpenMP architecture
+    int thread_num = 0; // master thread
+    gsl_rng_free(rngs[thread_num]);
+    gsl_rng* r_local = gsl_rng_alloc(gsl_rng_mt19937);
+    gsl_rng_set(r_local, seed);
+    rngs[thread_num] = r_local;
+    #endif
   }
 
   double get_uniform() {
     double r_val;
+    #ifndef NO_OMP
     int thread_num = omp_get_thread_num();
+    #else 
+    int thread_num = 0;
+    #endif
     r_val = gsl_rng_uniform(rngs[thread_num]);
     return r_val;
   }
 
   double get_gaussian_ziggurat() {
     double r_val;
+    #ifndef NO_OMP
     int thread_num = omp_get_thread_num();
+    #else 
+    int thread_num = 0;
+    #endif
     r_val = gsl_ran_gaussian_ziggurat(rngs[thread_num], 1.0);
     return r_val;
   }
 
   double get_ran_flat() {
     double r_val;
+    #ifndef NO_OMP
     int thread_num = omp_get_thread_num();
+    #else 
+    int thread_num = 0;
+    #endif
     r_val = gsl_ran_flat(rngs[thread_num], -1, 1);
     return r_val;
   }

src/set_omp_threads.cpp

@@ -1,4 +1,6 @@
-#include "omp.h"
+#ifndef NO_OMP
+  #include <omp.h>
+#endif
 
 #include <Rcpp.h>
 #include "seeder.h"
@@ -12,9 +14,17 @@ using namespace Rcpp;
 // output: none
 // [[Rcpp::export(".set_threads")]]
 void set_threads(int num_threads) {
-  if (num_threads > omp_get_num_threads()) {
-    Seeder* s = Seeder::getInstance();
-    omp_set_num_threads(num_threads);
-    s->reset_max_threads(num_threads);
+  #ifndef NO_OMP
+  if(omp_get_max_threads() > 1){
+    if (num_threads > omp_get_num_threads()) {
+      Seeder* s = Seeder::getInstance();
+      omp_set_num_threads(num_threads);
+      s->reset_max_threads(num_threads);
+    }
+  }else{
+    Rcout << "OMP will not be used for parallelization.";
   }
+  #else
+  Rcpp::Rcout << "OpenMP not supported on this architecure." << std::endl;
+  #endif
 }