Fix ASAN/Valgrind issues caused by LLVM and clang due to nlopt except…

…ions. Removed OpenMP

.Rbuildignore

@@ -1,4 +1,5 @@
 ^.*\.Rproj$
+^.*\.Rcheck$
 ^\.DS_Store$
 ^\.(RData|Rhistory|RProj\.user)$
 ^\.gitignore$

.gitattributes

@@ -0,0 +1 @@
+configure.ac text eol=lf

.github/workflows/builds.yml

@@ -11,8 +11,8 @@ name: Valgrind Check
 on:
   pull_request:
     branches: [ "main" ]
-  # push:
-  #   branches: [ "github-actions-build" ]
+  push:
+    branches: [ "seeder-valgrind" ]
   workflow_dispatch: 
 
 

.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:
@@ -56,54 +54,26 @@ 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: ${{matrix.compiler_version}}
-          env: true
-          directory: ".."
-      - name: Setup Xcode
-        if: runner.os == 'macOs'
-        uses: maxim-lobanov/setup-xcode@v1
-        with:
-          xcode-version: latest
+        run: |
+          install.packages("remotes")
+          remotes::install_github("coatless-mac/macrtools")
+          macrtools::macos_rtools_install()
+        shell: Rscript {0}
       - name: Build and Check ToxicR
         if: runner.os != 'Windows'
         run: |
-          R CMD build .
-          file config.log
-          cat config.log
           r_output=$(R CMD build .)
-          echo "$r_output"
-          package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p") 
-          echo "$package_name"
+          package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p")
           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: "."
+        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: "."

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/sanitizer.yml

@@ -3,8 +3,6 @@ name: UBSAN/ASAN Checks
 on:
   pull_request:
     branches: [ "main" ]
-  push:
-    branches: [ "github-actions-build", "brian-bk22-plotting-patch", "bounds-check-testing" ]
   workflow_dispatch: 
 
 

.gitignore

@@ -1,8 +1,10 @@
 *.o
 *.so
+*.Rproj
 .Rproj.user
 .Rhistory
 .vscode/*
 .RData
 *.tar.gz
-*.dll
+*.dll
+install.sh

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 23.10.1.2.4 
+## The following cumulative fixes are in version 23.10.1.2.4
 - 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: 24.1.1.2.1
-Date: 2024-07-02
+Version: 24.1.1.2.4
+Date: 2024-08-24
 Authors@R: 
     c(
     person(given = "Matt",
@@ -77,7 +77,7 @@ Imports: Rcpp (>= 1.0.0), ggplot2 (>= 3.3.2), shiny (>= 1.5.0), coda
         (>= 0.19-4), scales (>= 1.1.1), forcats, ggridges (>= 0.5.3),
         doBy (>= 4.6.11), multcomp (>= 1.4), dplyr (>= 1.0.7), remotes
 LinkingTo: Rcpp, RcppEigen, RcppGSL
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
 Suggests: plotly (>= 4.9.2.1), rmarkdown, actuar (>= 3.2-0),ggpubr (>=