Merge pull request #22 from SciomeLLC/nlopt-update

Only install missing cmake on Linux systems

.github/workflows/clang-check.yml

@@ -0,0 +1,69 @@
+name: clang-test
+on:
+  push:
+
+jobs:
+    clang-test:
+        runs-on: ubuntu-latest
+        name: clang-${{ matrix.compiler }}-R-${{matrix.R}}
+        strategy:
+          fail-fast: false
+          matrix:
+            compiler:
+                - llvm-16.0.6
+                - llvm-17.0.6
+                - llvm-18.1.8
+                - llvm-19.1.0
+                - llvm-20.0.0
+            R: ['release', 'devel']
+        steps:
+          - uses: actions/checkout@v3
+          - name: Cache
+            uses: actions/cache@v3
+            with:
+              path: |
+                ./build/
+                ~/vcpkg
+                ~/.cache/vcpkg/archives
+                ${{ env.LOCALAPPDATA }}/vcpkg/archives
+                ${{ env.APPDATA }}/vcpkg/archives
+                ${{ env.XDG_CACHE_HOME }}/vcpkg/archives
+                ~/.cache/ccache
+                ~/.ccache
+                ~/.config/ccache
+                ~/Library/Caches/ccache
+                ${{ env.LOCALAPPDATA }}/ccache
+                ${{ env.XDG_CACHE_HOME }}/ccache
+              key: ${{ runner.os }}-${{ matrix.compiler }}-${{ env.BUILD_TYPE }}-${{ hashFiles('**/CMakeLists.txt', './vcpkg.json') }}
+              restore-keys: |
+                ${{ runner.os }}-${{ env.BUILD_TYPE }}-
+          - uses: awalsh128/cache-apt-pkgs-action@latest
+            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
+          - name: Setup Cpp (C++ / C)
+            uses: aminya/setup-cpp@v1
+            with:
+              compiler: ${{ matrix.compiler }}
+              cmake: true
+              cache-tools: true
+              llvm: true
+              make: true
+          - uses: r-lib/actions/setup-r@v2
+            with:
+              r-version: ${{matrix.R}}
+              install-r: true
+          - uses: r-lib/actions/setup-r-dependencies@v2
+            with:
+              extra-packages: any::rcmdcheck, any::roxygen2
+              needs: check
+          - name: Build and Check ToxicR
+            run: |
+                r_output=$(R CMD build .)
+                package_name=$(echo "$r_output" | sed -n "s/.*building ‘\([^’]*\.tar\.gz\)’.*/\1/p")
+                R CMD check --as-cran --no-manual $package_name
+            shell: bash
+            working-directory: "." 

DESCRIPTION

@@ -75,8 +75,7 @@ URL: https://github.com/NIEHS/ToxicR
 LazyData: true
 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,
-        mvtnorm
+        doBy (>= 4.6.11), multcomp (>= 1.4), dplyr (>= 1.0.7), remotes
 LinkingTo: Rcpp, RcppEigen, RcppGSL
 RoxygenNote: 7.3.2
 Encoding: UTF-8

configure

@@ -3495,11 +3495,14 @@ fi
 
 
     if test x"${have_cmake}" == x"no"; then
-       . src/scripts/cmake_install.sh
-       if test -z "${CMAKE_BIN}"; then
-          ## also error to end configure here
-          as_fn_error $? "Could not find 'cmake'." "$LINENO" 5
-       fi
+
+        if test x"${OS_FLAG}" == x"Linux"; then
+            . src/scripts/cmake_install.sh
+            if test -z "${CMAKE_BIN}"; then
+                ## also error to end configure here
+                as_fn_error $? "Could not find 'cmake'." "$LINENO" 5
+            fi
+        fi
     fi
     ## 'uname -m' on M1 give x86_64 which is ... not helping
     machine=`"${R_HOME}/bin/Rscript" -e 'cat(Sys.info()["machine"])'`

configure.ac

@@ -78,11 +78,14 @@ if test x"${need_to_build}" != x"no"; then
     AC_PATH_PROG(have_cmake, cmake, no)
 
     if test x"${have_cmake}" == x"no"; then 
-       . src/scripts/cmake_install.sh
-       if test -z "${CMAKE_BIN}"; then
-          ## also error to end configure here
-          AC_MSG_ERROR([Could not find 'cmake'.])
-       fi
+
+        if test x"${OS_FLAG}" == x"Linux"; then
+            . src/scripts/cmake_install.sh
+            if test -z "${CMAKE_BIN}"; then
+                ## also error to end configure here
+                AC_MSG_ERROR([Could not find 'cmake'.])
+            fi
+        fi
     fi
     ## 'uname -m' on M1 give x86_64 which is ... not helping
     machine=`"${R_HOME}/bin/Rscript" -e 'cat(Sys.info()[["machine"]])'`

src/Makevars.in

@@ -1,5 +1,5 @@
 PKG_CXXFLAGS=-I./code_base -I./include @OPENMP@ @NLOPT_CPPFLAGS@ @GSL_CPPFLAGS@ -DR_COMPILATION -DNO_OMP -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @NLOPT_LIBS@  @GSL_LIBS@ @OPENMP@
+PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @NLOPT_LIBS@ @GSL_LIBS@ @OPENMP@
 
 # Debug / clear eigen warnings from compilation 
 #PKG_CXXFLAGS+=-Wno-ignored-attributes -DToxicR_DEBUG

src/Makevars.win

@@ -1,4 +1,4 @@
-PKG_CPPFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -I../windows/gsl-2.7/include -I../windows/nlopt-2.7.1/include  -I./ -I./code_base  -I./include -DR_COMPILATION -ftree-vectorize -Os -femulated-tls -DNO_OMP -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -I../windows/gsl-2.7/include -I../windows/nlopt-2.7.1/include -I./ -I./code_base -I./include -DR_COMPILATION -ftree-vectorize -Os -femulated-tls -DNO_OMP -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
 PKG_LIBS=$(SHLIB_OPENMP_CXXFLAGS) -L../windows/nlopt-2.7.1/lib${R_ARCH}${CRT}  -L../windows/gsl-2.7/lib${R_ARCH}${CRT} -lgsl -lgslcblas -lnlopt
 # Debug / clear eigen warnings from compilation 
 #PKG_CPPFLAGS += -Wno-ignored-attributes -DToxicR_DEBUG -g -O0