Merge pull request #21 from SciomeLLC/nlopt-update

Fix compiler directives to work with MacOS/Windows

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changes
-## Version 23.10.1.3
-## The following cumulative fixes are in version 23.10.1.3
+## Version 23.10.1.4
+## The following cumulative fixes are in version 23.10.1.4
 - Modify nlopt to avoid issues with LLVM-clang incompatibilities
 - Disable OpenMP temporarily to get approved for CRAN 
 ## Version 23.10.1.2.4 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ToxicR
 Type: Package
 Title: Analyzing Toxicology Dose-Response Data
-Version: 24.1.1.4
+Version: 23.10.1.4
 Date: 2024-11-12
 Authors@R: 
     c(
@@ -75,7 +75,8 @@ 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
+        doBy (>= 4.6.11), multcomp (>= 1.4), dplyr (>= 1.0.7), remotes,
+        mvtnorm
 LinkingTo: Rcpp, RcppEigen, RcppGSL
 RoxygenNote: 7.3.2
 Encoding: UTF-8

configure

@@ -3495,7 +3495,7 @@ fi
 
 
     if test x"${have_cmake}" == x"no"; then
-       . src/cmake_install.sh
+       . src/scripts/cmake_install.sh
        if test -z "${CMAKE_BIN}"; then
           ## also error to end configure here
           as_fn_error $? "Could not find 'cmake'." "$LINENO" 5

configure.ac

@@ -1,7 +1,5 @@
 # Configure Script for ToxicR
 # Modified 4/27/2022
-# Configure Script for ToxicR
-# Modified 4/27/2022
 
 AC_INIT([ToxicR], 1.0.1)  dnl Package version
 
@@ -11,15 +9,21 @@ CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 AC_LANG(C++)
 AC_PROG_CPP
 
-#determine the OS
-AC_MSG_CHECKING([Is OPENMP avaialble? ])
+# Determine the OS
+AC_MSG_CHECKING([Is OPENMP available?])
 OS_FLAG="$(uname)"
-if test x"${OS_FLAG}" == x"Darwin";then
+if test x"${OS_FLAG}" == x"Darwin"; then
      AC_MSG_RESULT([no])
      OPENMP="-DNO_OMP"
+     OSFLAG="-D__APPLE__"
+elif test x"${OS_FLAG}" == x"Linux"; then
+     AC_MSG_RESULT([yes])
+     OPENMP="\$(SHLIB_OPENMP_CXXFLAGS)"
+     OSFLAG=""
 else
      AC_MSG_RESULT([yes])
-     OPENMP="\$(SHLIB_OPENMP_CXXFLAGS) "
+     OPENMP="\$(SHLIB_OPENMP_CXXFLAGS)"
+     OSFLAG="-D__WIN32"
 fi
 
 AC_PATH_PROG([GSL_CONFIG], [gsl-config])
@@ -35,14 +39,14 @@ else
                  sudo apt install gsl 
                  To install GSL in Fedora Type:
                  sudo yum -y install gsl
-                 To iinstall GSL on macOS using homebrew type: 
+                 To install GSL on macOS using homebrew type: 
                  brew install gsl
                  ])
 fi
 
 ## Can we use pkg-config?
 AC_PATH_PROG(have_pkg_config, pkg-config, no)
-AC_MSG_CHECKING([Is pkg-config avaialble? ])
+AC_MSG_CHECKING([Is pkg-config available?])
 if test x"${have_pkg_config}" != x"no"; then
      AC_MSG_RESULT([yes])
      AC_MSG_CHECKING([if pkg-config knows NLopt])
@@ -58,24 +62,12 @@ if test x"${have_pkg_config}" != x"no"; then
                  AC_SUBST([NLOPT_LIBS],    "${nlopt_libs}")   
             else
                 AC_MSG_RESULT([no])
-                #if it is macOS just try link and use nlopt generically
-              need_to_build="yes"
+                need_to_build="yes"
             fi
     else
         AC_MSG_RESULT([no])
-            #if it is macOS just try link and use nlopt generically
-            if test x"${OS_FLAG}" == x"Darwin";then
-                    AC_MSG_RESULT([>= 2.6.0])
-                    nlopt_include=""
-                    nlopt_libs="-lnlopt"
-                    AC_SUBST([NLOPT_INCLUDE], "${nlopt_include}")
-                    AC_SUBST([NLOPT_LIBS],    "${nlopt_libs}")   
-            else
-                 need_to_build="yes"
-            fi
-
+        need_to_build="yes"
     fi
-
 else
     AC_MSG_RESULT([no])
     need_to_build="yes"
@@ -85,14 +77,12 @@ fi
 if test x"${need_to_build}" != x"no"; then
     AC_PATH_PROG(have_cmake, cmake, no)
 
-    if test x"${have_cmake}" == x"no"; then
-       . src/scripts/cmake_config.sh
+    if test x"${have_cmake}" == x"no"; then 
+       . src/scripts/cmake_install.sh
        if test -z "${CMAKE_BIN}"; then
           ## also error to end configure here
           AC_MSG_ERROR([Could not find 'cmake'.])
        fi
-    else
-        . src/scripts/cmake_install.sh
     fi
     ## 'uname -m' on M1 give x86_64 which is ... not helping
     machine=`"${R_HOME}/bin/Rscript" -e 'cat(Sys.info()[["machine"]])'`
@@ -107,6 +97,7 @@ SUBDIR_SOURCES="$(cd src/ && ls {code_base,polyK}/*.cpp | tr '\n' ' ')"
 SRC_SOURCES="$( cd src/ && ls *.cpp | tr '\n' ' ')"
 
 AC_SUBST(OPENMP)
+AC_SUBST(OSFLAG)
 AC_SUBST(SRC_SOURCES)
 AC_SUBST(SUBDIR_SOURCES)
 AC_SUBST([NLOPT_CPPFLAGS],["${nlopt_include}"])

src/Makevars.in

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

src/Makevars.ucrt

@@ -1,5 +1,5 @@
-PKG_CXXFLAGS=-I./code_base -I./include @OSFLAG@ $(SHLIB_OPENMP_CXXFLAGS) -I$(R_TOOLS_SOFT)/include/nlopt -I$(R_TOOLS_SOFT)/include/gsl -DR_COMPILATION -ftree-vectorize -Os -DNO_OMP -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -lgsl -lgslcblas -lnlopt -lgfortran
+PKG_CXXFLAGS=-I./code_base -I./include $(SHLIB_OPENMP_CXXFLAGS) -I$(R_TOOLS_SOFT)/include/nlopt -I$(R_TOOLS_SOFT)/include/gsl -DR_COMPILATION -ftree-vectorize -Os -DNO_OMP -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) -lgsl -lgslcblas -lnlopt
 # Debug / clear eigen warnings from compilation 
 #PKG_CXXFLAGS+=-Wno-ignored-attributes -DToxicR_DEBUG
 

src/include/cBMDstatmod.h

@@ -378,9 +378,13 @@ optimizationResult cfindMAX_W_EQUALITY(cBMDModel<LL, PR> *M,
     try {
       result = opt.optimize(x, minf);
       good_opt = true;
+    #if defined(_WIN32) || defined(__APPLE__)
+    } catch (nlopt::roundoff_limited &exc) {
+      good_opt = false;
+    #else 
     } catch (nlopt::roundoff_limited2 &exc) {
       good_opt = false;
-      // cout << "Error Round off" << endl;
+    #endif
     } catch (nlopt::forced_stop &exc) {
       good_opt = false;
       // cout << "Error Forced stop" << endl;
@@ -609,7 +613,7 @@ optimizationResult cfindMAX_W_BOUND(cBMDModel<LL, PR> *M, Eigen::MatrixXd start,
       // flush(file);
       good_opt = true;
 // opt_iter++;
-#ifdef _WIN32 || defined(__APPLE__)
+#if defined(_WIN32) || defined(__APPLE__)
     } catch (nlopt::roundoff_limited &exc) {
       good_opt = false;
       DEBUG_LOG(file, "opt_iter= " << opt_iter << ", error: roundoff_limited");

src/include/statmod.h

@@ -780,7 +780,7 @@ optimizationResult findMAP(statModel<LL, PR> *M, Eigen::MatrixXd startV,
 
     } // catch
 
-#ifdef _WIN32 || defined(__APPLE__)
+#if defined(_WIN32) || defined(__APPLE__)
     catch (nlopt::roundoff_limited &exce) {
       DEBUG_LOG(file, "opt_iter= " << opt_iter << ", error: roundoff_limited");
       // Rcpp::Rcout << "Roundoff_limited nlopt: " << exce.what() <<