# get version of CoGAPS from DESCRIPTION file

 AC_INIT(CoGAPS, m4_esyscmd_s([awk -e '/^Version:/ {print $2}' DESCRIPTION]))

 
 # get C++ compiler from R configuration
 CXX=`"${R_HOME}/bin/R" CMD config CXX`
 
 # Switch to a C++ compiler, and check if it works.
 AC_LANG(C++)
 AC_REQUIRE_CPP
 AC_PROG_CXX
 
 # Check if compiling debug version
 AC_ARG_ENABLE(debug, [AC_HELP_STRING([--enable-debug],
     [build debug version of CoGAPS])], [build_debug=yes], [build_debug=no])
 

 # Check if running C++ tests (this adds to compilation time)
 AC_ARG_ENABLE(cpp-tests, [AC_HELP_STRING([--enable-cpp-tests],
     [turn on C++ unit tests])], [cpp_tests=yes], [cpp_tests=no])
 

 # Check if running internal tests
 AC_ARG_ENABLE(internal-tests, [AC_HELP_STRING([--enable-internal-tests],
     [allow for testing private data])], [internal_tests=yes], [internal_tests=no])
 

 # Check if compiler warnings should be turned on
 AC_ARG_ENABLE(warnings, [AC_HELP_STRING([--enable-warnings],
     [compile CoGAPS with warning messages])], [warnings=yes], [warnings=no])
 

 # Use SIMD unless requested not to

 AC_ARG_ENABLE(simd, [AC_HELP_STRING([--enable-simd],

     [compile with SIMD support if available])],
     [use_simd=$enableval], [use_simd=yes])

 
 # default CoGAPS specific flags

 GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude"

 GAPS_CXX_FLAGS=
 GAPS_LIBS=
 
 # get compiler info
 AX_COMPILER_VENDOR
 AX_COMPILER_VERSION
 

 # set openmp flags, disable only if requested
 AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],
     [compile with openMP support if available])],
     [use_openmp=$enableval], [use_openmp=yes])
 

 AX_OPENMP

 if test "x$use_openmp" != "xno" ; then
     GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "
     GAPS_LIBS+=" $OPENMP_CXXFLAGS "
 fi

 
 echo "building on $ax_cv_cxx_compiler_vendor compiler version $ax_cv_cxx_compiler_version"
 
 # set compile flags for debug build
 if test "x$build_debug" = "xyes" ; then
     echo "Building Debug Version of CoGAPS"

     GAPS_CPP_FLAGS+=" -DGAPS_DEBUG "

 fi
 

 # set compile flags for internal tests
 if test "x$internal_tests" = "xyes" ; then
     echo "Enabling Internal Tests"
     GAPS_CPP_FLAGS+=" -DGAPS_INTERNAL_TESTS "
 fi
 

 # set compile flags if warnings enabled
 if test "x$warnings" = "xyes" ; then

     if test "x$ax_cv_cxx_compiler_vendor" = "xgnu" || test "x$ax_cv_cxx_compiler_vendor" = "xclang"; then

         GAPS_CXX_FLAGS+=" -Wall -Wextra -Werror -Wno-unused-parameter -Wno-unknown-pragmas"

     fi

 fi
 

 if test "x$use_simd" = "xno" ; then
     echo "Building without SIMD instructions"

 fi
 

 if test "x$use_simd" = "xsse" ; then
     echo "Disabling AVX instructions"
     GAPS_CXX_FLAGS+=" -mno-avx "
 fi
 

 if test "x$use_simd" != "xno" ; then

     echo "Using AVX instructions if available"

     GAPS_CXX_FLAGS+=" -march=native "

 fi
 

 GAPS_SOURCE_FILES+=" Cogaps.o"
 GAPS_SOURCE_FILES+=" GapsParameters.o"
 GAPS_SOURCE_FILES+=" GapsResult.o"
 GAPS_SOURCE_FILES+=" GapsRunner.o"
 GAPS_SOURCE_FILES+=" GapsStatistics.o"
 GAPS_SOURCE_FILES+=" RcppExports.o"
 GAPS_SOURCE_FILES+=" test-runner.o"
 GAPS_SOURCE_FILES+=" atomic/AtomicDomain.o"
 GAPS_SOURCE_FILES+=" atomic/ProposalQueue.o"
 GAPS_SOURCE_FILES+=" data_structures/HashSets.o"
 GAPS_SOURCE_FILES+=" data_structures/HybridMatrix.o"
 GAPS_SOURCE_FILES+=" data_structures/HybridVector.o"
 GAPS_SOURCE_FILES+=" data_structures/Matrix.o"
 GAPS_SOURCE_FILES+=" data_structures/SparseIterator.o"
 GAPS_SOURCE_FILES+=" data_structures/SparseMatrix.o"
 GAPS_SOURCE_FILES+=" data_structures/SparseVector.o"
 GAPS_SOURCE_FILES+=" data_structures/Vector.o"
 GAPS_SOURCE_FILES+=" file_parser/CsvParser.o"
 GAPS_SOURCE_FILES+=" file_parser/FileParser.o"

 GAPS_SOURCE_FILES+=" file_parser/GctParser.o"

 GAPS_SOURCE_FILES+=" file_parser/TsvParser.o"
 GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/AlphaParameters.o"
 GAPS_SOURCE_FILES+=" gibbs_sampler/DenseStoragePolicy.o"
 GAPS_SOURCE_FILES+=" gibbs_sampler/SparseStoragePolicy.o"

 GAPS_SOURCE_FILES+=" math/Math.o"
 GAPS_SOURCE_FILES+=" math/MatrixMath.o"
 GAPS_SOURCE_FILES+=" math/Random.o"
 GAPS_SOURCE_FILES+=" math/VectorMath.o"
 
 # add c++ tests to source list
 if test "x$cpp_tests" = "xyes" ; then
     echo "Enabling C++ Unit Tests"
     GAPS_CPP_FLAGS+=" -DGAPS_CPP_UNIT_TESTS "
 
     GAPS_SOURCE_FILES+=" cpp_tests/testAtomicDomain.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testDenseGibbsSampler.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testFileParsers.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testHashSets.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testHybridMatrix.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testHybridVector.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testMatrix.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testRandom.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testSerialization.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testSparseGibbsSampler.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testSparseIterator.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testSparseMatrix.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testSparseVector.o"
     GAPS_SOURCE_FILES+=" cpp_tests/testVector.o"
 fi
 

 # export variables containing flags
 AC_SUBST(GAPS_CPP_FLAGS)
 AC_SUBST(GAPS_CXX_FLAGS)
 AC_SUBST(GAPS_LIBS)

 AC_SUBST(GAPS_SOURCE_FILES)

 
 # create makefile, output configure file
 AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT