@@ -70,11 +70,6 @@ if test "x$use_simd" = "xsse" ; then

     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"

@@ -70,10 +70,10 @@ if test "x$use_simd" = "xsse" ; then

     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

+# 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"

@@ -27,7 +27,7 @@ AC_ARG_ENABLE(simd, [AC_HELP_STRING([--enable-simd],

     [use_simd=$enableval], [use_simd=yes])

 # default CoGAPS specific flags

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

+GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__"

 GAPS_CXX_FLAGS=

 GAPS_LIBS=

@@ -27,7 +27,7 @@ AC_ARG_ENABLE(simd, [AC_HELP_STRING([--enable-simd],

     [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_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude"

 GAPS_CXX_FLAGS=

 GAPS_LIBS=

@@ -17,10 +17,6 @@ AC_ARG_ENABLE(debug, [AC_HELP_STRING([--enable-debug],

 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])

@@ -58,12 +54,6 @@ if test "x$build_debug" = "xyes" ; then

     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

@@ -121,22 +121,7 @@ GAPS_SOURCE_FILES+=" math/VectorMath.o"

 if test "x$cpp_tests" = "xyes" ; then

     echo "Enabling C++ Unit Tests"

     GAPS_CPP_FLAGS+=" -DGAPS_CPP_UNIT_TESTS "

-

-    GAPS_SOURCE_FILES+=" cpp_tests/testSamplerHighLevel.cpp"

-    # 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"

+    GAPS_SOURCE_FILES+=" cpp_tests/testVector.o"

 fi

 # export variables containing flags

@@ -107,7 +107,7 @@ GAPS_SOURCE_FILES+=" data_structures/SparseVector.o"

 GAPS_SOURCE_FILES+=" data_structures/Vector.o"

 GAPS_SOURCE_FILES+=" file_parser/CharacterDelimitedParser.o"

 GAPS_SOURCE_FILES+=" file_parser/FileParser.o"

-GAPS_SOURCE_FILES+=" file_parser/GctParser.o"

+GAPS_SOURCE_FILES+=" file_parser/MatrixElement.o"

 GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/AlphaParameters.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/DenseNormalModel.o"

@@ -105,10 +105,9 @@ 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/CharacterDelimitedParser.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/DenseNormalModel.o"

@@ -1,5 +1,5 @@

 # get version of CoGAPS from DESCRIPTION file

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

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

 # get C++ compiler from R configuration

 CXX=`"${R_HOME}/bin/R" CMD config CXX`

@@ -93,6 +93,7 @@ GAPS_SOURCE_FILES+=" GapsStatistics.o"

 GAPS_SOURCE_FILES+=" RcppExports.o"

 GAPS_SOURCE_FILES+=" test-runner.o"

 GAPS_SOURCE_FILES+=" atomic/Atom.o"

+GAPS_SOURCE_FILES+=" atomic/ConcurrentAtom.o"

 GAPS_SOURCE_FILES+=" atomic/AtomicDomain.o"

 GAPS_SOURCE_FILES+=" atomic/ConcurrentAtomicDomain.o"

 GAPS_SOURCE_FILES+=" atomic/ProposalQueue.o"

@@ -92,6 +92,7 @@ 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/Atom.o"

 GAPS_SOURCE_FILES+=" atomic/AtomicDomain.o"

 GAPS_SOURCE_FILES+=" atomic/ConcurrentAtomicDomain.o"

 GAPS_SOURCE_FILES+=" atomic/ProposalQueue.o"

@@ -93,6 +93,7 @@ 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/ConcurrentAtomicDomain.o"

 GAPS_SOURCE_FILES+=" atomic/ProposalQueue.o"

 GAPS_SOURCE_FILES+=" data_structures/HashSets.o"

 GAPS_SOURCE_FILES+=" data_structures/HybridMatrix.o"

@@ -120,20 +120,21 @@ 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"

+    GAPS_SOURCE_FILES+=" cpp_tests/testSamplerHighLevel.cpp"

+    # 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

@@ -109,7 +109,6 @@ 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/DenseNormalModel.o"

-GAPS_SOURCE_FILES+=" gibbs_sampler/DenseNormalWithUncertaintyModel.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/SparseNormalModel.o"

 GAPS_SOURCE_FILES+=" math/Math.o"

 GAPS_SOURCE_FILES+=" math/MatrixMath.o"

@@ -109,6 +109,7 @@ 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/DenseNormalModel.o"

+GAPS_SOURCE_FILES+=" gibbs_sampler/DenseNormalWithUncertaintyModel.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/SparseNormalModel.o"

 GAPS_SOURCE_FILES+=" math/Math.o"

 GAPS_SOURCE_FILES+=" math/MatrixMath.o"

@@ -108,8 +108,8 @@ 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+=" gibbs_sampler/DenseNormalModel.o"

+GAPS_SOURCE_FILES+=" gibbs_sampler/SparseNormalModel.o"

 GAPS_SOURCE_FILES+=" math/Math.o"

 GAPS_SOURCE_FILES+=" math/MatrixMath.o"

 GAPS_SOURCE_FILES+=" math/Random.o"

@@ -105,7 +105,6 @@ 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/Hdf5Parser.o"

 GAPS_SOURCE_FILES+=" file_parser/TsvParser.o"

 GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/AlphaParameters.o"

@@ -97,8 +97,9 @@ 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/GctParser.o"

 GAPS_SOURCE_FILES+=" file_parser/FileParser.o"

+GAPS_SOURCE_FILES+=" file_parser/GctParser.o"

+GAPS_SOURCE_FILES+=" file_parser/Hdf5Parser.o"

 GAPS_SOURCE_FILES+=" file_parser/TsvParser.o"

 GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

 GAPS_SOURCE_FILES+=" gibbs_sampler/AlphaParameters.o"

@@ -101,8 +101,9 @@ GAPS_SOURCE_FILES+=" file_parser/GctParser.o"

 GAPS_SOURCE_FILES+=" file_parser/FileParser.o"

 GAPS_SOURCE_FILES+=" file_parser/TsvParser.o"

 GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

-GAPS_SOURCE_FILES+=" gibbs_sampler/DenseGibbsSampler.o"

-GAPS_SOURCE_FILES+=" gibbs_sampler/SparseGibbsSampler.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"

@@ -81,6 +81,7 @@ if test "x$use_simd" = "xsse" ; then

 fi

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

+    echo "Using AVX instructions if available"

     GAPS_CXX_FLAGS+=" -march=native "

 fi

@@ -75,6 +75,11 @@ 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

     GAPS_CXX_FLAGS+=" -march=native "

 fi

@@ -13,6 +13,10 @@ AC_PROG_CXX

 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])

@@ -75,10 +79,61 @@ if test "x$use_simd" != "xno" ; then

     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/GctParser.o"

+GAPS_SOURCE_FILES+=" file_parser/FileParser.o"

+GAPS_SOURCE_FILES+=" file_parser/TsvParser.o"

+GAPS_SOURCE_FILES+=" file_parser/MtxParser.o"

+GAPS_SOURCE_FILES+=" gibbs_sampler/DenseGibbsSampler.o"

+GAPS_SOURCE_FILES+=" gibbs_sampler/SparseGibbsSampler.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])

@@ -27,7 +27,7 @@ AC_ARG_ENABLE(simd, [AC_HELP_STRING([--enable-simd],

     [use_simd=$enableval], [use_simd=yes])

 # default CoGAPS specific flags

-GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ "

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

 GAPS_CXX_FLAGS=

 GAPS_LIBS=

@@ -1,6 +1,5 @@

 # get version of CoGAPS from DESCRIPTION file

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

-# AM_INIT_AUTOMAKE([-Wall -Werror foreign])

 # get C++ compiler from R configuration

 CXX=`"${R_HOME}/bin/R" CMD config CXX`

@@ -73,9 +73,7 @@ if test "x$use_simd" = "xno" ; then

 fi

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

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

-        GAPS_CXX_FLAGS+=" -march=native "

-    fi

+    GAPS_CXX_FLAGS+=" -march=native "

 fi

 # export variables containing flags

@@ -64,7 +64,7 @@ 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 "

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

     fi

 fi

@@ -1,6 +1,6 @@

 # get version of CoGAPS from DESCRIPTION file

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

-AM_INIT_AUTOMAKE([-Wall -Werror foreign])

+# AM_INIT_AUTOMAKE([-Wall -Werror foreign])

 # get C++ compiler from R configuration

 CXX=`"${R_HOME}/bin/R" CMD config CXX`

@@ -22,10 +22,10 @@ AC_ARG_ENABLE(internal-tests, [AC_HELP_STRING([--enable-internal-tests],

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

     [compile CoGAPS with warning messages])], [warnings=yes], [warnings=no])

-# Check if specific version of SIMD instructions requested

+# Use SIMD unless requested not to

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

-    [specify simd instruction set (sse, avx)])],

-    [simd_version=$enableval], [simd_version=avx])

+    [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__ "

@@ -47,9 +47,6 @@ if test "x$use_openmp" != "xno" ; then

     GAPS_LIBS+=" $OPENMP_CXXFLAGS "

 fi

-# detect SIMD support

-AX_EXT

-

 echo "building on $ax_cv_cxx_compiler_vendor compiler version $ax_cv_cxx_compiler_version"

 # set compile flags for debug build

@@ -71,48 +68,16 @@ if test "x$warnings" = "xyes" ; then

     fi

 fi

-# set compile flags for SIMD

-echo "Supported SIMD flags: " $SIMD_FLAGS

-

-if test "x$simd_version" != "xavx" && test "x$simd_version" != "xsse" && test "x$simd_version" != "xno" && test "x$simd_version" != "xyes" ; then

-    echo "Invalid SIMD Type, Defaulting to AVX"

-    simd_version=avx

-fi

-

-avx_supported=false

-if test "x$simd_version" = "xavx" || test "x$simd_version" = "xyes" ; then

-    for s in $SIMD_FLAGS; do

-        if test "x$s" = "x-mavx"; then

-            avx_supported=true

-            echo "Building with AVX instructions"

-            GAPS_CXX_FLAGS+=" -mavx "

-        fi

-    done

-    if test "x$avx_supported" = "xfalse" ; then

-        echo "Note: AVX not supported, trying for SSE"

-        simd_version=sse

-    fi

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

+    echo "Building without SIMD instructions"

 fi

-sse_supported=false

-if test "x$simd_version" = "xsse" ; then

-    for s in $SIMD_FLAGS; do

-        if test "x$s" = "x-msse4.2"; then

-            sse_supported=true

-            echo "Building with SSE instructions"

-            GAPS_CXX_FLAGS+=" -msse4.2 "

-        fi

-    done

-    if test "x$sse_supported" = "xfalse" ; then

-        echo "Note: SSE not supported"

-        simd_version=no

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

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

+        GAPS_CXX_FLAGS+=" -march=native "

     fi

 fi

-if test "x$simd_version" = "xno" ; then

-    echo "Building without SIMD instructions"

-fi

-

 # export variables containing flags

 AC_SUBST(GAPS_CPP_FLAGS)

 AC_SUBST(GAPS_CXX_FLAGS)

old mode 100644

new mode 100755

@@ -14,6 +14,10 @@ AC_PROG_CXX

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

     [build debug version of CoGAPS])], [build_debug=yes], [build_debug=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])

@@ -54,6 +58,12 @@ if test "x$build_debug" = "xyes" ; then

     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

@@ -32,10 +32,16 @@ GAPS_LIBS=

 AX_COMPILER_VENDOR

 AX_COMPILER_VERSION

-# set openmp flags

+# 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

-GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

-GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+if test "x$use_openmp" != "xno" ; then

+    GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

+    GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+fi

 # detect SIMD support

 AX_EXT

@@ -21,7 +21,7 @@ AC_ARG_ENABLE(warnings, [AC_HELP_STRING([--enable-warnings],

 # Check if specific version of SIMD instructions requested

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

     [specify simd instruction set (sse, avx)])],

-    [simd_version=$enableval], [simd_version=sse])

+    [simd_version=$enableval], [simd_version=avx])

 # default CoGAPS specific flags

 GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ "

@@ -37,6 +37,9 @@ AX_OPENMP

 GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

 GAPS_LIBS+=" $OPENMP_CXXFLAGS "

+# detect SIMD support

+AX_EXT

+

 echo "building on $ax_cv_cxx_compiler_vendor compiler version $ax_cv_cxx_compiler_version"

 # set compile flags for debug build

@@ -53,7 +56,6 @@ if test "x$warnings" = "xyes" ; then

 fi

 # set compile flags for SIMD

-AX_EXT

 echo "Supported SIMD flags: " $SIMD_FLAGS

 if test "x$simd_version" != "xavx" && test "x$simd_version" != "xsse" && test "x$simd_version" != "xno" && test "x$simd_version" != "xyes" ; then

@@ -1,5 +1,6 @@

 # get version of CoGAPS from DESCRIPTION file

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

+AM_INIT_AUTOMAKE([-Wall -Werror foreign])

 # get C++ compiler from R configuration

 CXX=`"${R_HOME}/bin/R" CMD config CXX`

@@ -30,9 +30,9 @@ GAPS_LIBS=

 # get compiler info

 AX_COMPILER_VENDOR

 AX_COMPILER_VERSION

-AX_OPENMP

 # set openmp flags

+AX_OPENMP

 GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

 GAPS_LIBS+=" $OPENMP_CXXFLAGS "

@@ -46,28 +46,52 @@ fi

 # set compile flags if warnings enabled

 if test "x$warnings" = "xyes" ; then

-    AX_CHECK_COMPILE_FLAG([-Wall], [GAPS_CXX_FLAGS+=" -Wall "])

-    AX_CHECK_COMPILE_FLAG([-Wextra], [GAPS_CXX_FLAGS+=" -Wextra "])

-    AX_CHECK_COMPILE_FLAG([-Werror], [GAPS_CXX_FLAGS+=" -Werror "])

-    AX_CHECK_COMPILE_FLAG([-Wno-unused-parameter],

-        [GAPS_CXX_FLAGS+=" -Wno-unused-parameter "])

+    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 "

+    fi

 fi

 # set compile flags for SIMD

+AX_EXT

+echo "Supported SIMD flags: " $SIMD_FLAGS

+

+if test "x$simd_version" != "xavx" && test "x$simd_version" != "xsse" && test "x$simd_version" != "xno" && test "x$simd_version" != "xyes" ; then

+    echo "Invalid SIMD Type, Defaulting to AVX"

+    simd_version=avx

+fi

+

+avx_supported=false

+if test "x$simd_version" = "xavx" || test "x$simd_version" = "xyes" ; then

+    for s in $SIMD_FLAGS; do

+        if test "x$s" = "x-mavx"; then

+            avx_supported=true

+            echo "Building with AVX instructions"

+            GAPS_CXX_FLAGS+=" -mavx "

+        fi

+    done

+    if test "x$avx_supported" = "xfalse" ; then

+        echo "Note: AVX not supported, trying for SSE"

+        simd_version=sse

+    fi

+fi

+

+sse_supported=false

 if test "x$simd_version" = "xsse" ; then

-    echo "Compiling with SSE instructions"

-    AX_CHECK_COMPILE_FLAG([-msse4.2], [GAPS_CXX_FLAGS+=" -msse4.2 "])

-elif test "x$simd_version" = "xyes" ; then

-    echo "Compiling with SSE instructions"

-    AX_CHECK_COMPILE_FLAG([-msse4.2], [GAPS_CXX_FLAGS+=" -msse4.2 "])

-elif test "x$simd_version" = "xavx" ; then

-    echo "Compiling with AVX instructions"

-    AX_CHECK_COMPILE_FLAG([-mavx], [GAPS_CXX_FLAGS+=" -mavx "])    

-elif test "x$simd_version" = "xno" ; then

-    echo "Compiling without SIMD instructions"

-else

-    echo "Error: Invalid SIMD type"

-    exit -1

+    for s in $SIMD_FLAGS; do

+        if test "x$s" = "x-msse4.2"; then

+            sse_supported=true

+            echo "Building with SSE instructions"

+            GAPS_CXX_FLAGS+=" -msse4.2 "

+        fi

+    done

+    if test "x$sse_supported" = "xfalse" ; then

+        echo "Note: SSE not supported"

+        simd_version=no

+    fi

+fi

+

+if test "x$simd_version" = "xno" ; then

+    echo "Building without SIMD instructions"

 fi

 # export variables containing flags

@@ -49,8 +49,8 @@ if test "x$warnings" = "xyes" ; then

     AX_CHECK_COMPILE_FLAG([-Wall], [GAPS_CXX_FLAGS+=" -Wall "])

     AX_CHECK_COMPILE_FLAG([-Wextra], [GAPS_CXX_FLAGS+=" -Wextra "])

     AX_CHECK_COMPILE_FLAG([-Werror], [GAPS_CXX_FLAGS+=" -Werror "])

-    AX_CHECK_COMPILE_FLAG([-Wno-unused-parameter], [GAPS_CXX_FLAGS+=" -Wno-unused-parameter "])

-    AX_CHECK_COMPILE_FLAG([-Wno-unused-function], [GAPS_CXX_FLAGS+=" -Wno-unused-function "])

+    AX_CHECK_COMPILE_FLAG([-Wno-unused-parameter],

+        [GAPS_CXX_FLAGS+=" -Wno-unused-parameter "])

 fi

 # set compile flags for SIMD

@@ -13,10 +13,6 @@ AC_PROG_CXX

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

     [build debug version of CoGAPS])], [build_debug=yes], [build_debug=no])

-# Check if compiling debug version with thread sanitizer

-AC_ARG_ENABLE(debug_tsan, [AC_HELP_STRING([--enable-debug-tsan],

-    [build debug version of CoGAPS])], [build_debug_tsan=yes], [build_debug_tsan=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])

@@ -45,21 +41,7 @@ echo "building on $ax_cv_cxx_compiler_vendor compiler version $ax_cv_cxx_compile

 # set compile flags for debug build

 if test "x$build_debug" = "xyes" ; then

     echo "Building Debug Version of CoGAPS"

-    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG -fno-omit-frame-pointer "

-    if test "x$ax_cv_cxx_compiler_vendor" = "xclang" ; then

-        GAPS_CPP_FLAGS+=" -fsanitize=address -fsanitize=undefined "

-        GAPS_LIBS+=" -fsanitize=address -fsanitize=undefined "

-    elif test "x$ax_cv_cxx_compiler_vendor" = "xgnu" ; then

-        GAPS_CPP_FLAGS+=" -fsanitize=address -fsanitize=undefined "

-        GAPS_LIBS+=" -fsanitize=address -fsanitize=undefined "

-    fi

-elif test "x$build_debug_tsan" = "xyes" ; then

-    echo "Building Debug Version of CoGAPS with thread sanitizer"

-    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG -fno-omit-frame-pointer "

-    if test "x$ax_cv_cxx_compiler_vendor" = "xclang" ; then

-        GAPS_CPP_FLAGS+=" -fsanitize=thread "

-        GAPS_LIBS+=" -fsanitize=thread "

-    fi

+    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG "

 fi

 # set compile flags if warnings enabled

@@ -1,11 +1,5 @@

-# include macros

-m4_builtin([include], m4/ax_check_compile_flag.m4)

-m4_builtin([include], m4/ax_compiler_vendor.m4)

-m4_builtin([include], m4/ax_compiler_version.m4)

-m4_builtin([include], m4/ax_openmp.m4)

-

 # get version of CoGAPS from DESCRIPTION file

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

+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`

@@ -29,7 +29,7 @@ AC_ARG_ENABLE(simd, [AC_HELP_STRING([--enable-simd],

     [simd_version=$enableval], [simd_version=sse])

 # default CoGAPS specific flags

-GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 "

+GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ "

 GAPS_CXX_FLAGS=

 GAPS_LIBS=

@@ -1,8 +1,8 @@

 # include macros

-m4_builtin([include], ax_check_compile_flag.m4)

-m4_builtin([include], ax_compiler_vendor.m4)

-m4_builtin([include], ax_compiler_version.m4)

-m4_builtin([include], ax_openmp.m4)

+m4_builtin([include], m4/ax_check_compile_flag.m4)

+m4_builtin([include], m4/ax_compiler_vendor.m4)

+m4_builtin([include], m4/ax_compiler_version.m4)

+m4_builtin([include], m4/ax_openmp.m4)

 # get version of CoGAPS from DESCRIPTION file

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

@@ -19,6 +19,10 @@ AC_PROG_CXX

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

     [build debug version of CoGAPS])], [build_debug=yes], [build_debug=no])

+# Check if compiling debug version with thread sanitizer

+AC_ARG_ENABLE(debug_tsan, [AC_HELP_STRING([--enable-debug-tsan],

+    [build debug version of CoGAPS])], [build_debug_tsan=yes], [build_debug_tsan=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])

@@ -47,7 +51,21 @@ echo "building on $ax_cv_cxx_compiler_vendor compiler version $ax_cv_cxx_compile

 # set compile flags for debug build

 if test "x$build_debug" = "xyes" ; then

     echo "Building Debug Version of CoGAPS"

-    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG "

+    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG -fno-omit-frame-pointer "

+    if test "x$ax_cv_cxx_compiler_vendor" = "xclang" ; then

+        GAPS_CPP_FLAGS+=" -fsanitize=address -fsanitize=undefined "

+        GAPS_LIBS+=" -fsanitize=address -fsanitize=undefined "

+    elif test "x$ax_cv_cxx_compiler_vendor" = "xgnu" ; then

+        GAPS_CPP_FLAGS+=" -fsanitize=address -fsanitize=undefined "

+        GAPS_LIBS+=" -fsanitize=address -fsanitize=undefined "

+    fi

+elif test "x$build_debug_tsan" = "xyes" ; then

+    echo "Building Debug Version of CoGAPS with thread sanitizer"

+    GAPS_CPP_FLAGS+=" -DGAPS_DEBUG -fno-omit-frame-pointer "

+    if test "x$ax_cv_cxx_compiler_vendor" = "xclang" ; then

+        GAPS_CPP_FLAGS+=" -fsanitize=thread "

+        GAPS_LIBS+=" -fsanitize=thread "

+    fi

 fi

 # set compile flags if warnings enabled

@@ -1,8 +1,8 @@

 # include macros

-m4_builtin([include], ax_check_compile_flag.m4)

-m4_builtin([include], ax_compiler_vendor.m4)

-m4_builtin([include], ax_compiler_version.m4)

-m4_builtin([include], ax_openmp.m4)

+m4_builtin([include], m4/ax_check_compile_flag.m4)

+m4_builtin([include], m4/ax_compiler_vendor.m4)

+m4_builtin([include], m4/ax_compiler_version.m4)

+m4_builtin([include], m4/ax_openmp.m4)

 # get version of CoGAPS from DESCRIPTION file

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

@@ -1,77 +1,87 @@

-# include macros

-m4_builtin([include], ax_check_compile_flag.m4)

-m4_builtin([include], ax_compiler_vendor.m4)

-m4_builtin([include], ax_compiler_version.m4)

-m4_builtin([include], ax_openmp.m4)

-

-# get version of CoGAPS from DESCRIPTION file

-AC_INIT(CoGAPS, m4_esyscmd_s([awk -e '/^Version:/ {print $2}' Repo/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 specific version of SIMD instructions requested

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

-    [specify simd instruction set (sse, avx)])],

-    [simd_version=$enableval], [simd_version=sse])

-

-# default CoGAPS specific flags

-GAPS_CPP_FLAGS=" -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 "

-GAPS_CXX_FLAGS=

-GAPS_LIBS=

-

-# get compiler info

-AX_COMPILER_VENDOR

-AX_COMPILER_VERSION

-AX_OPENMP

-

-# set openmp flags

-GAPS_CXX_FLAGS+=" $OPENMP_CXXFLAGS "

-GAPS_LIBS+=" $OPENMP_CXXFLAGS "

-

-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 "

-    AX_CHECK_COMPILE_FLAG([-Wall], [GAPS_CXX_FLAGS+=" -Wall "])

-    AX_CHECK_COMPILE_FLAG([-Wextra], [GAPS_CXX_FLAGS+=" -Wextra "])