From 22ae85100877c8c4c5c4e1c84c143a7643f1d34c Mon Sep 17 00:00:00 2001
From: James J Balamuta <james.balamuta@gmail.com>
Date: Sat, 26 Aug 2017 16:59:15 -0500
Subject: [PATCH 1/5] Block macOS system files from entering repo

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 0a747394..1f6cda3f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
 .Rproj.user
 .Rhistory
 .RData
+.DS_Store
 src/*.o
 src/*.so
 src/*.dll

From be5000662e773022d4dd878a9524e56ef70b1fc9 Mon Sep 17 00:00:00 2001
From: James J Balamuta <james.balamuta@gmail.com>
Date: Sat, 26 Aug 2017 18:41:20 -0500
Subject: [PATCH 2/5] Determine the appropriate OpenMP flags in configure.ac

---
 R/{inline.R => inline.R.in}                   |   4 +-
 cleanup                                       |   4 +-
 configure                                     | 828 +++++++++++++++++-
 configure.ac                                  |  87 +-
 .../include/RcppArmadilloConfigGenerated.h.in |   3 +
 src/{Makevars => Makevars.in}                 |   4 +-
 6 files changed, 885 insertions(+), 45 deletions(-)
 rename R/{inline.R => inline.R.in} (85%)
 rename src/{Makevars => Makevars.in} (84%)

diff --git a/R/inline.R b/R/inline.R.in
similarity index 85%
rename from R/inline.R
rename to R/inline.R.in
index 75a9298d..0c03b754 100644
--- a/R/inline.R
+++ b/R/inline.R.in
@@ -19,11 +19,11 @@ inlineCxxPlugin <- function(...) {
     plugin <-
         Rcpp::Rcpp.plugin.maker(
                    include.before = "#include <RcppArmadillo.h>",
-                   libs           = "$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)",
+                   libs           = "@HAVE_OPENMP_R_CFLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)",
                    package        = "RcppArmadillo"
                )
     settings <- plugin()
-    settings$env$PKG_CPPFLAGS <- "-I../inst/include $(SHLIB_OPENMP_CXXFLAGS)"
+    settings$env$PKG_CPPFLAGS <- "-I../inst/include @HAVE_OPENMP_R_CXXFLAG@"
     settings
 }
 
diff --git a/cleanup b/cleanup
index 294a0c25..b2383a5f 100755
--- a/cleanup
+++ b/cleanup
@@ -16,7 +16,9 @@ rm -f  config.log config.status confdefs.h \
        vignettes/*~ \
        */*~ *~ \
        inst/include/RcppArmadilloLapack.h \
-       inst/include/RcppArmadilloConfigGenerated.h
+       inst/include/RcppArmadilloConfigGenerated.h \
+       src/Makevars \
+       R/inline.R
 
 rm -rf autom4te.cache/ \
        vignettes/auto/
diff --git a/configure b/configure
index a609807e..3e717927 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for RcppArmadillo 0.7.960.1.1.
+# Generated by GNU Autoconf 2.69 for RcppArmadillo 0.7.960.1.1.1.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -576,16 +576,23 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RcppArmadillo'
 PACKAGE_TARNAME='rcpparmadillo'
-PACKAGE_VERSION='0.7.960.1.1'
-PACKAGE_STRING='RcppArmadillo 0.7.960.1.1'
+PACKAGE_VERSION='0.7.960.1.1.1'
+PACKAGE_STRING='RcppArmadillo 0.7.960.1.1.1'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+HAVE_OPENMP_R_CXXFLAG
+HAVE_OPENMP_R_CFLAG
+HAVE_OPENMP_WARNING
 HAVE_OPENMP
 ARMA_CRIPPLED_LAPACK
 HAVE_GOOD_LAPACK
+OPENMP_CXXFLAGS
+ac_ct_CC
+CFLAGS
+CC
 CXXCPP
 OBJEXT
 EXEEXT
@@ -636,6 +643,7 @@ SHELL'
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
+enable_openmp
 '
       ac_precious_vars='build_alias
 host_alias
@@ -646,7 +654,9 @@ LDFLAGS
 LIBS
 CPPFLAGS
 CCC
-CXXCPP'
+CXXCPP
+CC
+CFLAGS'
 
 
 # Initialize some variables set by options.
@@ -1197,7 +1207,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures RcppArmadillo 0.7.960.1.1 to adapt to many kinds of systems.
+\`configure' configures RcppArmadillo 0.7.960.1.1.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1259,10 +1269,16 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of RcppArmadillo 0.7.960.1.1:";;
+     short | recursive ) echo "Configuration of RcppArmadillo 0.7.960.1.1.1:";;
    esac
   cat <<\_ACEOF
 
+Optional Features:
+  --disable-option-checking  ignore unrecognized --enable/--with options
+  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
+  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
+  --disable-openmp        do not use OpenMP
+
 Some influential environment variables:
   CXX         C++ compiler command
   CXXFLAGS    C++ compiler flags
@@ -1272,6 +1288,8 @@ Some influential environment variables:
   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
   CXXCPP      C++ preprocessor
+  CC          C compiler command
+  CFLAGS      C compiler flags
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -1339,7 +1357,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-RcppArmadillo configure 0.7.960.1.1
+RcppArmadillo configure 0.7.960.1.1.1
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1427,11 +1445,95 @@ fi
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_cpp
+
+# ac_fn_c_try_compile LINENO
+# --------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_compile ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  rm -f conftest.$ac_objext
+  if { { ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_compile") 2>conftest.err
+  ac_status=$?
+  if test -s conftest.err; then
+    grep -v '^ *+' conftest.err >conftest.er1
+    cat conftest.er1 >&5
+    mv -f conftest.er1 conftest.err
+  fi
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then :
+  ac_retval=0
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_retval=1
+fi
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_compile
+
+# ac_fn_cxx_try_link LINENO
+# -------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_link ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  rm -f conftest.$ac_objext conftest$ac_exeext
+  if { { ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_link") 2>conftest.err
+  ac_status=$?
+  if test -s conftest.err; then
+    grep -v '^ *+' conftest.err >conftest.er1
+    cat conftest.er1 >&5
+    mv -f conftest.er1 conftest.err
+  fi
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } && {
+	 test -z "$ac_cxx_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 test -x conftest$ac_exeext
+       }; then :
+  ac_retval=0
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_retval=1
+fi
+  # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+  # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+  # interfere with the next link command; also delete a directory that is
+  # left behind by Apple's compiler.  We do this before executing the actions.
+  rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+  as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_link
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by RcppArmadillo $as_me 0.7.960.1.1, which was
+It was created by RcppArmadillo $as_me 0.7.960.1.1.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -1785,9 +1887,14 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 if test -z "${R_HOME}"; then
     as_fn_error $? "Could not determine R_HOME." "$LINENO" 5
 fi
-## Use R to set CXX and CXXFLAGS
+
+## Use R to set CC, CXX, CFLAGS, and CXXFLAGS
+RBIN="${R_HOME}/bin/R"
+CC=$(${R_HOME}/bin/R CMD config CC)
+CFLAGS=$(${R_HOME}/bin/R CMD config CFLAGS)
 CXX=$(${R_HOME}/bin/R CMD config CXX)
-CXXFLAGS=$("${R_HOME}/bin/R" CMD config CXXFLAGS)
+CXXFLAGS=$(${R_HOME}/bin/R CMD config CXXFLAGS)
+LIBS="${PKG_LIBS}"
 
 ## We are using C++
 ac_ext=cpp
@@ -2698,6 +2805,7 @@ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
+
 ## If it is g++, we have GXX set so let's examine it
 if test "${GXX}" = yes; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether g++ version is sufficient" >&5
@@ -2725,13 +2833,13 @@ fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking LAPACK_LIBS" >&5
 $as_echo_n "checking LAPACK_LIBS... " >&6; }
 
-## external LAPACK has the required function
+## External LAPACK has the required function
 lapack=$(${R_HOME}/bin/R CMD config LAPACK_LIBS)
 hasRlapack=$(echo ${lapack} | grep lRlapack)
 ## internal Rlapack now the required functions if "new enough": R 3.3.0 or later
 newR=$("${R_HOME}/bin/Rscript" --vanilla -e 'if (getRversion() >= "3.3.0") cat("yes") else cat("no")')
 
-## in what follows below we substitute both side of the define/undef
+## In what follows below we substitute both side of the define/undef
 ## while this may seem a little unusual we do it to fully reproduce the
 ## previous bash-based implementation
 
@@ -2759,33 +2867,701 @@ $as_echo "$as_me: WARNING: Some complex-valued LAPACK functions may not be avail
     fi
 fi
 
-## Check for OpenMP
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for OpenMP" >&5
-$as_echo_n "checking for OpenMP... " >&6; }
-## if R has -fopenmp we should be good
-allldflags=$(${R_HOME}/bin/R CMD config --ldflags)
-hasOpenMP=$(echo ${allldflags} | grep -- -fopenmp)
-if test x"${hasOpenMP}" == x""; then
-   { $as_echo "$as_me:${as_lineno-$LINENO}: result: missing" >&5
-$as_echo "missing" >&6; }
-   have_openmp="#define ARMA_DONT_USE_OPENMP 1"
+
+## Store whether openmp should be checked
+supported_openmp_os=yes
+
+## Simplify life to avoid AC_CANONICAL_HOST headaches
+OSNAME=`uname -s 2>/dev/null`
+
+if test "x$OSNAME" = xDarwin; then
+    supported_openmp_os=no
+fi
+
+## The next part has been modified slightly from simon's OpenMP check script
+## https://stat.ethz.ch/pipermail/r-devel/2010-September/058488.html
+
+## Account for systems with broken OMP libraries...
+ac_pkg_openmp=no
+
+## Checks for programs
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_CC="${ac_tool_prefix}gcc"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
 else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+  ac_ct_CC=$CC
+  # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$ac_ct_CC"; then
+  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_ac_ct_CC="gcc"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+  if test "x$ac_ct_CC" = x; then
+    CC=""
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+    CC=$ac_ct_CC
+  fi
+else
+  CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+          if test -n "$ac_tool_prefix"; then
+    # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_CC="${ac_tool_prefix}cc"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+  fi
+fi
+if test -z "$CC"; then
+  # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+  ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+       ac_prog_rejected=yes
+       continue
+     fi
+    ac_cv_prog_CC="cc"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+  # We found a bogon in the path, so make sure we never use it.
+  set dummy $ac_cv_prog_CC
+  shift
+  if test $# != 0; then
+    # We chose a different compiler from the bogus one.
+    # However, it has the same basename, so the bogon will be chosen
+    # first if we set CC to just the basename; use the full file name.
+    shift
+    ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+  fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+  if test -n "$ac_tool_prefix"; then
+  for ac_prog in cl.exe
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$CC"; then
+  ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+    test -n "$CC" && break
+  done
+fi
+if test -z "$CC"; then
+  ac_ct_CC=$CC
+  for ac_prog in cl.exe
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$ac_ct_CC"; then
+  ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_ac_ct_CC="$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+  test -n "$ac_ct_CC" && break
+done
+
+  if test "x$ac_ct_CC" = x; then
+    CC=""
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+    CC=$ac_ct_CC
+  fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "no acceptable C compiler found in \$PATH
+See \`config.log' for more details" "$LINENO" 5; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+for ac_option in --version -v -V -qversion; do
+  { { ac_try="$ac_compiler $ac_option >&5"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_compiler $ac_option >&5") 2>conftest.err
+  ac_status=$?
+  if test -s conftest.err; then
+    sed '10a\
+... rest of stderr output deleted ...
+         10q' conftest.err >conftest.er1
+    cat conftest.er1 >&5
+  fi
+  rm -f conftest.er1 conftest.err
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }
+done
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if ${ac_cv_c_compiler_gnu+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+#ifndef __GNUC__
+       choke me
+#endif
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_compiler_gnu=yes
+else
+  ac_compiler_gnu=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+  GCC=yes
+else
+  GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if ${ac_cv_prog_cc_g+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_save_c_werror_flag=$ac_c_werror_flag
+   ac_c_werror_flag=yes
+   ac_cv_prog_cc_g=no
+   CFLAGS="-g"
+   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_prog_cc_g=yes
+else
+  CFLAGS=""
+      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+
+else
+  ac_c_werror_flag=$ac_save_c_werror_flag
+	 CFLAGS="-g"
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_prog_cc_g=yes
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+   ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+  CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+  if test "$GCC" = yes; then
+    CFLAGS="-g -O2"
+  else
+    CFLAGS="-g"
+  fi
+else
+  if test "$GCC" = yes; then
+    CFLAGS="-O2"
+  else
+    CFLAGS=
+  fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if ${ac_cv_prog_cc_c89+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <stdarg.h>
+#include <stdio.h>
+struct stat;
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh.  */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+     char **p;
+     int i;
+{
+  return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+  char *s;
+  va_list v;
+  va_start (v,p);
+  s = g (p, va_arg (v,int));
+  va_end (v);
+  return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default.  It has
+   function prototypes and stuff, but not '\xHH' hex character constants.
+   These don't provoke an error unfortunately, instead are silently treated
+   as 'x'.  The following induces an error, until -std is added to get
+   proper ANSI mode.  Curiously '\x00'!='x' always comes out true, for an
+   array size at least.  It's necessary to write '\x00'==0 to get something
+   that's true only with -std.  */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+   inside strings and character constants.  */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0]  ||  f (e, argv, 1) != argv[1];
+  ;
+  return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+	-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+  CC="$ac_save_CC $ac_arg"
+  if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+  test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+  x)
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+  xno)
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+  *)
+    CC="$CC $ac_cv_prog_cc_c89"
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+## Only run checks if openmp is supported on the os
+if test "${supported_openmp_os}" = "yes"; then
+
+  ## Checks for OpenMP
+
+  OPENMP_CXXFLAGS=
+  # Check whether --enable-openmp was given.
+if test "${enable_openmp+set}" = set; then :
+  enableval=$enable_openmp;
+fi
+
+  if test "$enable_openmp" != no; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CXX option to support OpenMP" >&5
+$as_echo_n "checking for $CXX option to support OpenMP... " >&6; }
+if ${ac_cv_prog_cxx_openmp+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+#ifndef _OPENMP
+ choke me
+#endif
+#include <omp.h>
+int main () { return omp_get_num_threads (); }
+
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+  ac_cv_prog_cxx_openmp='none needed'
+else
+  ac_cv_prog_cxx_openmp='unsupported'
+	  	  	  	  	  	  	                                	  	  	  	  	  	  for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp -homp \
+                           -Popenmp --openmp; do
+	    ac_save_CXXFLAGS=$CXXFLAGS
+	    CXXFLAGS="$CXXFLAGS $ac_option"
+	    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+#ifndef _OPENMP
+ choke me
+#endif
+#include <omp.h>
+int main () { return omp_get_num_threads (); }
+
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+  ac_cv_prog_cxx_openmp=$ac_option
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+	    CXXFLAGS=$ac_save_CXXFLAGS
+	    if test "$ac_cv_prog_cxx_openmp" != unsupported; then
+	      break
+	    fi
+	  done
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_openmp" >&5
+$as_echo "$ac_cv_prog_cxx_openmp" >&6; }
+    case $ac_cv_prog_cxx_openmp in #(
+      "none needed" | unsupported)
+	;; #(
+      *)
+	OPENMP_CXXFLAGS=$ac_cv_prog_cxx_openmp ;;
+    esac
+  fi
+
+
+
+  if test -n "${OPENMP_CFLAGS}"; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether OpenMP will work in a package" >&5
+$as_echo_n "checking whether OpenMP will work in a package... " >&6; }
+    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <omp.h>
+int
+main ()
+{
+ return omp_get_num_threads ();
+  ;
+  return 0;
+}
+_ACEOF
+    PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "${R_HOME}/bin/R" CMD SHLIB conftest.c 1>&5 2>&5 && "${R_HOME}/bin/R" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&5 2>&5 && ac_pkg_openmp=yes
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${ac_pkg_openmp}" >&5
+$as_echo "${ac_pkg_openmp}" >&6; }
+  fi
+fi
+
+if test "${ac_pkg_openmp}" = "yes"; then
    { $as_echo "$as_me:${as_lineno-$LINENO}: result: found" >&5
 $as_echo "found" >&6; }
    have_openmp="#define ARMA_USE_OPENMP 1"
+   have_openmp_warning=""
+   have_openmp_r_cflag='$(SHLIB_OPENMP_CFLAGS)'
+   have_openmp_r_cxxflag='$(SHLIB_OPENMP_CXXFLAGS)'
 fi
 
+if test "${ac_pkg_openmp}" = "no"; then
+
+   if test "${supported_openmp_os}" = "no"; then
+      { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: OpenMP support on macOS has been temporarily disabled due to detection issues with the binary." >&5
+$as_echo "$as_me: WARNING: OpenMP support on macOS has been temporarily disabled due to detection issues with the binary." >&2;}
+   else
+      { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2. If using clang, upgrade to >= 3.8.0" >&5
+$as_echo "$as_me: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2. If using clang, upgrade to >= 3.8.0" >&2;}
+   fi
 
+   have_openmp="#define ARMA_DONT_USE_OPENMP 1"
+   have_openmp_warning="#define ARMA_DONT_PRINT_OPENMP_WARNING 1"
+   have_openmp_r_cflag=""
+   have_openmp_r_cxxflag=""
+fi
 
-## now use all these
+## Now use all these
 HAVE_GOOD_LAPACK="${have_good_lapack}"
 
 ARMA_CRIPPLED_LAPACK="${arma_crippled_lapack}"
 
 HAVE_OPENMP="${have_openmp}"
 
+HAVE_OPENMP_WARNING="${have_openmp_warning}"
+
+HAVE_OPENMP_R_CFLAG="${have_openmp_r_cflag}"
+
+HAVE_OPENMP_R_CXXFLAG="${have_openmp_r_cxxflag}"
+
 ac_config_files="$ac_config_files inst/include/RcppArmadilloConfigGenerated.h"
 
+# Set flags for inline.R
+ac_config_files="$ac_config_files R/inline.R"
+
+# Also needed in the Makevars
+ac_config_files="$ac_config_files src/Makevars"
+
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
 # tests run on this system so they can be shared between configure
@@ -3328,7 +4104,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by RcppArmadillo $as_me 0.7.960.1.1, which was
+This file was extended by RcppArmadillo $as_me 0.7.960.1.1.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3381,7 +4157,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-RcppArmadillo config.status 0.7.960.1.1
+RcppArmadillo config.status 0.7.960.1.1.1
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
@@ -3492,6 +4268,8 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "inst/include/RcppArmadilloConfigGenerated.h") CONFIG_FILES="$CONFIG_FILES inst/include/RcppArmadilloConfigGenerated.h" ;;
+    "R/inline.R") CONFIG_FILES="$CONFIG_FILES R/inline.R" ;;
+    "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac
diff --git a/configure.ac b/configure.ac
index c5214e6c..13d2bd64 100644
--- a/configure.ac
+++ b/configure.ac
@@ -8,7 +8,9 @@
 ##
 ##  Licensed under GPL-2 or later
 
-## require at least autoconf 2.61
+## Run this script using autoconf -i under the RcppArmadillo package directory
+
+## Require at least autoconf 2.61
 AC_PREREQ(2.61)
 
 ## Process this file with autoconf to produce a configure script.
@@ -19,9 +21,14 @@ AC_INIT(RcppArmadillo, m4_esyscmd_s([awk -e '/^Version:/ {print $2}' DESCRIPTION
 if test -z "${R_HOME}"; then
     AC_MSG_ERROR([Could not determine R_HOME.])   
 fi
-## Use R to set CXX and CXXFLAGS
+
+## Use R to set CC, CXX, CFLAGS, and CXXFLAGS
+RBIN="${R_HOME}/bin/R"
+CC=$(${R_HOME}/bin/R CMD config CC)
+CFLAGS=$(${R_HOME}/bin/R CMD config CFLAGS)
 CXX=$(${R_HOME}/bin/R CMD config CXX)
-CXXFLAGS=$("${R_HOME}/bin/R" CMD config CXXFLAGS)
+CXXFLAGS=$(${R_HOME}/bin/R CMD config CXXFLAGS)
+LIBS="${PKG_LIBS}"
 
 ## We are using C++
 AC_LANG(C++)
@@ -29,6 +36,7 @@ AC_REQUIRE_CPP
 
 ## Check the C++ compiler using the CXX value set
 AC_PROG_CXX
+
 ## If it is g++, we have GXX set so let's examine it
 if test "${GXX}" = yes; then
     AC_MSG_CHECKING([whether g++ version is sufficient])
@@ -51,13 +59,13 @@ fi
 ## Check for suitable LAPACK_LIBS
 AC_MSG_CHECKING([LAPACK_LIBS])
 
-## external LAPACK has the required function
+## External LAPACK has the required function
 lapack=$(${R_HOME}/bin/R CMD config LAPACK_LIBS)
 hasRlapack=$(echo ${lapack} | grep lRlapack)
 ## internal Rlapack now the required functions if "new enough": R 3.3.0 or later
 newR=$("${R_HOME}/bin/Rscript" --vanilla -e 'if (getRversion() >= "3.3.0") cat("yes") else cat("no")')
 
-## in what follows below we substitute both side of the define/undef
+## In what follows below we substitute both side of the define/undef
 ## while this may seem a little unusual we do it to fully reproduce the
 ## previous bash-based implementation
 
@@ -81,24 +89,73 @@ else
     fi
 fi
 
-## Check for OpenMP
-AC_MSG_CHECKING([for OpenMP])
-## if R has -fopenmp we should be good
-allldflags=$(${R_HOME}/bin/R CMD config --ldflags)
-hasOpenMP=$(echo ${allldflags} | grep -- -fopenmp)
-if test x"${hasOpenMP}" == x""; then
-   AC_MSG_RESULT([missing])
-   have_openmp="#define ARMA_DONT_USE_OPENMP 1"
-else   
+
+## Store whether openmp should be checked
+supported_openmp_os=yes
+
+## Simplify life to avoid AC_CANONICAL_HOST headaches
+OSNAME=`uname -s 2>/dev/null`
+
+if test "x$OSNAME" = xDarwin; then
+    supported_openmp_os=no
+fi
+
+## The next part has been modified slightly from simon's OpenMP check script
+## https://stat.ethz.ch/pipermail/r-devel/2010-September/058488.html
+
+## Account for systems with broken OMP libraries...
+ac_pkg_openmp=no
+
+## Checks for programs
+AC_PROG_CC
+  
+## Only run checks if openmp is supported on the os
+if test "${supported_openmp_os}" = "yes"; then
+  
+  ## Checks for OpenMP
+  AC_OPENMP
+  
+  if test -n "${OPENMP_CFLAGS}"; then
+    AC_MSG_CHECKING([whether OpenMP will work in a package])
+    AC_LANG_CONFTEST(
+    [AC_LANG_PROGRAM([[#include <omp.h>]], [[ return omp_get_num_threads (); ]])])
+    PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "${R_HOME}/bin/R" CMD SHLIB conftest.c 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && "${R_HOME}/bin/R" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && ac_pkg_openmp=yes
+    AC_MSG_RESULT([${ac_pkg_openmp}])
+  fi
+fi 
+
+if test "${ac_pkg_openmp}" = "yes"; then
    AC_MSG_RESULT([found])
    have_openmp="#define ARMA_USE_OPENMP 1"
+   have_openmp_warning=""
+   have_openmp_r_cflag='$(SHLIB_OPENMP_CFLAGS)'
+   have_openmp_r_cxxflag='$(SHLIB_OPENMP_CXXFLAGS)'
 fi
 
+if test "${ac_pkg_openmp}" = "no"; then
+   
+   if test "${supported_openmp_os}" = "no"; then
+      AC_MSG_WARN([OpenMP support on macOS has been temporarily disabled due to detection issues with the binary.])
+   else
+      AC_MSG_WARN([No OpenMP support. If using GCC, upgrade to >= 4.2. If using clang, upgrade to >= 3.8.0])   
+   fi
 
+   have_openmp="#define ARMA_DONT_USE_OPENMP 1"
+   have_openmp_warning="#define ARMA_DONT_PRINT_OPENMP_WARNING 1"
+   have_openmp_r_cflag=""
+   have_openmp_r_cxxflag=""
+fi
 
-## now use all these
+## Now use all these
 AC_SUBST([HAVE_GOOD_LAPACK],["${have_good_lapack}"])
 AC_SUBST([ARMA_CRIPPLED_LAPACK], ["${arma_crippled_lapack}"])
 AC_SUBST([HAVE_OPENMP], ["${have_openmp}"])
+AC_SUBST([HAVE_OPENMP_WARNING], ["${have_openmp_warning}"])
+AC_SUBST([HAVE_OPENMP_R_CFLAG], ["${have_openmp_r_cflag}"])
+AC_SUBST([HAVE_OPENMP_R_CXXFLAG], ["${have_openmp_r_cxxflag}"])
 AC_CONFIG_FILES([inst/include/RcppArmadilloConfigGenerated.h])
+# Set flags for inline.R
+AC_CONFIG_FILES([R/inline.R])
+# Also needed in the Makevars
+AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT
diff --git a/inst/include/RcppArmadilloConfigGenerated.h.in b/inst/include/RcppArmadilloConfigGenerated.h.in
index c1bd0211..5bfc4c27 100644
--- a/inst/include/RcppArmadilloConfigGenerated.h.in
+++ b/inst/include/RcppArmadilloConfigGenerated.h.in
@@ -28,4 +28,7 @@
 // from configure test for OpenMP
 @HAVE_OPENMP@
 
+// disables warning if compiler does not support OpenMP
+@HAVE_OPENMP_WARNING@
+
 #endif
diff --git a/src/Makevars b/src/Makevars.in
similarity index 84%
rename from src/Makevars
rename to src/Makevars.in
index 8022bfb6..af2c4772 100644
--- a/src/Makevars
+++ b/src/Makevars.in
@@ -1,7 +1,7 @@
 ## -*- mode: makefile; -*-
 
-PKG_CXXFLAGS = -I../inst/include $(SHLIB_OPENMP_CXXFLAGS) 
-PKG_LIBS= $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_CXXFLAGS=-I../inst/include @HAVE_OPENMP_R_CXXFLAG@
+PKG_LIBS=@HAVE_OPENMP_R_CFLAG@ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
 ## With R 3.1.0 or later, you can uncomment the following line to tell R to 
 ## enable compilation with C++11 (where available)

From 6921ff5c4e6e1d1caf2322be683948ad6a7acbe4 Mon Sep 17 00:00:00 2001
From: James J Balamuta <james.balamuta@gmail.com>
Date: Sat, 26 Aug 2017 18:42:52 -0500
Subject: [PATCH 3/5] Fix for the vignette engine hiccup

---
 DESCRIPTION                              | 2 +-
 vignettes/RcppArmadillo-sparseMatrix.Rnw | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e21c4e59..3bb45261 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -23,6 +23,6 @@ License: GPL (>= 2)
 LazyLoad: yes
 LinkingTo: Rcpp
 Imports: Rcpp (>= 0.11.0), stats, utils, methods
-Suggests: RUnit, Matrix, pkgKitten, reticulate
+Suggests: RUnit, Matrix, pkgKitten, reticulate, highlight
 URL: http://dirk.eddelbuettel.com/code/rcpp.armadillo.html
 BugReports: https://github.com/RcppCore/RcppArmadillo/issues
diff --git a/vignettes/RcppArmadillo-sparseMatrix.Rnw b/vignettes/RcppArmadillo-sparseMatrix.Rnw
index 2561adbc..bc7f5f41 100644
--- a/vignettes/RcppArmadillo-sparseMatrix.Rnw
+++ b/vignettes/RcppArmadillo-sparseMatrix.Rnw
@@ -3,7 +3,7 @@
 %\VignetteIndexEntry{RcppArmadillo-sparseMatrix}
 %\VignetteEngine{highlight::highlight}
 %\VignetteKeywords{R, C++, Armadillo, linear algebra, sparse matrix}
-%\VignettePackage{RcppArmadillo}
+%\VignetteDepends{RcppArmadillo}
 
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}

From 7272da378fe921fe9b972aecd06abc6de9625674 Mon Sep 17 00:00:00 2001
From: James J Balamuta <james.balamuta@gmail.com>
Date: Sat, 26 Aug 2017 18:43:08 -0500
Subject: [PATCH 4/5] Add gitignore for vignette files...

---
 vignettes/.gitignore | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 vignettes/.gitignore

diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 00000000..5e469eb9
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,9 @@
+RcppArmadillo-*.aux
+RcppArmadillo-*.out
+RcppArmadillo-*.toc
+RcppArmadillo-*.bbl
+RcppArmadillo-*.blg
+RcppArmadillo-*.log
+RcppArmadillo-*.tex
+RcppArmadillo-*.pdf
+unitTests-results/
\ No newline at end of file

From 46270192b8e9a8a85f2a28427f185baa7cf67c4a Mon Sep 17 00:00:00 2001
From: James J Balamuta <james.balamuta@gmail.com>
Date: Sat, 26 Aug 2017 20:04:34 -0500
Subject: [PATCH 5/5] Adds highlight dependency in travis

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 3f298854..029075dc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -13,7 +13,7 @@ before_install:
   - ./run.sh bootstrap
 
 install:
-  - ./run.sh install_aptget  r-cran-rcpp r-cran-runit r-cran-matrix r-cran-pkgkitten r-cran-jsonlite python-scipy
+  - ./run.sh install_aptget  r-cran-rcpp r-cran-runit r-cran-matrix r-cran-pkgkitten r-cran-jsonlite python-scipy r-cran-highlight
   - ./run.sh install_r reticulate
 
 script: