@@ -55,7 +55,14 @@ if test "x$use_pthread_stack_min" = xno; then

 fi

-

+AC_MSG_CHECKING([if R is using flexiblas])

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

+if echo "${BLAS_LIBS}" | grep flexiblas > /dev/null; then

+    AC_MSG_RESULT([flexiblas found. preprocessCore specific threading will be disabled])

+    use_pthreads=no

+else

+    AC_MSG_RESULT([flexiblas not found. preprocessCore threading will not be disabled])

+fi

 AC_ARG_ENABLE([threading],

 	AS_HELP_STRING([--disable-threading],[Disable threading]))

@@ -55,14 +55,6 @@ if test "x$use_pthread_stack_min" = xno; then

 fi

-AC_MSG_CHECKING([if R is using openblas])

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

-if echo "${BLAS_LIBS}" | grep openblas > /dev/null; then

-    AC_MSG_RESULT([openblas found. preprocessCore threading will be disabled])

-    use_pthreads=no

-else

-    AC_MSG_RESULT([openblas not found. preprocessCore threading will not be disabled])

-fi

 AC_ARG_ENABLE([threading],

@@ -25,8 +25,6 @@ AC_PROG_CPP

 AC_LANG(C)

-

-

 # Checks for libraries.

 use_pthreads=no

 AC_SEARCH_LIBS([pthread_create], [pthread],

@@ -57,10 +55,21 @@ if test "x$use_pthread_stack_min" = xno; then

 fi

+AC_MSG_CHECKING([if R is using openblas])

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

+if echo "${BLAS_LIBS}" | grep openblas > /dev/null; then

+    AC_MSG_RESULT([openblas found. preprocessCore threading will be disabled])

+    use_pthreads=no

+else

+    AC_MSG_RESULT([openblas not found. preprocessCore threading will not be disabled])

+fi

+

+

 AC_ARG_ENABLE([threading],

 	AS_HELP_STRING([--disable-threading],[Disable threading]))

+

 AS_IF([test "x$enable_threading" != "xno" ],[

 	    if test "x${use_pthreads}" = "xno"; then

 	       AC_MSG_NOTICE(------------------------------------------)

@@ -76,7 +76,7 @@ AS_IF([test "x$enable_threading" != "xno" ],[

 	    fi

 	    ],

 	    [

-	    AC_MSG_NOTICE(Disabling threading for\ preprocessCore)

+	    AC_MSG_NOTICE(Disabling threading for preprocessCore)

 	    ])

@@ -76,7 +76,7 @@ AS_IF([test "x$enable_threading" != "xno" ],[

 	    fi

 	    ],

 	    [

-	    AC_MSG_NOTICE("Disabling threading for\n preprocessCore")

+	    AC_MSG_NOTICE(Disabling threading for\ preprocessCore)

 	    ])

@@ -1,12 +1,6 @@

 dnl

-dnl Configuration things for affyR.

-dnl (http://www.cbs.dtu.dk/laurent/download/affyR/

-dnl What is below (and in the other configuration fiels 

-dnl was taken from different configuration scripts for R version 1.3.0.

+dnl Configuration things for preprocessCore

 dnl

-dnl Acknowledgments: The author(s) of the R configure scripts, Kurt Hornik for the tip with autoconf.

-dnl

-dnl Laurent 2001

 AC_INIT("DESCRIPTION")

@@ -29,6 +23,7 @@ AC_PROG_CC

 AC_PROG_CPP

+AC_LANG(C)

@@ -48,13 +43,13 @@ fi

 AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])

-AC_COMPILE_IFELSE([

+AC_COMPILE_IFELSE([AC_LANG_SOURCE([

 	#include <pthread.h>

 	#include <limits.h>

       int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;

 }     	  

-    ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])

+    ])],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])

 AC_MSG_RESULT($use_pthread_stack_min)

 if test "x$use_pthread_stack_min" = xno; then

@@ -62,17 +57,28 @@ if test "x$use_pthread_stack_min" = xno; then

 fi

+AC_ARG_ENABLE([threading],

+	AS_HELP_STRING([--disable-threading],[Disable threading]))

-if test "x${use_pthreads}" = "xno"; then

-  echo "------------------------------------------"

-  echo " Unable to find pthreads on this system.  "

-  echo " Building a single-threaded version.      "

-  echo "------------------------------------------"

-fi

-if test "x${use_pthreads}" = "xyes"; then

-  AC_DEFINE(USE_PTHREADS, 1)

-fi

+AS_IF([test "x$enable_threading" != "xno" ],[

+	    if test "x${use_pthreads}" = "xno"; then

+	       AC_MSG_NOTICE(------------------------------------------)

+	       AC_MSG_NOTICE( Unable to find pthreads on this system.  )

+	       AC_MSG_NOTICE( Building a single-threaded version.      )

+	       AC_MSG_NOTICE(------------------------------------------)

+	    fi

+

+

+	    if test "x${use_pthreads}" = "xyes"; then

+  	       AC_MSG_NOTICE(Enabling threading for preprocessCore)

+  	       AC_DEFINE(USE_PTHREADS, 1)

+	    fi

+	    ],

+	    [

+	    AC_MSG_NOTICE("Disabling threading for\n preprocessCore")

+	    ])

+

new file mode 100644

@@ -0,0 +1,80 @@

+dnl

+dnl Configuration things for affyR.

+dnl (http://www.cbs.dtu.dk/laurent/download/affyR/

+dnl What is below (and in the other configuration fiels 

+dnl was taken from different configuration scripts for R version 1.3.0.

+dnl

+dnl Acknowledgments: The author(s) of the R configure scripts, Kurt Hornik for the tip with autoconf.

+dnl

+dnl Laurent 2001

+

+

+AC_INIT("DESCRIPTION")

+

+dnl

+dnl Are things (still) the same ?

+dnl (taken from the 'writing R extensions manual')

+

+dnl Now find the compiler and compiler flags to use

+: ${R_HOME=`R RHOME`}

+if test -z "${R_HOME}"; then

+       echo "could not determine R_HOME"

+       exit 1

+fi

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

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

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

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

+AC_PROG_CC

+AC_PROG_CPP

+

+

+

+

+

+# Checks for libraries.

+use_pthreads=no

+AC_SEARCH_LIBS([pthread_create], [pthread],

+  [use_pthreads=yes])

+

+# Checks for header files.

+AC_HEADER_STDC

+AC_CHECK_HEADERS([stdlib.h])

+

+if test "x${have_pthreads}" = xyes; then

+  AC_CHECK_HEADERS([pthread.h], [],

+    [use_pthreads=no])

+fi

+

+

+AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])

+AC_COMPILE_IFELSE([

+	#include <pthread.h>

+	#include <limits.h>

+

+      int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;

+}     	  

+    ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])

+AC_MSG_RESULT($use_pthread_stack_min)

+

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

+	use_pthreads=no

+fi

+

+

+

+if test "x${use_pthreads}" = "xno"; then

+  echo "------------------------------------------"

+  echo " Unable to find pthreads on this system.  "

+  echo " Building a single-threaded version.      "

+  echo "------------------------------------------"

+fi

+

+if test "x${use_pthreads}" = "xyes"; then

+  AC_DEFINE(USE_PTHREADS, 1)

+fi

+

+

+

+

+AC_OUTPUT(src/Makevars)