first cut at support for J Azevedo and Rui Camacho's YapR.

.gitmodules

@@ -31,3 +31,6 @@
 [submodule "packages/R"]
 	path = packages/R
 	url = ssh://vsc@yap.git.sourceforge.net/gitroot/yap/R
+[submodule "packages/YapR"]
+	path = packages/YapR
+	url = ssh://vsc@yap.git.sourceforge.net/gitroot/yap/YapR

Makefile.in

@@ -673,6 +673,7 @@ all: startup.yss
 	@INSTALL_DLLS@ (cd packages/RDF; $(MAKE))
 	@INSTALL_DLLS@ (cd packages/semweb; $(MAKE))
 	@INSTALL_DLLS@ (cd packages/sgml; $(MAKE))
+	@INSTALL_YAPR@ (cd packages/YapR; $(MAKE))
 	@USE_MINISAT@ (cd packages/CLPBN/clpbn/bp ; $(MAKE))
 	@USE_MINISAT@ (cd packages/swi-minisat2/C; $(MAKE))
 	@INSTALL_DLLS@ (cd packages/zlib; $(MAKE))
@@ -735,6 +736,7 @@ install_unix: startup.yss libYap.a
 	@INSTALL_DLLS@ (cd packages/CLPBN/clpbn/bp ; $(MAKE) install)
 	@USE_MINISAT@ (cd packages/swi-minisat2/C; $(MAKE) install)
 	@INSTALL_MATLAB@ (cd library/matlab; $(MAKE) install)
+	@INSTALL_YAPR@ (cd packages/YapR; $(MAKE) install)
 	@ENABLE_JPL@ @INSTALL_DLLS@ (cd packages/jpl; $(MAKE) install)
 	#@ENABLE_JPL@ @INSTALL_DLLS@ (cd packages/pyswip; $(MAKE) install)
 	mkdir -p $(DESTDIR)$(INCLUDEDIR)
@@ -775,6 +777,7 @@ install_win32: startup.yss
 	(cd library/system; $(MAKE) install)
 	@ENABLE_WINCONSOLE@ (cd LGPL/swi_console; $(MAKE) install)
 	@INSTALL_MATLAB@ (cd library/matlab; $(MAKE) install)
+	@INSTALL_YAPR@ (cd packages/YapR; $(MAKE) install)
 	(cd library/tries; $(MAKE) install)
 	(cd packages/clib; $(MAKE) install)
 	(cd packages/plunit; $(MAKE) install)
@@ -841,6 +844,7 @@ clean: clean_docs
 	@INSTALL_DLLS@ (cd packages/RDF; $(MAKE) clean)
 	@INSTALL_DLLS@ (cd packages/semweb; $(MAKE) clean)
 	@INSTALL_DLLS@ (cd packages/sgml; $(MAKE) clean)
+	@INSTALL_YAPR@ (cd packages/YapR; $(MAKE) clean)
 	@USE_MINISAT@ (cd packages/swi-minisat2; $(MAKE) clean)
 	@USE_MINISAT@ (cd packages/CLPBN/clpbn/bp; $(MAKE) clean)
 	@INSTALL_DLLS@ (cd packages/tai/libtai; $(MAKE) clean)

configure

@@ -609,6 +609,8 @@ PROLOG_SYSTEM
 M4GENABSMI
 MATLAB_INCLUDE
 INSTALL_MATLAB
+YAPR_INCLUDES
+INSTALL_YAPR
 USE_MINISAT
 CUDD_CPPFLAGS
 CUDD_LDFLAGS
@@ -776,6 +778,7 @@ enable_april
 enable_dlcompat
 enable_cplint
 with_gmp
+with_yapr
 with_minisat
 with_cudd
 enable_myddas
@@ -1454,6 +1457,7 @@ Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
  --with-gmp=DIR           use GNU Multiple Precision in DIR
+ --with-yapr=DIR           use GNU Multiple Precision in DIR
  --enable-minisat           use minisat interface
  --with-cudd=DIR           use CUDD package in DIR
  --with-java=JAVA_HOME       use Java instalation in JAVA_HOME
@@ -3877,6 +3881,23 @@ fi
 
 
 
+# Check whether --with-yapr was given.
+if test "${with_yapr+set}" = set; then :
+  withval=$with_yapr; if test "$withval" = yes; then
+		YAPR_INCLUDES="-I/usr/share/R/include"
+		yap_cv_yapr=yes
+	elif test "$withval" = no; then
+		yap_cv_yapr=no
+	else
+		yap_cv_yapr=$with_yapr
+		YAPR_INCLUDES="-I${yap_cv_yapr}/share/R/include"
+	fi
+else
+  yap_cv_yapr=no
+fi
+
+
+
 # Check whether --with-minisat was given.
 if test "${with_minisat+set}" = set; then :
   withval=$with_minisat; if test "$withval" = yes; then
@@ -4363,6 +4384,15 @@ else
   INSTALL_MATLAB=""
 fi
 
+if test "$yap_cv_yapr" = no
+then
+  INSTALL_YAPR="@# "
+else
+  INSTALL_YAPR=""
+fi
+
+
+
 if test "$yap_cv_cudd" = no
 then
   USE_CUDD="@# "
@@ -5703,6 +5733,88 @@ fi
 
 fi
 
+if test "$yap_cv_yapr" != "no"
+then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lR" >&5
+$as_echo_n "checking for main in -lR... " >&6; }
+if test "${ac_cv_lib_R_main+set}" = set; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lR  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+
+int
+main ()
+{
+return main ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_R_main=yes
+else
+  ac_cv_lib_R_main=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_R_main" >&5
+$as_echo "$ac_cv_lib_R_main" >&6; }
+if test "x$ac_cv_lib_R_main" = x""yes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBR 1
+_ACEOF
+
+  LIBS="-lR $LIBS"
+
+fi
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lRmath" >&5
+$as_echo_n "checking for main in -lRmath... " >&6; }
+if test "${ac_cv_lib_Rmath_main+set}" = set; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lRmath  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+
+int
+main ()
+{
+return main ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_Rmath_main=yes
+else
+  ac_cv_lib_Rmath_main=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_Rmath_main" >&5
+$as_echo "$ac_cv_lib_Rmath_main" >&6; }
+if test "x$ac_cv_lib_Rmath_main" = x""yes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBRMATH 1
+_ACEOF
+
+  LIBS="-lRmath $LIBS"
+
+fi
+
+fi
+
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for zlibVersion in -lz" >&5
 $as_echo_n "checking for zlibVersion in -lz... " >&6; }
@@ -8470,6 +8582,8 @@ fi
 
 
 
+
+
 
 
 
@@ -9720,6 +9834,7 @@ mkdir -p  packages/R
 mkdir -p  packages/RDF
 mkdir -p  packages/semweb
 mkdir -p  packages/sgml
+mkdir -p  packages/YapR
 mkdir -p  packages/zlib
 
 ac_config_files="$ac_config_files Makefile"
@@ -9790,6 +9905,8 @@ ac_config_files="$ac_config_files packages/semweb/Makefile"
 
 ac_config_files="$ac_config_files packages/sgml/Makefile"
 
+ac_config_files="$ac_config_files packages/YapR/Makefile"
+
 ac_config_files="$ac_config_files packages/zlib/Makefile"
 
 
@@ -10546,6 +10663,7 @@ do
     "packages/RDF/Makefile") CONFIG_FILES="$CONFIG_FILES packages/RDF/Makefile" ;;
     "packages/semweb/Makefile") CONFIG_FILES="$CONFIG_FILES packages/semweb/Makefile" ;;
     "packages/sgml/Makefile") CONFIG_FILES="$CONFIG_FILES packages/sgml/Makefile" ;;
+    "packages/YapR/Makefile") CONFIG_FILES="$CONFIG_FILES packages/YapR/Makefile" ;;
     "packages/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES packages/zlib/Makefile" ;;
     "packages/chr/Makefile") CONFIG_FILES="$CONFIG_FILES packages/chr/Makefile" ;;
     "packages/clpqr/Makefile") CONFIG_FILES="$CONFIG_FILES packages/clpqr/Makefile" ;;

configure.in

@@ -147,6 +147,19 @@ AC_ARG_WITH(gmp,
 	fi,
 	[yap_cv_gmp=yes])
 
+AC_ARG_WITH(yapr,
+	[ --with-yapr[=DIR]           use GNU Multiple Precision in DIR],
+	if test "$withval" = yes; then
+		YAPR_INCLUDES="-I/usr/share/R/include"
+		yap_cv_yapr=yes
+	elif test "$withval" = no; then
+		yap_cv_yapr=no
+	else
+		yap_cv_yapr=$with_yapr
+		YAPR_INCLUDES="-I${yap_cv_yapr}/share/R/include"
+	fi,
+	[yap_cv_yapr=no])
+
 dnl best test we could do.
 AC_ARG_WITH(minisat,
 	[ --enable-minisat           use minisat interface],
@@ -409,6 +422,15 @@ else
   INSTALL_MATLAB=""
 fi
 
+if test "$yap_cv_yapr" = no 
+then
+  INSTALL_YAPR="@# "
+else
+  INSTALL_YAPR=""
+fi
+
+
+
 if test "$yap_cv_cudd" = no 
 then
   USE_CUDD="@# "
@@ -630,6 +652,12 @@ then
   AC_CHECK_LIB(gmp,main)
 fi
 
+if test "$yap_cv_yapr" != "no"
+then
+  AC_CHECK_LIB(R,main)
+  AC_CHECK_LIB(Rmath,main)
+fi
+
 dnl if test "$yap_cv_cudd" != "no"
 dnl then
 dnl   AC_CHECK_LIB(cudd,Cudd_Init)
@@ -1513,6 +1541,8 @@ AC_SUBST(USE_CUDD)
 AC_SUBST(CUDD_LDFLAGS)
 AC_SUBST(CUDD_CPPFLAGS)
 AC_SUBST(USE_MINISAT)
+AC_SUBST(INSTALL_YAPR)
+AC_SUBST(YAPR_INCLUDES)
 AC_SUBST(INSTALL_MATLAB)
 AC_SUBST(MATLAB_INCLUDE)
 
@@ -1999,6 +2029,7 @@ mkdir -p  packages/R
 mkdir -p  packages/RDF
 mkdir -p  packages/semweb
 mkdir -p  packages/sgml
+mkdir -p  packages/YapR
 mkdir -p  packages/zlib
 
 AC_CONFIG_FILES([Makefile])
@@ -2035,6 +2066,7 @@ AC_CONFIG_FILES([packages/R/Makefile])
 AC_CONFIG_FILES([packages/RDF/Makefile])
 AC_CONFIG_FILES([packages/semweb/Makefile])
 AC_CONFIG_FILES([packages/sgml/Makefile])
+AC_CONFIG_FILES([packages/YapR/Makefile])
 AC_CONFIG_FILES([packages/zlib/Makefile])
 
 if test "$ENABLE_CHR" = ""; then

packages/YapR

@@ -0,0 +1 @@
+Subproject commit 121c0909062150dc547c271a9e44827c45459b4f