configure.in

dnl	This file is an input file used by the GNU "autoconf" program to
dnl	generate the file "configure", which is run to configure the 
dnl	Makefile in this directory.

# Version: $Id$
# Copyright (c) 1997-2017 The Regents of the University of California.
# All rights reserved. 
#
# Permission is hereby granted, without written agreement and without
# license or royalty fees, to use, copy, modify, and distribute this
# software and its documentation for any purpose, provided that the
# above copyright notice and the following two paragraphs appear in all
# copies of this software.
#
# IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
# FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
# ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
# THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#
# THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
# PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
# CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
# ENHANCEMENTS, OR MODIFICATIONS.
#
# 						PT_COPYRIGHT_VERSION_2
# 						COPYRIGHTENDKEY

# configure is derived from configure.in by running GNU autoconf
# on configure.in.  Sadly, autoconf now requires Perl and is much
# slower than it used to be.
# See $PTII/doc/coding/develsetup.htm for details about how configure
# works.
# To modify configure:
# 1. Edit configure.in
# 2. Run: cd "$PTII"; rm config.*; autoconf; ./configure
# 3. When you are satisfied with your changes, check in configure.in:
#       cvs commit -m "Added xxx package" configure.in
# 4. Since configure.in will have a more recent modification time than
#    configure, be sure to run autoconf again
# 5. Check in configure:
#       cvs commit -m "configure.in changed" configure
# NOTE: sometimes the order that the files are updated when cvs update
# is run can cause configure.in to have a more recent mod time than
# configure.  If this is the case, try editing configure and adding
# a space to a comment line and commiting the change.

dnl Don't look for ptolemy/kernel/util/NamedObj.java here, or
dnl else we won't be able to rebuild after make extraclean.
AC_INIT(mk/ptII.mk.in)

#PT_VERBOSE=1

AC_ARG_ENABLE(verbose, [  --enable-verbose,	configure prints verbose msgs],
    PTVERBOSE=1)

if test "${PTVERBOSE:-none}" = "none"; then
    AC_MSG_RESULT([For more verbose output, run ./configure --enable-verbose])
fi

dnl Define our own messages so that we can control verbosity.

dnl PT_MSG_RESULT prints 'ok' if PTVERBOSE is not set, otherwise
dnl PT_MSG_RESULT prints its first argument.
AC_DEFUN([PT_MSG_RESULT],
[if test "${PTVERBOSE:-none}" = "none"; then AC_MSG_RESULT([ok]); else AC_MSG_RESULT([$1]); fi ])# PT_MSG_RESULT

dnl PT_MSG_RESULT prints nothing if PTVERBOSE is not  set, otherwise
dnl PT_MSG_RESULT prints its first argument. 
AC_DEFUN([PT_MSG_STATUS],
[if test "${PTVERBOSE:-none}" != "none"; then AC_MSG_RESULT([$1]); fi ])# PT_MSG_STATUS 


# Fix permissions on files.
# If the distribution was in a jar file, then some files might not be executable.
execFiles="ptolemy/util/test/junit/javachdir configure bin/ant bin/node bin/npm"
for file in $execFiles
do
    if test -f $file -a ! -x $file; then
        # PT_MSG_RESULT(Making $file executable.)
        chmod a+x $file
    fi
done

# Java does not find things in c:/program files/java
AC_MSG_CHECKING([if your path has 'program files/java' instead of 'Program Files/Java' ])
echo "$PATH" | egrep 'program files/java' > /dev/null
status=$?
if test "$status" -eq 0 ; then
   AC_MSG_WARN([
    Temporarily changing your path within configure for Java because
    Java can't find c:/program files/java, but can find
    c:/Program files/Java].)
   PATH="`echo $PATH | sed 's@program files/java@Program Files/Java@g'`"
else
   PT_MSG_RESULT([ok])
fi

# We must have PTII set before running configure.
if test -z "$PTII"; then
    if test -n "$PTOLEMY"; then
	if test -d "$PTOLEMY/tycho/java"; then
	    echo "\$PTOLEMY/tycho/java exists, setting PTII to that value"
	    PTII="$PTOLEMY/tycho/java"
	    # We should not have to call AC_PREFIX_DEFAULT($PTII) here
	    # but autoconf shuffles things around, so the call to
	    # AC_PREFIX_DEFAULT($PTII) that is 15 or so lines below
	    # actually appears at the top of configure.
	    ac_default_prefix=$PTII
	else
	    echo "You must set the PTII environment variable before running configure"
	    exit 3
	fi
    else
	echo "You must set the PTII environment variable before running configure"
	exit 3
    fi

fi

if test  ! -d "$PTII"; then
    echo "\$PTII is set to '$PTII', but it does not exist"
    exit 3
fi

if test  ! -w "$PTII"; then
    echo "Warning: \$PTII is set to '$PTII', but it is not writable by you."
    echo "This may or may not be a problem.  If you are running under"
    echo "Windows, then you might be able to ignore this problem and"
    echo "proceed with the build.  If you continue to have problems,"
    echo "try upgrading to cygwin1.1.0 or later"
fi

AC_MSG_CHECKING([if \$PTII ('$PTII') has backslashes])
echo "$PTII" | egrep '\\' > /dev/null
status=$?
if test "$status" -eq 1 ; then
       PT_MSG_RESULT([ok
    '$PTII' does not contain backslashes])
else
    AC_MSG_ERROR([
    \$PTII == $PTII,
    which contains backslashes.  Even under Windows, please set
    PTII to use forward slashes.])
fi

AC_MSG_CHECKING([if \$PTII ('$PTII') and the current directory are the same"])
canonicalPTII=`cd "$PTII"; pwd`
if test "$canonicalPTII" != "`pwd`" ; then
    currentDirectory="`pwd`"
    FINAL_WARNING="Perhaps $PTII is set to a directory other \
    than the current directory? \
    'cd \"$PTII\"; pwd' yields \"$canonicalPTII\", which is not the \
    same as 'pwd', which is \"$currentDirectory\""
    AC_MSG_WARN([$FINAL_WARNING])
fi

AC_MSG_CHECKING([if \$PTII ('$PTII') contains "cygdrive"])
echo "$PTII" | egrep 'cygdrive|cygwin' > /dev/null
status=$?
if test "$status" -eq 1 ; then
    PT_MSG_RESULT([ok
    '$PTII' does not contain cygdrive or cygwin, which is right.])
else
    AC_MSG_WARN(['\$PTII == $PTII,
which contains 'cygdrive' or 'cygwin'.
It could be that you have incorrectly set PTII.
If you have installed Cygwin in c:/cygwin, and your Ptolemy II installation
is in a directory outside of the c:/cygwin tree, then Cygwin may
change your PTII variable to include "/cygdrive/c".  This
will cause problems with non-Cygwin tools like javac that do
not understand /cygdrive/c

PTII can end up with cygdrive or cygwin in it if
you mistakenly do something like PTII=`pwd`.

Under Cygwin, try permanently setting PTII in the control panel 
(Start->Control Panels->Advanced->Environment Variables)
or temporary set it within bash:
  export PTII=c:/Users/YourLogin/ptII
and then rerun
  ./configure
See $PTII/doc/install.htm for details.'])
fi


case "`uname -s`" in
    CYGWIN_NT-*)
        AC_MSG_CHECKING([if \$PTII ('$PTII') contains "cygwin"])
        cygpath -w "$PTII" | grep cygwin > /dev/null
        status=$?
        if test "$status" -eq 1 ; then
	     PT_MSG_RESULT([ok
  \$PTII is '$PTII', which does not contain cygwin, which is right.])
        else
    AC_MSG_WARN([
'cygpath -w \$PTII' == '`cygpath -w $PTII`'
which contains 'cygwin'.
This could happen if your home directory is in the default location
for cygwin which cygwin thinks is /home/yourname,
but windows thinks is c:\\cygwin\\home\\yourname.
This will cause problems with non-Cygwin tools like javac that do
not understand Cygwin directory structure and mounts will not
be able to find files in $PTII.
The solution is to move the Ptolemy II tree outside of
c:\\cygwin and to set the PTII variable to point to that location
and then rerun
  cd \$PTII  
  ./configure
See $PTII/doc/install.htm for details.'])
     fi
     ;;
esac 


# If we are under Cygwin, check that we can find CMD
case "`uname -s`" in
    CYGWIN_NT-*)
	AC_PATH_PROG(CMD_PATH, cmd)
	if test ! -x "$CMD_PATH"; then
			AC_MSG_WARN([Failed to find the 'cmd' command, which
    is used by the $PTII/bin/ptolemy script.
    Under Windows 2000, cmd is usually found at c:\\winnt\\system32\\cmd.exe.
    Under Windows XP, cmd is usually found at c:\\windows\\system32\\cmd.exe.
    You may need to modify your PATH to explicitly include 
    c:\\winnt\\system32 by going or c:\\windows\\system32 by going to
    to Start->Settings->Control Panels->System->Environment and changing
    %SystemRoot%\\system32 to c:\\winnt\\system32 or c:\\windows\\system32.])
	fi
	;;

    *) ;;
esac

PTII_DEFAULT=$PTII
# The default value of prefix
AC_PREFIX_DEFAULT($PTII)


#--------------------------------------------------------------------
#	The PTII directory as a URL
#--------------------------------------------------------------------

# Read the PTII variable and substitute forward slashes
# for backward slashes

case "`uname -s`" in
CYGWIN_ME-*)
	windows="yes"
	# Windows ME is not a real os, and it does not have CMD.
	# So, we punt
	PTII_DIR=$PTII
	;;
CYGWIN_98-*) 
	windows="yes" 
	# Windows 98 is not a real os, and it does not have CMD.
	# So, we punt
	PTII_DIR=$PTII
	;;
CYGWIN*)
	windows="yes"
	# We use cmd /c chdir here to get rid of /cygwin/c
	PTII_DIR=`(cd "$PTII"; cmd /c chdir) | tr -d '\r' | sed 's@\\\@/@g'`
	;;
*)
	windows="no"
	PTII_DIR=$PTII
	;;
esac

#--------------------------------------------------------------------
#       Look for the "find" command
#--------------------------------------------------------------------
AC_ARG_WITH(find, [  --with-find=PATH         use the find command from PATH,
                           PTJAVA_DIR environment variable],
    FIND=$withval,
    FIND=/usr/bin/find)
AC_PATH_PROG(FIND, find)
if test `echo "$FIND" | grep system32`; then
    AC_MSG_WARN([Your path is probably messed up, you have a system32
    directory in your path before /bin])
    FIND=/bin/find
fi

if test ! -f "$FIND"; then
    AC_MSG_WARN([Could not find the "find" command, looked in \"$FIND\"])
fi    

# Substitute %20 for any spaces.
PTII_LOCALURL=`echo "file:///$PTII_DIR" | sed 's/ /%20/g'`
#--------------------------------------------------------------------
#	See if there was a command-line option for where Java is;  if
#	not, check to see if the PTJAVA_DIR environment variable is set;
#       if it is not, look for javac on the path.
#       NOTE: If your javac compiler is in /usr/bin, then PTJAVA_DIR is
#       likely to be set to /usr.  Consider using PTJAVA_HOME if
#       you are looking for Java jar files.
#       Note that PTJAVA_HOME is set to the jre directory, wheras
#       PTJAVA_DIR is set to the directory above the jre directory.
#       PTJAVA_HOME will _not_ have a trailing slash.
#--------------------------------------------------------------------

AC_ARG_WITH(java, [  --with-java=DIR         use Java binaries from DIR,
                           defaults to the value of the
                           PTJAVA_DIR environment variable],
    PTJAVA_DIR=$withval)

if test -d "$PTJAVA_DIR"; then
	PT_MSG_STATUS([
    PTJAVA_DIR environment variable was set to
    '$PTJAVA_DIR', and there is a directory
    at that location, so we will try it.])
else
    if test -z "$PTJAVA_DIR"; then
	PT_MSG_STATUS([PTJAVA_DIR environment variable was not set,
    so we search for the java compiler.])
    else
	AC_MSG_WARN([PTJAVA_DIR environment variable is set to
    '${PTJAVA_DIR}', which is not a directory,
    so we search for the java compiler.])
    fi
    AC_PATH_PROG(JAVAC, javac)
    if test -x "$JAVAC"; then
	JAVABIN=`dirname "$JAVAC"`
	PTJAVA_DIR=`dirname "$JAVABIN"`
	if test "$PTJAVA_DIR" = "/"; then
	    if test -d /usr/java; then
		PTJAVA_DIR=/usr/java
	        AC_MSG_WARN([ Found javac in "$JAVABIN", /usr/java exists, so
  we are setting PTJAVA_DIR to '$PTJAVA_DIR'])
	    fi
	fi
        if test "$PTJAVA_DIR" = "/usr"; then
	    # $PTII/vendors/ptinyos/tinyos-1.x/contrib/ptII/ptinyos/tools/make/ptII/ptII.rules
	    # uses -I$(PTJAVA_DIR).  If PTJAVA_DIR is /usr, then compilation of the ptinyos
	    # demos fails.
	    AC_MSG_CHECKING([PTJAVA_DIR == /usr, checking for links])
	    startdir=$PTII
	    cd "$srcdir/config"
	    if "$JAVAC" RootDirectory.java ; then
	        AC_MSG_CHECKING([the value of the Java directory ])
		AC_PATH_PROG(JAVA, java)
		if env "$JAVA" -classpath "$PTII/config" RootDirectory "$JAVAC"> /dev/null; then

		    PTJAVA_DIR_TMP=`"$JAVA" -classpath "$PTII/config" RootDirectory "$JAVAC"`

		    # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
	            # Remove /cygdrive so we can compile with MSVC
		    #PTJAVA_DIR_REAL=`echo "$PTJAVA_HOME_TMP" | sed 's@/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl
       	            if test -d "$PTJAVA_DIR_TMP"; then
		        PTJAVA_DIR="$PTJAVA_DIR_TMP"
		        PT_MSG_RESULT('$PTJAVA_DIR');
		    else	
		        AC_MSG_WARN(['$JAVA -classpath "$PTII/config" RootDirectory "$JAVAC"' failed.
    We will not be able to search for the canonical Java home directory.]);
		    fi
	        else
		    AC_MSG_WARN(['cd config; $JAVAC RootDirectory.java' failed.
    We will not be able to search for the canonical Java home directory.]);
	        fi
	        cd "$startdir"
            fi
        fi
    else
        AC_MSG_WARN([ Failed to find javac, perhaps Java is not installed?])
    fi

    # The default location that we look for the JDK.  This should probably
    # be a list that includes /usr/local/jdk and /opt/jdk
    if test ! -d "$PTJAVA_DIR"; then
	DEFAULT_JDK=/opt/jdk1.7
	if test -d "$DEFAULT_JDK"; then
	    PTJAVA_DIR=`cd "$DEFAULT_JDK"; pwd`
	    AC_MSG_WARN(['${PTJAVA_DIR}' is not a directory, using the default '${DEFAULT_JDK}'])

	else
	    DEFAULT_JDK=/usr/java
	    if test -d "$DEFAULT_JDK"; then
		PTJAVA_DIR=`cd "$DEFAULT_JDK"; pwd`
		AC_MSG_WARN(['${PTJAVA_DIR}' is not a directory, using the default '${DEFAULT_JDK}'])
	    else
			    AC_MSG_ERROR([
Java directory $DEFAULT_JDK doesn't exist.
Be sure that the directory that contains javac and java is in your path.
Typically, under Windows, this directory might be c:\Program Files\Java\jdk1.8.0_45\bin
For instructions about adding to a directory to your path permanently,
consult your user documentation.
Under bash, you may temporarily add a directory with something like:
  PATH=/cygdrive/c/Program\ Files/Java/jdk1.8.0_45/bin:\$PATH
  export PATH
  rm config.*; ./configure
You may also try --with-java=DIR, or set the PTJAVA_DIR environment variable
to the directory where your jdk is located:
  export PTJAVA_DIR=/cygdrive/c/Program\ Files/Java/jdk1.8.0_45
  rm config.*; ./configure
but adding the directory to your path is likely to work best.])
	    fi
	fi
    fi
fi

# PTJAVA_DIR without /cygdrive
# Use changequote here to preserve square brackets
changequote(<<, >>)dnl
PTJAVA_DIR_NO_CYGDRIVE="`echo "$PTJAVA_DIR" | sed 's@/cygdrive/\([a-z]\)/@\1:/@'`"
changequote([, ])dnl





if test ! -d "ptolemy/actor/lib/fmi/"; then
    PT_MSG_STATUS([ptolemy/actor/lib/ is not present,
    so we need not find a 32-bit JVM for testing.])
else
#--------------------------------------------------------------------
#	See if there was a command-line option for where the 32-bit Java is;  if
#	not, check to see if the PTJAVA32_DIR environment variable is set;
#       if it is not, look for javac on the path.
#       NOTE: If your javac compiler is in /usr/bin, then PTJAVA32_DIR is
#       likely to be set to /usr.  Consider using PTJAVA32_HOME if
#       you are looking for Java jar files.
#       Note that PTJAVA_HOME is set to the jre directory, wheras
#       PTJAVA_DIR is set to the directory above the jre directory.
#       PTJAVA_HOME will _not_ have a trailing slash.
#--------------------------------------------------------------------

AC_ARG_WITH(java32, [  --with-java32=DIR         use 32-bit Java binaries from DIR,
                           defaults to the value of the
                           PTJAVA32_DIR environment variable],
    PTJAVA32_DIR=$withval)

if test -d "$PTJAVA32_DIR"; then
	PT_MSG_STATUS([
    PTJAVA32_DIR environment variable was set to
    '$PTJAVA32_DIR', and there is a directory
    at that location, so we will try it.])
else
    if test -z "$PTJAVA32_DIR"; then
	PT_MSG_STATUS([PTJAVA32_DIR environment variable was not set,
    so we search for the java compiler.])
    else
	AC_MSG_WARN([PTJAVA32_DIR environment variable is set to
    '${PTJAVA32_DIR}', which is not a directory,
    so we search for the java compiler.])
    fi
    java -d32 -version > /dev/null
    retval=$?
    if test $retval = 0; then
        PTJAVA32_DIR=${PTJAVA_DIR}
	PT_MSG_STATUS([Running java -d32 -version succeeded,
    so PTJAVA32_DIR is $PTJAVA_32DIR])
    else
        AC_PATH_PROG(JAVA32, java32)
	JAVA32BIN=`dirname "$JAVA32"`
	PTJAVA32_DIR=`dirname "$JAVA32BIN"`
	if test -x "$JAVA32"; then
	 if test "$PTJAV32_DIR" = "/"; then
	    if test -d /usr/java; then
		PTJAVA32_DIR=/usr/java
	        AC_MSG_WARN([ Found java32 in "$JAVA32BIN", /usr/java exists, so
  we are setting PTJAVA32_DIR to '$PTJAVA32_DIR'])
	    fi
	  fi
          if test "$PTJAVA32_DIR" = "/usr" -o "$PTJAVA32_DIR" = "/usr/local"; then
	    # $PTII/vendors/ptinyos/tinyos-1.x/contrib/ptII/ptinyos/tools/make/ptII/ptII.rules
	    # uses -I$(PTJAVA_DIR).  If PTJAVA_DIR is /usr, then compilation of the ptinyos
	    # demos fails.
	    AC_MSG_CHECKING([PTJAVA32_DIR == /usr or /usr/local, checking for links])
	    startdir=$PTII
	    cd "$srcdir/config"
	    if "$JAVAC" RootDirectory.java ; then
	        AC_MSG_CHECKING([the value of the Java directory ])
		if env "$JAVA32" -classpath "$PTII/config" RootDirectory "$JAVA32"> /dev/null; then

		    PTJAVA32_DIR_TMP=`"$JAVA32" -classpath "$PTII/config" RootDirectory "$JAVA32"`

		    # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
	            # Remove /cygdrive so we can compile with MSVC
		    #PTJAVA_DIR_REAL=`echo "$PTJAVA_HOME_TMP" | sed 's@/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl
       	            if test -d "$PTJAVA32_DIR_TMP"; then
		        PTJAVA32_DIR="$PTJAVA32_DIR_TMP"
		        PT_MSG_RESULT('$PTJAVA_DIR');
		    else	
		        AC_MSG_WARN(['$JAVA32 -classpath "$PTII/config" RootDirectory "$JAVA32"' failed.
    We will not be able to search for the canonical 32-bit Java home directory.]);
		    fi
	        else
		    AC_MSG_WARN(['cd "$PTII/config"; $JAVAC RootDirectory.java' failed.
    We will not be able to search for the canonical 32-bit Java home directory.]);
	        fi
	        cd "$startdir"
            fi
          fi
        fi
	if test ! -x "$PTJAVA32_DIR/bin/java"; then
	   AC_MSG_WARN([Running java -d32 -version failed,
    and $PTJAVA32_DIR/bin/java does not exist.
    Perhaps you need to install a separate 32-bit JVM
    or rerun configure with --with-java32?
    The 32-bit JVM is only needed for certain 32-bit FMI tests.
    In general, under a 64-bit JVM, FMI will work fine without a 32-bit JVM.])
        fi
    fi
fi

# PTJAVA32_DIR without /cygdrive
# Use changequote here to preserve square brackets
changequote(<<, >>)dnl
PTJAVA32_DIR_NO_CYGDRIVE="`echo "$PTJAVA32_DIR" | sed 's@/cygdrive/\([a-z]\)/@\1:/@'`"
changequote([, ])dnl

fi # Test for ptolemy/actor/lib/fmi


#
# Check that we have the javac that corresponds with PTJAVA_DIR in our path
#
AC_MSG_CHECKING([for the java runtime in $PTJAVA_DIR/bin])
if test -f "$PTJAVA_DIR/bin/java" -o -f "$PTJAVA_DIR/bin/java.exe"; then
    PT_MSG_RESULT($PTJAVA_DIR/bin/java)
    AC_PATH_PROG(JAVA, java)
    if test "$PTJAVA_DIR/bin/java" = "$JAVA"; then
	PT_MSG_STATUS([    You have the right java in your path,
    "$PTJAVA_DIR/bin/java"
      = "$JAVA"])
    else
	AC_MSG_WARN(['$PTJAVA_DIR/bin/java' is not
    the same as '$JAVA'.
    Perhaps '$JAVA' is in your path before
    '$PTJAVA_DIR/bin/java'?
    If you have problems later, be sure that you don't have a mismatch
    in JDK versions.])
	JAVA="$PTJAVA_DIR/bin/java"
    fi
else
   if test -f "$PTJAVA_DIR/Commands/java"; then
       PT_MSG_RESULT($PTJAVA_DIR/Commands/java)
       AC_PATH_PROG(JAVA, java)
       if test "$PTJAVA_DIR/Commands/java" = "$JAVA"; then
           PT_MSG_STATUS([    You have the right java in your path,
    "$PTJAVA_DIR/Commands/java"
      = "$JAVA"])
       else
           AC_MSG_WARN(['$PTJAVA_DIR/Commands/java' is not
    the same as '$JAVA'.
    Perhaps '$JAVA' is in your path before
    '$PTJAVA_DIR/Commands/java'?
    If you have problems later, be sure that you don't have a mismatch
    in JDK versions.])
	JAVA="$PTJAVA_DIR/Commands/java"
      fi
   else 
       AC_MSG_ERROR([
  Cannot find '$PTJAVA_DIR/bin/java' or '$PTJAVA_DIR/Commands/java'.
  Try --with-java=DIR, or set the PTJAVA_DIR environment variable.
])
   fi

fi

#
# Check that we have the javac that corresponds with PTJAVA_DIR in our path
#
AC_MSG_CHECKING([for the java compiler in $PTJAVA_DIR/bin])
if test -f "$PTJAVA_DIR/bin/javac"; then
    PT_MSG_RESULT($PTJAVA_DIR/bin/javac)
    AC_PATH_PROG(JAVAC, javac)
    if test ! -x "$JAVAC"; then
	AC_MSG_WARN([Failed to find the 'javac' command in your path.
        This is not necessarily a problem, since
	'$PTJAVA_DIR/bin/javac' was found, but if you have problems,
	then you may want to adjust your path])
    fi
    if test "$PTJAVA_DIR/bin/javac" = "$JAVAC"; then
        PT_MSG_STATUS([    You have the right javac in your path,
    "$PTJAVA_DIR/bin/javac"
      = "$JAVAC"])
    else
        AC_MSG_WARN(['$PTJAVA_DIR/bin/javac' is not
	 the same as '$JAVAC'.
	 Perhaps '$JAVAC' is in your path
	 before '$PTJAVA_DIR/bin/javac'?
	 If you have problems later, be sure that you don't have a mismatch
	 in JDK versions.])
	JAVAC="$PTJAVA_DIR/bin/javac"
    fi
else
   if test -f "$PTJAVA_DIR/Commands/javac"; then
       PT_MSG_RESULT($PTJAVA_DIR/Commands/javac)
       AC_PATH_PROG(JAVAC, javac)
       if test "$PTJAVA_DIR/Commands/javac" = "$JAVAC"; then
           PT_MSG_STATUS([    You have the right java in your path,
    "$PTJAVA_DIR/Commands/javac"
      = "$JAVAC"])
       else
           AC_MSG_WARN(['$PTJAVA_DIR/Commands/javac' is not
    the same as '$JAVAC'.
    Perhaps '$JAVAC' is in your path before
    '$PTJAVA_DIR/Commands/javac'?
    If you have problems later, be sure that you don't have a mismatch
    in JDK versions.])
	JAVAC="$PTJAVA_DIR/Commands/javac"
      fi
   else 
       AC_MSG_ERROR([
  Cannot find '$PTJAVA_DIR/bin/javac' or '$PTJAVA_DIR/Commands/javac'.
  Try --with-java=DIR, or set the PTJAVA_DIR environment variable.])
   fi 
fi

#--------------------------------------------------------------------
#	Test the Java Compiler (javac)
#--------------------------------------------------------------------
AC_MSG_CHECKING([the Java compiler with a simple compile])
JVERSION=unknown
# We need to run javac in the config directory so that javac from jdk1.1.6
# under NT and cygwin works properly
startdir="$PTII"

cd "$srcdir/config"
rm -f *.class
if "$JAVAC" confTest.java ; then
    PT_MSG_RESULT(confTest.java compiled)

    AC_MSG_CHECKING([the value of the java.version Property ])
    # Older versions of cygwin might not have env, but 1.1 does
    if env "$JAVA" -classpath "$PTII/config" confTest > /dev/null; then
	# Run it again and get the results
	JVERSION=`"$JAVA" -classpath "$PTII/config" confTest`
	PT_MSG_RESULT($JVERSION)
    else	
        case "`uname -s`" in
            CYGWIN_NT-*)
	        # If $PTII is in /home, then suggest moving it.
	        echo "$PTII" | egrep "^/home/" > /dev/null
		status=$?

		if test "$status" -eq 0; then
		    AC_MSG_ERROR(['"$JAVA" -classpath "$PTII/config" confTest failed.
    If java fails, then you will not be able to run Ptolemy II.'

    You are running under Cygwin and $PTII and starts with /home/.

    By default, Cygwin puts user home directories in /home.
    However, Java will not be able to find directories in Cygwin's /home/ tree.

    The fix is to move $PTII to the /cygdrive/Users/$USERNAME and set
    PTII to c:/Users/$USERNAME/ptII:

       mv $PTII /cygdrive/c/Users/$USERNAME
       export PTII=c:/Users/c/$USERNAME/ptII
       cd \$PTII
       ./configure
    '])
		fi

	        AC_MSG_ERROR(['"$JAVA" -classpath "$PTII/config" confTest failed.
    If java fails, then you will not be able to run Ptolemy II.'
    This could be because your PTII variable is set incorrectly, perhaps
    it has 'cygwin' or 'cygdrive' in it?

    Under Cygwin, try setting PTII in the control panel 
    (Start->Control Panels->Advanced->Environment Variables)
    or temporary set it within bash:
        export PTII=c:/Users/$USERNAME/ptII
    and then rerun
        ./configure
    See $PTII/doc/install.htm for details.'])

            ;;

            *)
	        AC_MSG_ERROR(['"$JAVA" -classpath "$PTII/config" confTest failed.
    If java fails, then you will not be able to run Ptolemy II.'])
            ;;
        esac
   fi

else
   AC_MSG_ERROR(['cd "$PTII/config"; "$JAVAC" confTest.java failed.
    If javac fails, then you will not be able to compile Ptolemy II.

    This could be because your PTII variable is set incorrectly.

    Under Cygwin, try setting PTII in the control panel 
    (Start->Control Panels->Advanced->Environment Variables)
    or temporary set it within bash:
       export PTII=c:/Users/YourLogin/ptII
    and then rerun
      ./configure
      See $PTII/doc/install.htm for details.'])

fi

# The Major and Minor version of the JDK.  1.6, 1.8 etc.  Used by ant in build.xml.in.
changequote(<<, >>)dnl
JVERSION_TARGET=`echo "$JVERSION" | sed 's/\([1-9]*\.[^._]*\).*/\1/'`
changequote([, ])dnl

cd "$startdir"

#--------------------------------------------------------------------
#	We require JDK 1.8 preferred
#--------------------------------------------------------------------

AC_MSG_CHECKING([the JDK version])
JDOCSIZE=
UPGRADE_JVM=no
# Ptalon uses generics, which are present only in Java 1.5 and later
HAS_GENERICS=no
JAVA1_6_OR_LATER=no
case "$JVERSION" in
	1.1.*) UPGRADE_JVM=yes;;
	1.2.*) UPGRADE_JVM=yes;;
	1.3.*) UPGRADE_JVM=yes;;
	1.4.*) UPGRADE_JVM=yes;;
	1.5.*) UPGRADE_JVM=yes;;
	1.6.*) case "`uname -s`" in
	           Darwin) AC_MSG_WARN([Java 1.6.x is the first JVM in your path.
    Ptolemy II can be built and run with Java 1.6, but under Mac OS X, the Java 1.6 JVM
    from Apple has bugs including occaisionally crashing when closing a window.
    A possible solution is to download Java 1.7 or later for Oracle and be sure that
    the path to the Oracle JDK is in your path before the path to the Apple JDK.
    Typically, the Oracle JDK is installed at
    /Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home.
    To adjust the path in Bash, use
    export PATH=/Library/Java/JavaVirtualMachines/1.7.0.jdk/Contents/Home/bin:\${PATH}])
               esac
	       UPGRADE_JVM=yes;;
	1.7.*) UPGRADE_JVM=yes;;
       	*)     ;;
esac

if test "$UPGRADE_JVM" = "yes"; then
    case "`uname -s`" in
        Darwin) 
     	    upgradeMessage="Mac OS X, ships with Java 1.6 from Apple, but 
    later versions of Java are available from Oracle";;
        *)
	    upgradeMessage="";;
    esac

		AC_MSG_ERROR([Ptolemy II requires JDK 1.8 or later.

    JDK 1.2.2 has a bug involving compiling inner classes with protected
    methods.
    The RTOS domain uses java.util.Timer, which is present in JDK 1.3
    and later.
    ptolemy/kernel/attributes/URIAttribute.java uses java.net.URI, which
    is present in JDK 1.4 and later. 
    JDK 1.5 or later is required so that these packages can use generics:
	- actor/gui/run, which uses org/mlc/swing
	- actor/lib/vhdl
	- backtrack
	- ptalon
    JDK 1.6 or later is needed for ptdb to use javax.swing.GroupLayout.
    JDK 1.8 is needed for Nashorn, nio and many other features.
    Please upgrade your JDK to 1.8 or later and try again.
    $upgradeMessage]) 	
else
   # -breakiterator is only present in jdk1.4 and later
   JDOCBREAKITERATOR=-breakiterator
   # Ptalon uses generics, assume 1.5 or greater here
   HAS_GENERICS=yes
   PT_MSG_RESULT([ok, you are running $JVERSION])
fi


# Set PTJAVA_HOME
# Under Cygwin, PTJAVA_HOME will not contain /cygdrive/c
# Under Cygwin, PTJAVA_DIR _will_ contain /cygdrive/c
# We need to run javac in the config directory so that javac from
# jdk1.1.6 under NT and cygwin works properly
startdir=$PTII
cd "$srcdir/config"
AC_MSG_CHECKING([for java.home property by compiling a test program ])
# Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
if "$JAVAC" JavaHome.java ; then
   PT_MSG_RESULT(JavaHome.java compiled)
   AC_MSG_CHECKING([for java.home property by running a test program ])
   if env "$JAVA" -classpath "$PTII/config" JavaHome > /dev/null; then
      # Run it again and get the results with \ converted to /
      PTJAVA_HOME=`"$JAVA" -classpath "$PTII/config" JavaHome`
      PT_MSG_RESULT($PTJAVA_HOME)
      PTDOCLETS_DIR=doclets
   else   
      AC_MSG_WARN(['$JAVA -classpath "$PTII/config" JavaHome' failed.
   Since we cannot determine where the JRE is, we cannot set PTJAVA_HOME.
   for use with doclets or the serial communications protocol])
    fi
fi
cd "$startdir"

#
# Check that jar can handle the -i argument
#
AC_MSG_CHECKING([for the jar command])
if test -f "$PTJAVA_DIR/bin/jar"; then
    PT_MSG_RESULT($PTJAVA_DIR/bin/jar)
    JAR="$PTJAVA_DIR/bin/jar"
else
   if test -f "$PTJAVA_DIR/Commands/java"; then
       PT_MSG_RESULT($PTJAVA_DIR/Commands/java)
       JAR="$PTJAVA_DIR/Commands/jar"
   else
       AC_MSG_WARN([Cannot find '$PTJAVA_DIR/bin/jar'.
       or '$PTJAVA/Commands/jar', looking in the path.
       This is usually only a problem if you run 'make install'])
       AC_PATH_PROG(JAR, jar)
   fi
fi

AC_MSG_CHECKING([that $JAR can handle -i])
if test -x "$JAR"; then
    cd "$srcdir/config"

    "$JAR" -cf jarTest.jar confTest.class
    if "$JAR" -i jarTest.jar; then
        PT_MSG_RESULT([$JAR -i worked])
	# JAR_INDEX now includes the JAR_FLAGS flag so that we can
	# pass -J-Xss100m for linux
	JAR_INDEX='"$(JAR)" $(JAR_FLAGS) -i $@'
    else
        AC_MSG_WARN([$JAR -i jarTest.jar failed,
    so we will not index the jar files])
	JAR_INDEX=""
    fi

    cd "$startdir"
else
     AC_MSG_WARN([jar command "$JAR" is not executable or not found.
       This is usually only a problem if you run 'make install'])
fi

#
# The jarsigner command is used to create signed jar files for Webstart JNLP files
#
AC_MSG_CHECKING([for the jarsigner command])
if test -f "$PTJAVA_DIR/bin/jarsigner"; then
    PT_MSG_RESULT($PTJAVA_DIR/bin/jarsigner)
    JARSIGNER="$PTJAVA_DIR/bin/jarsigner"
else
   if test -f "$PTJAVA_DIR/Commands/java"; then
       PT_MSG_RESULT($PTJAVA_DIR/Commands/java)
       JARSIGNER="$PTJAVA_DIR/Commands/jarsigner"
   else
       AC_MSG_WARN([Cannot find '$PTJAVA_DIR/bin/jarsigner'.
       or '$PTJAVA/Commands/jarsigner', looking in the path.
       This is only a problem when testing the security actors.])
       AC_PATH_PROG(JARSIGNER, jarsigner)
   fi
fi

if test ! -x "$JARSIGNER"; then
     AC_MSG_WARN([The jarsigner command "$JARSIGNER" is not executable or not found.
       This is only a problem when testing the security actors.])
fi

#
# The javaws command is used to test Webstart JNLP files.
#
if test ! -f "mk/jnlp.mk"; then
    PT_MSG_STATUS([mk/jnlp.mk is not present,
    so we need not find javaws, the Java Web Start binary.])
else
    AC_MSG_CHECKING([for the javaws command])
    if test -f "$PTJAVA_DIR/bin/javaws"; then
        PT_MSG_RESULT($PTJAVA_DIR/bin/javaws)
        JAVAWS="$PTJAVA_DIR/bin/javaws"
    else
        if test -f "$PTJAVA_DIR/Commands/java"; then
            PT_MSG_RESULT($PTJAVA_DIR/Commands/java)
            JAVAWS="$PTJAVA_DIR/Commands/javaws"
        else
            AC_MSG_WARN([Cannot find '$PTJAVA_DIR/bin/javaws'.
    or '$PTJAVA/Commands/javaws', looking in the path.
    This is only a problem when testing the Java Webstart (JNLP) files.])
            AC_PATH_PROG(JAVAWS, javaws)
        fi
    fi
    if test ! -x "$JAVAWS"; then
        AC_MSG_WARN([The javaws command "$JAVAWS" is not executable or not found.
    This is only a problem when testing the Java Webstart (JNLP) files.])
    fi
fi

#
# keytool command used to generate a certificate for testing actor.lib.security actors
#
if test ! -d "ptolemy/actor/lib/security/"; then
    PT_MSG_STATUS([ptolemy/actor/lib/security/ is not present,
    so we need not find keytool, the certifate command.])
else
    AC_MSG_CHECKING([for the keytool command])
    if test -f "$PTJAVA_DIR/bin/keytool"; then
        PT_MSG_RESULT($PTJAVA_DIR/bin/keytool)
        KEYTOOL="$PTJAVA_DIR/bin/keytool"
    else
        if test -f "$PTJAVA_DIR/Commands/java"; then
            PT_MSG_RESULT($PTJAVA_DIR/Commands/java)
            KEYTOOL="$PTJAVA_DIR/Commands/keytool"
        else
            AC_MSG_WARN([Cannot find '$PTJAVA_DIR/bin/keytool'.
    or '$PTJAVA/Commands/keytool', looking in the path.
    This is only a problem when testing the security actors.])
            AC_PATH_PROG(KEYTOOL, keytool)
        fi
    fi

    if test ! -x "$KEYTOOL"; then
        AC_MSG_WARN([The keytool command "$KEYTOOL" is not executable or not found.
    This is only a problem when testing the security actors.])
    fi
fi


#--------------------------------------------------------------------
#	Figure out which separator to use for CLASSPATH
#	So much for write once, run everywhere.
#       Find NT4 and Windows 2000 (CYGWIN_NT-4.0 and
#       CYGWIN_NT-5.0 respectively)
#--------------------------------------------------------------------
AC_MSG_CHECKING([for the proper CLASSPATH separator])

# If you mess with this, consider changing the jdkClassPathSeparator
# proc in ptII/util/testsuite/jdktools.tcl
case "`uname -s`" in
    CYGWIN_ME-*) CLASSPATHSEPARATOR=";";;
    CYGWIN_NT-*) CLASSPATHSEPARATOR=";";;
    CYGWIN_98-*) CLASSPATHSEPARATOR=";";;
    *) CLASSPATHSEPARATOR=":";;
esac
PT_MSG_RESULT(['$CLASSPATHSEPARATOR'])


#--------------------------------------------------------------------
#	Get ready to accumulate information for Eclipse and Ant
#--------------------------------------------------------------------

# These directories are always excluded from Eclipse
# To add to this list, edit .classpath.in
ECLIPSE_EXCLUDING_SRC="ptolemy/actor/lib/reactable/"

# Jar files to include in the Eclipse library
#ECLIPSE_CLASSPATHENTRY_LIBS='<classpathentry kind="lib" path="lib/diva.jar"/>'
ECLIPSE_CLASSPATHENTRY_LIBS=''

# Add any jar files in $HOME/.ptolemyII
# FIXME: Eclipse should support Java 1.6 style * classpaths

# The Cygwin value of $HOME is not understood by Java under Windows.
if test  "$windows" = "yes"; then
    tmpHOME="`cygpath --mixed $HOME`"
else
    tmpHOME="$HOME"
fi
for jar in $tmpHOME/.ptolemyII/*.jar 
do
    if test -f "$jar"; then

        if test "$windows" = "yes" ; then
	   # Avoid /cygdrive/c in .classpath
	   jar=`cygpath --mixed "$jar"`
	fi

        # Avoid adding .ptolemyII/*.jar to .classpath
	ECLIPSE_CLASSPATHENTRY_LIBS="$ECLIPSE_CLASSPATHENTRY_LIBS \
	        <classpathentry kind=\"lib\" path=\"$jar\"/> "
	# Ant understands * style classpaths, so no need to update Ant.	
    fi
done

# Paths to always exclude in Ant's build.xml
# IMPORTANT: If you update the list below, also update .classpath.in and .classpath.default
ANT_ALWAYS_EXCLUDE='<exclude name="**/CVS/"/>
<exclude name="**/adm/dists/" />
<exclude name="**/adm/gen-*/" />
<exclude name="**/codeDoc/"/>
<exclude name="**/cobertura.ser" />
<exclude name="**/makefile" />
<exclude name="**/.*" />
<exclude name="**/*.bat" />
<exclude name="**/*.class" />
<exclude name="**/*.html" />
<exclude name="**/*.in" />
<exclude name="**/*.png" />
<exclude name="**/*.tcl" />
<exclude name="**/*.xml" />
<exclude name="adm/cvs2svn/"/>
<exclude name="build/"/>
<exclude name="config/"/>
<exclude name="doc/coding/templates/"/>
<exclude name="jni/test/jni/meaningOfLife/"/>
<exclude name="jni/test/jni/testDeux/"/>
<exclude name="jni/test/jni/testTrois/"/>
<exclude name="org/terraswarm/accessor/accessors/web/node_modules/" />
<exclude name="org/terraswarm/accessor/accessors/web/hosts/cordova/demo/" />
<exclude name="org/terraswarm/accessor/accessors/web/hosts/cordova/plugins/" />
<exclude name="org/terraswarm/accessor/accessors-svn/" />
<exclude name="pt-modules/"/>
<exclude name="ptolemy/apps/agilent/"/>
<exclude name="ptolemy/apps/anytimecontrol/"/>
<exclude name="ptolemy/apps/apes/"/>
<exclude name="ptolemy/apps/charon/"/>
<exclude name="ptolemy/apps/crazyboard/"/>
<exclude name="ptolemy/apps/eclipse/"/>
<exclude name="ptolemy/apps/etherealSting/"/>
<exclude name="ptolemy/apps/fullscreen/"/>
<exclude name="ptolemy/apps/giotto/"/>
<exclude name="ptolemy/apps/ia/"/>
<exclude name="ptolemy/apps/interfaces/"/>
<exclude name="ptolemy/apps/jmf/"/>
<exclude name="ptolemy/apps/kurt/"/>
<exclude name="ptolemy/apps/kvm/"/>
<exclude name="ptolemy/apps/lego/"/>
<exclude name="ptolemy/apps/lejos/"/>
<exclude name="ptolemy/apps/midp/"/>
<exclude name="ptolemy/apps/mobileCoding/"/>
<exclude name="ptolemy/apps/pendulum/"/>
<exclude name="ptolemy/apps/rijndael/"/>
<exclude name="ptolemy/apps/robot/"/>
<exclude name="ptolemy/apps/security/"/>
<exclude name="ptolemy/apps/sobel/"/>
<exclude name="ptolemy/apps/soot/"/>
<exclude name="ptolemy/apps/throttle/"/>
<exclude name="ptolemy/apps/tini/"/>
<exclude name="ptolemy/apps/transmission/"/>
<exclude name="ptolemy/apps/vergil/"/>
<exclude name="ptolemy/apps/waba/"/>
<exclude name="ptolemy/apps/websensor/"/>
<exclude name="ptolemy/apps/webstart/"/>
<exclude name="ptolemy/apps/xsl/"/>
<exclude name="ptolemy/apps/zaurus/"/>
<exclude name="ptolemy/backtrack/eclipse/plugin/"/>
<exclude name="ptolemy/backtrack/test/"/>
<exclude name="ptolemy/codegen/c/actor/lib/oldJavaFiles/"/>
<exclude name="ptolemy/codegen/dsp/lib/"/>
<exclude name="ptolemy/codegen/kernel/newInterfaces/"/>
<exclude name="ptolemy/codegen/lib/"/>
<exclude name="ptolemy/copernicus/kernel/fragment/"/>
<exclude name="ptolemy/copernicus/shallow/cg/"/>
<exclude name="ptolemy/domains/giotto/demo/Hierarchy/Hierarchy/"/>
<exclude name="ptolemy/domains/giotto/demo/Multimode/Multimode/"/>
<exclude name="ptolemy/domains/giotto/demo/Simple/Simple/"/>
<exclude name="ptolemy/domains/gr/lib/experimental/"/>
<exclude name="ptolemy/domains/gro/"/>
<exclude name="ptolemy/domains/pdf/"/>
<exclude name="ptolemy/domains/ptinyos/demo/Surge/output/"/>
<exclude name="ptolemy/moml/test/NoPackageActor.java"/>
<exclude name="ptolemy/plot/adm/"/>
<exclude name="ptolemy/plot/servlet/"/>
<exclude name="reports/"/>
<exclude name="signed/" />
<exclude name="src/"/>
<exclude name="target/"/>
<exclude name="vendors/"/>'

# Jar files to include in Ant's build.xml
ANT_CLASSPATH=''

# if maven-ant-tasks/*.jar was found
# and if $PTII/ptolemy/apps/websensor was found.

# Paths to exclude in Ant's build.xml
ANT_EXCLUDE=''

# Path of directories that contain source, used by the Ant's build rule.
ANT_SRC=''

# Paths of tests to exclude in Ant's build.xml
ANT_EXCLUDE_TESTS=''

# A shell function that adds its argument to the ECLIPSE_CLASSPATH_ENTRY_LIBS
# and to ANT_CLASSPATH
updateClasspath () {
        if test ! -z "$1"; then
            ECLIPSE_CLASSPATHENTRY_LIBS="$ECLIPSE_CLASSPATHENTRY_LIBS \
	        <classpathentry kind=\"lib\" path=\"$1\"/> "
            ANT_CLASSPATH="$ANT_CLASSPATH <pathelement location=\"$1\"/> "
        else
            echo "INTERNAL WARNING: updateClasspath called with an empty string as the jar file?"
        fi
}

# A shell function that adds its argument to ECLIPSE_EXCLUDING_SRC
# and ANT_EXCLUDE
updateExcludes () {
   ECLIPSE_EXCLUDING_SRC="$ECLIPSE_EXCLUDING_SRC|$1"
   ANT_EXCLUDE="$ANT_EXCLUDE <exclude name=\"$1\" />"
}

# A shell function that adds its arguments to ANT_EXCLUDE_TESTS.
updateExcludeTests () {
   ANT_EXCLUDE_TESTS="$ANT_EXCLUDE_TESTS <exclude name=\"$1\" />"
}


########################################################################

if test ! -d "ptolemy/backtrack/eclipse"; then
    PT_MSG_STATUS([ptolemy/backtrack/eclipse/ is not present,
    no need to print message about Darwin.])
else
    case "`uname -s`" in
        Darwin) 
            AC_MSG_WARN([Under Eclipse on Mac OS X, there are various
    problems with Eclipse.	 
    - Eclipse-3.4.0 has problems with Eclipse plugins on the Mac.
      Note that the backtracking and other Eclipse code will
      _not_ work on the Mac from within Eclipse. Backtracking will work 
      on the Mac _outside_ of Eclipse.
    For details, see
    http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Mac2008 and follow the
    'Problems with Eclipse and Ptolemy on the Mac' link.])
            if test -d ptolemy/apps/eclipse/awt/; then
	        AC_MSG_WARN([Under Eclipse on Mac OS X, ptolemy/apps/eclipse/awt
    is not supported.])
	        updateExcludes "ptolemy/apps/eclipse/awt/"
            fi	    
     	    ;;
            *)
            ECLIPSE_CLASSPATHENTRY_PDE_REQUIREDPLUGINS='<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>'
            ;;
    esac
fi

PRE_JDK17=no
PRE_JDK18=no
case "$JVERSION" in
     1.6.*) PRE_JDK18=yes
     	    PRE_JDK17=yes;;
     1.7.*) PRE_JDK18=yes;;
esac

if test "$PRE_JDK17" = "yes" ; then
    # These must have trailing slash or the updateExcludes shell function will not work.
    pre1_7packages="ptolemy/cg/"
    AC_MSG_WARN([A version of Java ($JVERSION) earlier than Java 1.7 is the first JVM in your path.
    The following packages will not be compiled:
        $pre1_7packages])
    for package in $pre1_7packages
    do
	updateExcludes $package
    done
fi

# Set to jjs if Nashorn (present in Java 1.8) is found.
PTJJS_DIR=
# Set to accessor and used in org/terraswarm/makefile if Nashorn is found.
PTACCESSOR_DIR=
# Set to include packages that require Java 1.8, but do not require Vertx or other optional packages and used in doc/makefile.
PTJAVA18_PACKAGES=

if test "$PRE_JDK18" = "yes" ; then
    # These must have trailing slash or the updateExcludes shell function will not work.
    pre1_8packages="org/hlacerti/ org/ptolemy/machineLearning/particleFilter/ org/ptolemy/machineLearning/hsmm/ org/ptolemy/osc/ org/ptolemy/ssm/ ptolemy/apps/hardrealtime/ ptolemy/actor/lib/fmi/ ptolemy/actor/lib/conversions/ ptolemy/actor/lib/jjs/ ptolemy/actor/lib/jjs/modules/ ptolemy/actor/lib/jjs/modules/cameras/ ptolemy/actor/lib/jjs/modules/imageDisplay/ ptolemy/cg/adapter/generic/program/procedural/fmimahybrid/ /ptolemy/cg/adapter/generic/program/procedural/adapters/org/terraswarm/accessor/ ptolemy/vergil/basic/imprt/accessor/ ptolemy/vergil/basic/imprt/fmu/ org/terraswarm/accessor/ ptolemy/domains/wireless/lib/bluetooth/ ptolemy/actor/lib/security/ ptolemy/domains/atc/ ptolemy/domains/tcs/"
    AC_MSG_WARN([A version of Java ($JVERSION) earlier than Java 1.8 is the first JVM in your path.
    The following packages will not be compiled:
        $pre1_8packages])
    FINAL_WARNING="$FINAL_WARNING You are compiling with a pre-JDK1.8 Java, which means that accessors will NOT be built. Is this what you want?"
    for package in $pre1_8packages
    do
	updateExcludes $package
    done
else

        # Packages that do not use vertx or other packages, but do use Java 1.8.
        PTJAVA18_PACKAGES="org.ptolemy.machineLearning.hsmm org.ptolemy.machineLearning.particleFilter org.ptolemy.ssm ptolemy.actor.lib.jjs ptolemy.actor.lib.jjs.modules.audio ptolemy.actor.lib.jjs.modules.contextAware ptolemy.actor.lib.jjs.modules.contextAwareTest ptolemy.actor.lib.jjs.modules.crypto ptolemy.actor.lib.jjs.modules.dataConverter ptolemy.actor.lib.jjs.modules.imageDisplay ptolemy.actor.lib.jjs.modules.iotAuth ptolemy.actor.lib.jjs.modules.discovery ptolemy.actor.lib.jjs ptolemy.actor.lib.jjs.modules.shell"
        # Set to accessor and used in org/terraswarm/accessors/makefile if Nashorn is found.
        PTJJS_DIR=jjs
        # org.terraswarm.accessor depends on jjs/JavaScript.java so we
        # list org.terraswarm.accessor with jjs/JavaScript
        PTACCESSOR_DIR=accessor
        PTACCESSOR_DIR_FULL="$PTII/org/terraswarm/$PTACCESSOR_DIR"

        if test -d "$PTACCESSOR_DIR_FULL" ; then
                  
           ACCESSORS_REPO=https://github.com/icyphy/accessors

           if test -d "$PTACCESSOR_DIR_FULL/accessors/.svn" ; then
              AC_MSG_CHECKING([$PTACCESSOR_DIR_FULL/accessors/.svn exists, but we are now using git for the accessors repo.])
              if test -d "$PTACCESSOR_DIR_FULL/accessors-svn" ; then
                  AC_MSG_WARN([$PTACCESSOR_DIR_FULL/accessors-svn exists, but so does $PTACCESSOR_DIR_FULL/accessors/.svn?
    Please remove $PTACCESSOR_DIR_FULL/accessors.])
              else
                  mv "$PTACCESSOR_DIR_FULL/accessors" "$PTACCESSOR_DIR_FULL/accessors-svn"
                  AC_MSG_RESULT([The $PTACCESSOR_DIR_FULL/accessors directory has been moved to $PTACCESSORS_DIR_FULL/accessors-svn and the accessors git repo will be checked out.])
              fi                  
           fi               

           AC_MSG_CHECKING([for $PTACCESSOR_DIR_FULL/accessors/, used by CapeCode and Accessors])

           if test -d "$PTACCESSOR_DIR_FULL/accessors" ; then
              PT_MSG_RESULT([ok])
           else
              # The accessors mechanism needs to have a repo checked out.

              # If the git command is present, try to check out the repo
              AC_MSG_CHECKING([for git])
              AC_PATH_PROG(GIT, git)
              if test ! -x "$GIT"; then
                  AC_MSG_WARN([Could not find a git binary so accessors that extend the TerraSwarm accessors will not work.])
              else
                  GIT_CLONE_COMMAND="git clone $ACCESSORS_REPO"
                  AC_MSG_RESULT([About to check out the accessors repo using
    $GIT_CLONE_COMMAND])

                  (cd $PTACCESSOR_DIR_FULL; $GIT_CLONE_COMMAND)
              fi

              AC_MSG_CHECKING([for the $PTACCESSOR_DIR_FULL/accessors directory again])

              if test ! -d "$PTACCESSOR_DIR_FULL/accessors" ; then
                  FINAL_WARNING="$FINAL_WARNING Could not check out the accessor repo in $PTACCESSOR_DIR_FULL.  Accessors probably won't work.  See above for details."

                  AC_MSG_WARN([Could not check out the accessors git repo.
    Accessors that extend the TerraSwarm accessors will probably not work well unless the repo is checked out.
    To check out the accessors repo:

      cd org/terraswarm/accessor
      git clone $ACCESSORS_REPO
      cd $PTII
      ./configure

])
               else
                   PT_MSG_RESULT([ok])
              fi
           fi
        fi
fi

# ptolemy/media/viewer/AudioPlayer.java uses internal sun.* classes not present in Java 9.
# PTVIEWER_DIR is set to viewer and used in ptolemy/media/makefile for JVM < 9
PTVIEWER_DIR=viewer
# PTVIEWER_PACKAGES is used in doc/makefile
PTVIEWER_PACKAGES=ptolemy.media.viewer

# Handle Java 9 fails.
case "$JVERSION" in
        9*)    # We use to need to add a module so that
               # javax.xml.bind.DatatypeConverter can be found.
               # However, we no longer need that class.

               # ANT_JAVAC_COMPILERARG='     <compilerarg line="--add-modules java.xml.bind"/>';
               # JAVAC_MODULES="--add-modules java.xml.bind"
               PTVIEWER_DIR=
               PTVIEWER_PACKAGES=
               updateExcludes "ptolemy/copernicus/applet/"
               updateExcludes "ptolemy/media/viewer"

               ;;
esac



#####################################################################
#####################################################################
#       Below here we look for various packages.
#       Not all Ptolemy software products need all packages, so
#       we usually look for a directory that uses the package first
#
#       Please try to keep the packages vaguely alphabetical
#####################################################################
#####################################################################

#--------------------------------------------------------------------
#       Look for the maven-ant-tasks-*.jar file used
#       to run Maven from ant.
#
#--------------------------------------------------------------------

# Set to 'xmlns:artifact="antlib:org.apache.maven.artifact.ant"' if 
# maven-ant-tasks-*.jar is found
ANT_MAVEN_ARTIFACT=''

# The ant rule to build $PTII/ptolemy/apps/websensor.
ANT_MAVEN_BUILD_WEBSENSOR=''

# Set to 'build-websensor'
# if maven-ant-tasks/*.jar was found
# and if $PTII/ptolemy/apps/websensor was found.
ANT_MAVEN_SUBPROJECTS=''

# Set to '<fileset dir="${basedir}/ptolemy/apps/websensor"/>'
# if maven-ant-tasks/*.jar was found
# and if $PTII/ptolemy/apps/websensor was found.
ANT_WEBSENSOR_FILESET=''

# Set to <sourcePath path="${basedir}/ptolemy/apps/websensor"/>'
ANT_WEBSENSOR_SOURCEPATH=''

# Set to '<src path="${basedir}/ptolemy/apps/websensor"/>'
# if maven-ant-tasks*.jar was found
# and if $PTII/ptolemy/apps/websensor was found.
ANT_WEBSENSOR_SRC=''

AC_MSG_CHECKING([for the Apache ant binary])

ANT="$PTII/bin/ant"
if test -d "$PTII/ant"; then
   case "`uname -s`" in
         CYGWIN_NT-*)
         # Not sure if we should use ant.bat or ant.cmd here
         ANT=$PTII/ant/bin/ant.cmd
         ;;
   *) ANT=$PTII/ant/bin/ant
   esac
fi

if test -f "$ANT" -a ! -x "$ANT"; then
   chmod a+x "$ANT"
fi

if test ! -f "$ANT"; then
    AC_MSG_WARN([$ANT not found?
    Apche Ant, is the best way to build Ptolemy II from sources.

    Usually, a copy of Apache Ant may be found in $PTII/ant/bin/ant and
    $PTII/bin/ant will execute $PTII/ant/bin/ant.
    
    Apache Ant is available from http://ant.apache.org/bindownload.cgi])
    case "`uname -s`" in
        Darwin) 
            AC_MSG_WARN([Under Mac OS X, the easiest way to install ant is to install
    MacPorts from https://www.macports.org/ and then run
        sudo port install apache-ant])
    esac
else
    if test ! -x "$ANT"; then
    AC_MSG_WARN([$ANT is present, but not executable?])
    else
        PT_MSG_RESULT($ANT)
        # Path to the ant binary, stored in lib/ptII.properteries, used
        # while importing accessors in
        # org/terraswarm/accessor/JSAccessor.java
        ANT_PATH="$ANT"
    fi
fi

#--------------------------------------------------------------------
#       Look for the "gawk" command, used by maven
#--------------------------------------------------------------------
AC_ARG_WITH(gawk, [  --with-gawk=PATH         use the gawk command from PATH with maven and ptolemy/configs/doc/makefile,
                   /usr/bin/gawk],
		   GAWK=$withval,
		   GAWK=gawk)
AC_PATH_PROG(GAWK, gawk)
if test ! -x "$GAWK"; then
    AC_MSG_WARN([Couldn't find gawk, looking for awk. gawk or awk is used by maven and in ptolemy/configs/doc/makefile.])
    AC_PATH_PROG(GAWK, awk)
    if test ! -x "$GAWK"; then
        GAWK=awk
    fi	
fi

if test ! -f pom.xml; then
    PT_MSG_STATUS([pom.xml is not present
    so we need not find Maven.])
else
    AC_PATH_PROGS(MVN, mvn mvn32)
    if test -x "$ANT" -a -x "$MVN"; then
        cat > maven-ant-tasks-test.xml << EoF
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project basedir="." default="build" name="ptII"
 xmlns:artifact="antlib:org.apache.maven.artifact.ant">
 <target name="help">
    <artifact:mvn pom="pom.xml">
      <arg value="help"/>
    </artifact:mvn>
  </target>
</project>
EoF

       AC_MSG_CHECKING([for maven ant task.  This could take a minute the first time configure is run.])
       if "$ANT" -f maven-ant-tasks-test.xml help > /dev/null 2>&1 ; then
          PT_MSG_RESULT([ok])
          ANT_MAVEN_ARTIFACT='xmlns:artifact="antlib:org.apache.maven.artifact.ant"'
          AC_MSG_CHECKING([for websensor in \$PTII/ptolemy/apps/websensor])
          if test -d "$PTII/ptolemy/apps/websensor" ; then
              PT_MSG_RESULT([ok])
	      ANT_MAVEN_BUILD_WEBSENSOR="
  <!-- Maven ant task is from http://maven.apache.org/ant-tasks/
       It is no longer supported by the maven community.
       ant-task should be found at $PTII/ant/lib/maven-ant-tasks-2.1.3.jar
       $PTII/configure checks to see if maven ant task is present,
       but the nightly build failed once because configure was expecting
       maven ant task to be present, but at ant runtime, it was not present.
       -->
  <target name=\"-check-maven-ant-task\">
    <condition property=\"maven-ant-task-exists\">
      <typefound uri=\"antlib:org.apache.maven.artifact.ant\" name=\"artifact\"/>
    </condition>
  </target>

  <!-- The build-websensor target depends on maven and
       maven ant tasks being installed.
       $PTII/configure checks for these conditions,
       as does the -check-maven-ant-task condition.
       If you get errors with this target, then try
       rerunning (cd $PTII; ./configure)
   -->
       
  <target name=\"build-websensor\"
          depends=\"-check-maven-ant-task\"
          if=\"${maven-ant-task-exists}\"
          >
    <artifact:mvn pom=\"ptolemy/apps/websensor/pom.xml\">
      <arg value=\"compile\"/>
    </artifact:mvn>
  </target>"

	      ANT_MAVEN_SUBPROJECTS=',build-websensor'
      	      ANT_WEBSENSOR_FILESET='<fileset dir="${basedir}/ptolemy/apps/websensor"/>'
	      ANT_WEBSENSOR_SOURCEPATH='<sourcePath path="${basedir}/ptolemy/apps/websensor"/>'
	      ANT_WEBSENSOR_SRC='<src path="${basedir}/ptolemy/apps/websensor"/>'
          fi
      else
          AC_MSG_WARN([ant did not find the maven-ant-tasks*.jar file,
    so we will not build in $PTII/ptolemy/apps/websensor.
    maven-ant-tasks-*.jar is available from
    https://maven.apache.org/ant-tasks/download.html])
      fi
      rm -f maven-ant-tasks-test.xml
    else
        AC_MSG_WARN([The ant and/or mvn binaries could not be found,
    so we will not build in $PTII/ptolemy/apps/websensor.])
    fi
fi

#--------------------------------------------------------------------
#       Boost was used by Mescal and is now used by FMI++
#	See http://www.boost.org
#--------------------------------------------------------------------

# Set to the directory that contains boost/numeric/odeint.hpp
# and used in actor/lib/fmi/fmipp
PTBOOST_INCLUDE_DIR=

# Set to yes if we found boost
PTBOOST=no

# Set to fmipp and used in ptolemy/actor/lib/fmi/makefile if odeint.hpp is found.
PTFMIPP_DIR=
# We only need to look for Boost if mescal is present
FMIPP_USER_DIR=$PTII/ptolemy/actor/lib/fmi/fmipp

if test ! -d "$FMIPP_USER_DIR"; then
    PT_MSG_STATUS([$FMIPP_USER_DIR is not present,
    so we need not find Boost.])
else
    if test "$PTBOOST" = "no"; then
        AC_MSG_CHECKING([for Boost])
        AC_ARG_WITH(boost, [  --with-boost-include=DIR      use boost includes from DIR DIR/boost/numeric/odeint.hpp should exist,
                          defaults to /usr/local/include],
	PTBOOST_INCLUDE_DIR=$withval,
	PTBOOST_INCLUDE_DIR=/usr/local/include)

	if test -f "$PTBOOST_INCLUDE_DIR/boost/numeric/odeint.hpp"; then
	    PT_MSG_RESULT($PTBOOST_INCLUDE_DIR)
	else
            boostdirs="/usr/local/boost* /opt/local/include /usr/local/include /usr/include"
	    for boostdir in $boostdirs
            do
	        if test -f "$boostdir/boost/numeric/odeint.hpp"; then
                    PTBOOST_INCLUDE_DIR=$boostdir
                    PT_MSG_RESULT($PTBOOST_INCLUDE_DIR)
		    break
                fi
            done
	    if test ! -f "$PTBOOST_INCLUDE_DIR/boost/numeric/odeint.hpp"; then
	        AC_MSG_WARN([Failed to find $PTBOOST_INCLUDE_DIR/boost/numeric/odeint.hpp
    This is only a problem if you want to rebuild the Functional
    Mock-up Interface ++ C files in actor/lib/fmi/fmipp.
    Most users can use the shared libraries in $PTII/lib or $PTII/bin.])
	    fi
        fi
    fi

    # We check for boost later in expat
fi

#--------------------------------------------------------------------
#       BSH is the Java Beanshell 
#       It is used by the Run Control panel that uses FormLayoutManager
#	For more information, see
#       http://www.beanshell.org
#--------------------------------------------------------------------

# PTBSH_RUN_DIR is set to run and used in
# $PTII/ptolemy/actor/gui/makefile if bsh.jar was found.
PTBSH_RUN_DIR=

# PTBSH_MLC_DIR is set to mlc and used in
# $PTII/org/makefile if BSH was found.
PTBSH_MLC_DIR=

# BSH jar file.  We ship $PTII/lib/bsh-2.0b4.jar.
PTBSH_JAR=

# We only need to look for if $PTII/ptolemy/actor/gui exists
BSH_USER_DIR="$PTII/ptolemy/actor/gui/run"
if test ! -d "$BSH_USER_DIR"; then
    PT_MSG_STATUS([$BSH_USER_DIR is not present,
    so we need not find BSH, the Java Bean Shell.])
else
    AC_MSG_CHECKING([for BSH, the Java Bean Shell])
    if test -f "$PTII/lib/bsh-2.0b4.jar"; then
        PT_MSG_RESULT($PTII/lib/bsh-2.0b4.jar)
        PTBSH_JAR="$PTII/lib/bsh-2.0b4.jar"
	PTBSH_MLC_DIR=mlc
	PTBSH_RUN_DIR=run
	# PTBSH_PACKAGES is used in ptII/doc/makefile
	PTBSH_PACKAGES="com.jgoodies.forms.builder com.jgoodies.forms.debug com.jgoodies.forms.factories com.jgoodies.forms.layout com.jgoodies.forms.util org.mlc.swing.example org.mlc.swing.layout ptolemy.actor.gui.run"
	updateClasspath $PTBSH_JAR
    else
        AC_MSG_WARN([Failed to find $PTII/lib/bsh-2.0b4.jar,
    BSH is the Java Bean Shell, which is used by the
    Ptolemy Run Control Panel.  BSH is optional.])
    fi
fi

if test -z "$PTBSH_RUN_DIR"; then
   updateExcludes "ptolemy/actor/gui/run/"
fi 


#--------------------------------------------------------------------
#       The CaffeineMark Kit is a Java benchmark kit
#	that is used by C code generation
#       See http://www-sor.inria.fr/~java/tools/cmkit
#--------------------------------------------------------------------

# Directory that contains the CaffeineMark Java Benchmark kit
# used by C code generation in copernicus/c
CMKIT_DIR='${PTII}/vendors/cm'

# PTCM_DIR is set to cm and used in $PTII/ptolemy/copernicus/c/test/makefile
# if the CaffeineMark Java Benchmark kit is found
PTCM_DIR= 

# We only need to look for cm if $PTII/ptolemy/copernicus/c exists
if test ! -d "$PTII/ptolemy/copernicus/c"; then
    PT_MSG_STATUS([$PTII/ptolemy/copernicus/c is not present,
    so we need not find the CaffeineMark Kit.])
else
    AC_MSG_CHECKING([for CaffeineMarkEmbeddedApp.class])
    AC_ARG_WITH(cmkit, [  --with-cmkit=DIR       use CaffeineMark from DIR,
                          defaults to \$PTII/vendors/cm],
	CMKIT_DIR=$withval,
	CMKIT_DIR=$PTII/vendors/cm)

    if test -f "$CMKIT_DIR/CaffeineMarkEmbeddedApp.class"; then
	PT_MSG_RESULT([$CMKIT_DIR])
	PTCM_DIR=cm
    else
        AC_MSG_WARN([Failed to find $CMKIT_DIR/CaffeineMarkEmbeddedApp.class
    perhaps CaffeineMark is not installed?
    You need not download CaffeineMark unless you plan on using C code
    generation using the older Copernicus C code generator.
    The newer codegen C code generator does  not require CaffeineMark.
    The CaffeineMark kit can be downloaded from
    http://www-sor.inria.fr/~java/tools/cmkit/embed.zip])
	# Note that we don't substitute in the ${PTII} here
	CMKIT_DIR='${PTII}/vendors/cm'
    fi
fi

#--------------------------------------------------------------------
#       Caltrop is an language used to define actors
#	For more information, 
#       see http://embedded.eecs.berkeley.edu/caltrop/
#       See if there was a command-line option for where Caltrop is.
#--------------------------------------------------------------------

# PTCALTROP_DIR is set to caltrop and used in
# $PTII/ptolemy/makefile if Cal was found.
PTCALTROP_DIR=

# Directory that contains the ptCal jar file
CALTROP_DIR='${PTII}/lib'

# We only need to look for on if $PTII/ptolemy/caltrop exists
CAL_USER_DIR="$PTII/ptolemy/caltrop"
if test ! -d "$CAL_USER_DIR"; then
    PT_MSG_STATUS([$CAL_USER_DIR is not present,
    so we need not find the Cal, the actor language.])
else
    AC_MSG_CHECKING([for Cal, the actor language])
    AC_ARG_WITH(cal, [  --with-cal=DIR       use ptCal.jar from DIR,
                          defaults to \$PTII/lib],
	CALTROP_DIR=$withval,
	CALTROP_DIR=$PTII/lib)

    if test -f "$CALTROP_DIR/ptCal.jar"; then
	PT_MSG_RESULT([$CALTROP_DIR])
	# We found cal
	AC_MSG_CHECKING([for saxon8.jar (used by caltrop)])
	if test -f "$CALTROP_DIR/saxon8.jar"; then
	   PT_MSG_RESULT([$CALTROP_DIR/saxon8.jar])

	   AC_MSG_CHECKING([for saxon8-dom.jar (used by caltrop)])
	   if test -f "$CALTROP_DIR/saxon8-dom.jar"; then
	       PT_MSG_RESULT([$CALTROP_DIR/saxon8-dom.jar])
	       AC_MSG_CHECKING([for java_cup.jar (used by caltrop)])
	       if test -f "$CALTROP_DIR/java_cup.jar"; then
	           PT_MSG_RESULT([$CALTROP_DIR/java_cup.jar])
	           PTCALTROP_DIR=caltrop
	       else     
                   AC_MSG_WARN([Failed to find $CALTROP_DIR/java_cup.jar
    which is required by Cal, the actor language.
    You can download java_cup from 
    http://www.cs.princeton.edu/~appel/modern/java/CUP/
    If it is not present, you will not be able to use the Cal actor
    or run the demonstrations  in ptolemy/caltrop])
	           # Note that we don't substitute in the ${PTII} here
	           CALTROP_DIR='${PTII}/lib/'
               fi
           else
               AC_MSG_WARN([Failed to find $CALTROP_DIR/saxon8-dom.jar
    which is required by Cal, the actor language.
    You can download saxon from http://saxon.sourceforge.net/
    If it is not present, you will not be able to use the Cal actor
    or run the demonstrations  in ptolemy/caltrop])
	       # Note that we don't substitute in the ${PTII} here
	       CALTROP_DIR='${PTII}/lib/'
	   fi    
	else   
           AC_MSG_WARN([Failed to find $CALTROP_DIR/saxon8.jar
    which is required by Cal, the actor language.
    You can download saxon from http://saxon.sourceforge.net/
    If it is not present, you will not be able to use the Cal actor
    or run the demonstrations  in ptolemy/caltrop])
	   # Note that we don't substitute in the ${PTII} here
	   CALTROP_DIR='${PTII}/lib/'
        fi
    else  
        AC_MSG_WARN([Failed to find PTII/lib/ptCal.jar
    ptCal.jar should be present in your distribution.  
    If it is not present, you will not be able to use the Cal actor
    or run the demonstrations  in ptolemy/caltrop])
	# Note that we don't substitute in the ${PTII} here
	CALTROP_DIR='${PTII}/lib/'
    fi
fi

if test -z "$PTCALTROP_DIR"; then
   updateExcludes "ptolemy/caltrop/"
else
   updateClasspath "$CALTROP_DIR/ptCal.jar"
   updateClasspath "$CALTROP_DIR/java_cup.jar"
   updateClasspath "$CALTROP_DIR/saxon8.jar"
   updateClasspath "$CALTROP_DIR/saxon8-dom.jar"
fi 

#--------------------------------------------------------------------
#       Checkstyle is used to check the style of java files by ant.
#	
#	
#--------------------------------------------------------------------
# We only need to look for CHECKSTYLE if this directory is present
CHECKSTYLE_USER_DIR="$PTII/ptolemy/actor/test/junit"

CHECKSTYLE_VERSION=-6.2
CHECKSTYLE_JAR="checkstyle$CHECKSTYLE_VERSION.jar"

if test ! -d "$CHECKSTYLE_USER_DIR"; then
    PT_MSG_STATUS([$CHECKSTYLE_USER_DIR is not present,
    so we need not find Checkstyle for testing])
else
    AC_MSG_CHECKING([for Checkstyle, optionally used to check the style of Java files.])
    AC_ARG_WITH(checkstyle, [  --with-checkstyle=DIR    use Checkstyle from DIR,
                          defaults to $PTII/vendors/checkstyle-6.2],
	CHECKSTYLE_DIR=$withval,
	CHECKSTYLE_DIR=$PTII/vendors/checkstyle$CHECKSTYLE_VERSION)
changequote(<<, >>)dnl
    CHECKSTYLE_VERSION=`basename "$CHECKSTYLE_DIR" | sed 's/checkstyle\(.*\)$/\1/'`
changequote([, ])dnl
    if test -r "$CHECKSTYLE_DIR/checkstyle$CHECKSTYLE_VERSION-all.jar" ; then
        PT_MSG_RESULT([$CHECKSTYLE_DIR])
        CHECKSTYLE_JAR="checkstyle$CHECKSTYLE_VERSION-all.jar"
    fi

    if test ! -f "$CHECKSTYLE_DIR/$CHECKSTYLE_JAR"; then
        AC_MSG_WARN([Failed to find Checkstyle in $PTII/vendors/checkstyle$CHECKSTYLE_VERSION
    Checkstyle is only necessary for code cleaning.
    Checkstyle is LGPL'd, so while it could be in the ptII repo, we don't add it.
    Checkstyle may be downloaded from http://checkstyle.sourceforge.net/])
    fi
fi

#--------------------------------------------------------------------
#       "CHIC is a modular verifier for behavioral compatibility checking
#	 of software and hardware components"
#
#	For more information, 
#       see https://embedded.eecs.berkeley.edu/research/chic/
#--------------------------------------------------------------------

# PTCHIC_DIR is set to chic and used in
# $PTII/ptolemy/makefile if Chic was found.
PTCHIC_DIR=

# Directory that contains the chic jar file
CHIC_DIR='${PTII}/lib'

# We only need to look for if $PTII/ptolemy/chic exists
CHIC_USER_DIR="$PTII/ptolemy/chic"
if test ! -d "$CHIC_USER_DIR"; then
    PT_MSG_STATUS([$CHIC_USER_DIR is not present,
    so we need not find Chic, the modular verifier for
    behavioral compatibility checking of software and hardware components.]) 
else
    AC_MSG_CHECKING([for Chic, the model checker])
    AC_ARG_WITH(chic, [  --with-chic=DIR       use chic.jar from DIR,
                          defaults to \$PTII/lib],
	CHIC_DIR=$withval,
	CHIC_DIR=$PTII/lib)

    if test -f "$CHIC_DIR/chic.jar"; then
        PT_MSG_RESULT($CHIC_DIR)
	# We found chic
	PTCHIC_DIR=chic
    else  
        AC_MSG_WARN([Failed to find PTII/lib/chic.jar
    chic.jar should be present in your distribution.  
    Chic is a modular verifier for behavioral compatibility checking
    of software and hardware components.
    If it is not present, you will not be able to use the Chic facilities
    or run the demonstrations in ptolemy/chic.])
	# Note that we don't substitute in the ${PTII} here
	CHIC_DIR='${PTII}/lib'
    fi
fi

if test -z "$PTCHIC_DIR"; then
   updateExcludes "ptolemy/chic/"
else
   updateClasspath "$CHIC_DIR/chic.jar"
fi 


case "`uname -s`" in
   Darwin) ECLIPSE_SWT_JAR=org.eclipse.swt.carbon.macosx_
  	   # Darwin has problems with echo -n?
   	   PT_ECHO="/bin/echo -n"
	   ;;
   *)      PT_ECHO=echo
  	   ;;
esac


#--------------------------------------------------------------------
#       COLT is a 
#       "Open Source Libraries for High Performance Scientific and Technical
#       Computing in Java"
#	For more information, see
#       http://hoschek.home.cern.ch/hoschek/colt/
#--------------------------------------------------------------------

# PTCOLT_DIR is set to colt and used in
# $PTII/ptolemy/actor/lib/makefile if Colt was found.
PTCOLT_DIR=

# Colt jar files.  We ship $PTII/lib/ptcolt.jar, which is a subset
# of $PTII/vendors/misc/colt.jar
PTCOLT_JARS=

# Directory that contains the colt jar file
COLT_DIR='${PTII}/vendors/misc/colt'

# We only need to look for if $PTII/ptolemy/actor/lib/colt exists
COLT_USER_DIR="$PTII/ptolemy/actor/lib/colt"
if test ! -d "$COLT_USER_DIR"; then
    PT_MSG_STATUS([$COLT_USER_DIR is not present,
    so we need not find Colt, the 
    Open Source Libraries for High Performance Scientific and Technical
    Computing in Java.])
else
    AC_MSG_CHECKING([for Ptolemy subset of Colt, the scientific computing lib])
    if test -f "$PTII/lib/ptcolt.jar"; then
        PT_MSG_RESULT($PTII/lib/colt.jar)
        PTCOLT_JAR="$PTII/lib/ptcolt.jar"
	PTCOLT_DIR=colt
	# PTCOLT_PACKAGES is used in ptII/doc/makefile
	PTCOLT_PACKAGES=ptolemy.actor.lib.colt
    else
        AC_MSG_WARN([Failed to find $PTII/lib/ptcolt.jar, will look for
    full colt.jar])
        PTCOLT_JAR=    
    fi

    AC_MSG_CHECKING([for Full version of Colt, the scientific computing lib])
    AC_ARG_WITH(colt, [  --with-colt=DIR       use colt.jar from DIR,
                          defaults to \$PTII/vendors/misc/colt],
	COLT_DIR=$withval,
	COLT_DIR=$PTII/vendors/misc/colt)

    if test -f "$COLT_DIR/colt.jar"; then
        PT_MSG_RESULT($COLT_DIR/colt.jar)
	PTCOLT_JARS=$COLT_DIR/colt.jar$CLASSPATHSEPARATOR$PTCOLT_JAR
	# Put the ptcolt.jar second, after $COLT_DIR/colt.jar
        updateClasspath "$PTCOLT_JAR"
	updateClasspath "$COLT_DIR/colt.jar"
	# We found colt
	PTCOLT_DIR=colt
	# PTCOLT_PACKAGES is used in ptII/doc/makefile
	PTCOLT_PACKAGES=ptolemy.actor.lib.colt
    else  
	if test -z "PTCOLT_DIR"; then
            AC_MSG_WARN([Failed to find $PTII/lib/ptcolt.jar
    and $COLT_DIR/colt.jar.
    Colt is the 'Open Source Libraries for High Performance
    Scientific and Technical Computing in Java'
    For more information, see http://hoschek.home.cern.ch/hoschek/colt/
    If it is not present, you will not be able to use the Colt facilities
    or run the demonstrations in ptolemy/actor/lib/colt.])
	    # Note that we don't substitute in the ${PTII} here
	    COLT_DIR='${PTII}/vendors/misc/colt'
        else 
	    AC_MSG_WARN([Did not find $COLT_DIR/colt.jar,
    using $PTCOLT_JAR])
    	    PTCOLT_JARS=$PTCOLT_JAR
	    updateClasspath "$PTCOLT_JAR"
        fi
    fi
fi

if test -z "$PTCOLT_DIR"; then
   updateExcludes "ptolemy/actor/lib/colt/"
fi 


#--------------------------------------------------------------------
#       org.omg.CORBA.Object is part of the JDK 1.9 module system
#       The error is:
#   [javac]   (package org.omg.CORBA is declared in module java.corba, which is not in the module graph)
#       
#--------------------------------------------------------------------

# PTCORBA_DIR is used in ptolemy/actor/makefile
PTCORBA_DIR=

# PTCORBA_PACKAGES is used in ptII/doc/makefile
PTCORBA_PACKAGES=

# We only need look for Corba if this directory exists
CORBA_USER_DIR="$PTII/ptolemy/actor/corba"
if test ! -d "$CORBA_USER_DIR"; then
    PT_MSG_STATUS([$CORBA_USER_DIR is not present,
    so we need not check for CORBA.])
else
    AC_MSG_CHECKING([for CORBA])
    # We need to run javac in the config directory so that javac from jdk1.1.6
    # under NT and cygwin works properly
    startdir=$PTII
    cd "$srcdir/config"
    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" CORBATest.java ; then
        PT_MSG_RESULT(CORBA found in the default classpath)
        # PTCORBA_DIR is used in ptolemy/actor/lib/jjs/modules
        PTCORBA_DIR=corba
        # PTCORBA_PACKAGES is used in ptII/doc/makefile
        PTCORBA_PACKAGES="ptolemy.actor.corba ptolemy.actor.corba.util"
    else
       AC_MSG_WARN(['"$JAVAC" CORBATest.java' failed.
    perhaps you are running an JDK 1.9?
    You will not be able to run the ptolemy.actor.corba actors,
    which is probably not a problem.])
       updateExcludes "ptolemy/actor/corba/"
       updateExcludes "ptolemy/domains/openmodelica/"
    fi
    cd "$startdir"

fi

#--------------------------------------------------------------------
#       Cobertura is used for code coverage
#	
#	
#--------------------------------------------------------------------
# We only need to look for COBERTURA if this directory is present
COBERTURA_USER_DIR="$PTII/ptolemy/actor/test/junit"

COBERTURA_VERSION=-2.0.3
COBERTURA_JAR="cobertura$COBERTURA_VERSION.jar"

if test ! -d "$COBERTURA_USER_DIR"; then
    PT_MSG_STATUS([$COBERTURA_USER_DIR is not present,
    so we need not find Cobertura for testing])
else
    AC_MSG_CHECKING([for Cobertura, optionally used for Java code coverage.])
    AC_ARG_WITH(cobertura, [  --with-cobertura=DIR    use Cobertura from DIR,
                          defaults to $PTII/vendors/cobertura-2.0.3],
	COBERTURA_DIR=$withval,
	COBERTURA_DIR=$PTII/vendors/cobertura$COBERTURA_VERSION)
changequote(<<, >>)dnl
    COBERTURA_VERSION=`basename "$COBERTURA_DIR" | sed 's/cobertura\(.*\)$/\1/'`
changequote([, ])dnl
    if test -r "$COBERTURA_DIR/cobertura$COBERTURA_VERSION.jar" ; then
        COBERTURA_JAR="cobertura$COBERTURA_VERSION.jar"
        PT_MSG_RESULT([$COBERTURA_JAR])
    fi

    if test ! -f "$COBERTURA_DIR/$COBERTURA_JAR"; then
        AC_MSG_WARN([Failed to find Cobertura in $PTII/vendors/corbertura$COBERTURA_VERSION
    Cobertura is only necessary to for code coverage.
    Cobertura is GPL'd, so we don't check it in to the ptII repository.
    Cobertura may be downloaded from http://cobertura.github.io/cobertura/])
    fi
fi

#--------------------------------------------------------------------
#       CUnit is used to test C Code in the code generator
#	
#	
#--------------------------------------------------------------------
# We only need to look for CUnit if this directory is present
CUNIT_USER_DIR="$PTII/ptolemy/cg/kernel/generic/program/procedural/c/type"

# PTCUNIT_DIR is set to test and used in 
# $PTII/ptolemy/cg/kernel/generic/program/procedural/c/type
# if CUnit is found
PTCUNIT_DIR=

if test ! -d "$CUNIT_USER_DIR"; then
    PT_MSG_STATUS([$CUNIT_USER_DIR is not present,
    so we need not find CUnit for testing])
else
    AC_MSG_CHECKING([for CUnit to be used to test the C cg templates])
    AC_ARG_WITH(cunit, [  --with-cunit=DIR    use CUnit from DIR,
                          defaults to /usr/local or $PTII/vendors/CUnit],
	CUNIT_DIR=$withval,
	CUNIT_DIR=/usr/local)
    if test -r "$CUNIT_DIR/include/CUnit/Basic.h" ; then
        PT_MSG_RESULT([$CUNIT_DIR])
        #PTCUNIT_INCLUDE_DIR="$CUNIT_DIR/include"
        #PTCUNIT_LIB_DIR="$CUNIT_DIR/lib"
        PTCUNIT_DIR=test
    else
        if test -r /usr/local/include/CUnit/Basic.h ; then
	    PT_MSG_RESULT([/usr/include])
            #PTCUNIT_INCLUDE_DIR=/usr/local/include
            #PTCUNIT_LIB_DIR=/usr/local/lib
            PTCUNIT_DIR=test
        else 
	    if test -r "$PTII/vendors/CUnit/include/CUnit/Basic.h" ; then
	        PT_MSG_RESULT([$PTII/vendors/CUnit])
                #PTCUNIT_INCLUDE_DIR="$PTII/vendors/CUnit/include"
	        #PTCUNIT_LIB_DIR="$PTII/vendors/CUnit/lib"
	        PTCUNIT_DIR=test
            else 
   	        AC_MSG_WARN([Failed to find CUnit in /usr/local or
    $PTII/vendors/CUnit.
    CUnit is only necessary to test the C templates of the code generation facility])
    	        updateExcludeTests **/ptolemy/cg/kernel/generic/program/procedural/c/type/test/junit/JUnitTclTest.java
		updateExcludeTests **/ptolemy/cg/adapter/generic/program/procedural/c/adapters/ptolemy/domains/de/kernel/test/junit/JUnitTclTest.java
            fi
        fi
    fi
fi

#--------------------------------------------------------------------
#       doclets are used to control javadoc
#	The Ptolemy II doclets are in $PTII/doc/doclets
#	and use $PTJAVA_HOME/../tools.jar to compile
#--------------------------------------------------------------------

# We only need to look for doclet if $PTII/doc/doclets is present
DOCLETS_USER_DIR="$PTII/doc/doclets"
DOCLETS_PRESENT=no

# Location of tools.jar, usually $(PTJAVA_HOME)/../lib/tools.jar
TOOLS_JAR=

# PTDOCLETS_DIR is set to doclets and used in 
# $PTII/doc if com.sun.tools.doclets.Taglet can be found
PTDOCLETS_DIR=

# If we can compile in doc/doclets, we set JDOCTAGLET appropriately
# and use JDOCTAGLET in doc/makefile
JDOCTAGLET=

if test ! -d "$DOCLETS_USER_DIR"; then
    PT_MSG_STATUS([$DOCLETS_USER_DIR is not present,
    so we need not find tools.jar in the JRE.])
    # Use curly brackets around PTII so that if tools.jar is not present

    TOOLS_JAR='${PTJAVA_HOME}/../lib/tools.jar'
else
    AC_MSG_CHECKING([for tools.jar for use with doclets])
    AC_ARG_WITH(tools_jar, [  --with-tools_jar=DIR    use tools.jar from DIR,
                          defaults to \$PTJAVA_HOME/../lib/tools.jar],
	TOOLS_JAR=$withval,
	TOOLS_JAR=${PTJAVA_HOME}/../lib/tools.jar)
    if test -f "$TOOLS_JAR"; then
	PT_MSG_RESULT([$TOOLS_JAR])
	PTDOCLETS_DIR=doclets
    else	
        AC_MSG_WARN([Could not find tools.jar, checking for classes.jar])
	AC_MSG_CHECKING([for classes.jar for use with doclets])
	TOOLS_JAR=${PTJAVA_HOME}/../Classes/classes.jar
        if test -f "$TOOLS_JAR"; then
	    PT_MSG_RESULT([$TOOLS_JAR])
	    PTDOCLETS_DIR=doclets
        else 
	    AC_MSG_WARN([Could not find tools.jar or classes.jar in
    PTJAVA_HOME = $PTJAVA_HOME
    Usually, tools.jar is in PTJAVA_HOME/../lib/tools.jar
    or classes.jar is in PTJAVA_HOME/../Classes/classes.jar
    Since tools.jar and classes.jar cannot be found,
    we will not use doclets from ptII/doc/doclets, which
    means that the actor documentation index system will not work.])
        fi
    fi	
fi
if test -z "$PTDOCLETS_DIR"; then
   updateExcludes "doc/doclets/"
else
   addToolsJarToEclipse=yes

#   case "`uname -s`" in
#	Darwin) 
#	    case "$TOOLS_JAR" in
#		*/Classes/classes.jar)
#		    addToolsJarToEclipse=no
#  	            AC_MSG_WARN([Not including $TOOLS_JAR 
#   to the Eclipse classpath under Darwin because it is already present.]);;
#            esac;;
#   esac

    if test "$addToolsJarToEclipse" = "yes" ; then
       updateClasspath "$TOOLS_JAR"
    fi
    JDOCTAG="-tag Pt.AcceptedRating -tag Pt.ProposedRating"
    # Use curly brackets so PTII gets expanded in the makefile
    JDOCTAGLET='-tagletpath "${PTII}" -taglet doc.doclets.RatingTaglet'
fi 

# The javadoc program
AC_PATH_PROG(JAVADOC, javadoc)
if test -x "$JAVADOC"; then
    case "`uname -s`" in
    CYGWIN*) 	
		# We use cygpath here
		# so that we can run make from within the doc builder gui.  The reason is that
		# the doc builder gui runs make within a cmd shell, not a bash shell, which
		# means that /cygdrive/c notation will not be understood.
		AC_MSG_CHECKING([Under windows, javadoc should use the non-cywin path])
		JAVADOC=`cygpath --mixed "$JAVADOC"`
	        PT_MSG_RESULT([$JAVADOC])
    ;;  
    esac
fi


#--------------------------------------------------------------------
#       We use Eclipse for parsing java backtracking.
#       Eclipse is an integrated development environment, see
#	http://www.eclipse.org
#       See if there was a command-line option for where Eclipse can be found
#       is
#       If not, look for for $PTII/vendors/eclipse
#--------------------------------------------------------------------

# PTBACKTRACK_DIR is set to backtrack and used in
# $PTII/ptolemy/makefile if we can handle generics (Java 1.5)
PTBACKTRACK_DIR=backtrack

# PTBACKTRACK_ECLIPSE_DIR is set to eclipse and used in
# $PTII/ptolemy/backtrack/makefile if Eclipse was found
# and the jar files were found
PTBACKTRACK_ECLIPSE_DIR=

# Jar files used by ptolemy/backtrack/eclipse
PTBACKTRACK_ECLIPSE_JARS=

# Default to looking for Eclipse
PTECLIPSE_PLUGINS=yes

eclipseMessage="The backtracking facility requires Eclipse 3.2 or greater.
    You need not download Eclipse unless you plan on using the backtracking
    facility in ptolemy.backtrack.
    Eclipse may be downloaded from http://www.eclipse.org/"

if test ! -d "$PTII/ptolemy/backtrack/eclipse" -o "x$ECLIPSE_CLASSPATHENTRY_PDE_REQUIREDPLUGINS" == "x"; then
    if test ! -d "$PTII/ptolemy/backtrack/eclipse"; then
        PT_MSG_STATUS([$PTII/ptolemy/backtrack/eclipse is not present,
	so we need not find Eclipse.])
    fi
    if test "x$ECLIPSE_CLASSPATHENTRY_PDE_REQUIREDPLUGINS" == "x"; then
	PT_MSG_STATUS([You are running under Mac OS X, and backtracking
    is not currently supported.  See 
    http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Mac])
    fi  
else
    if test ! "$HAS_GENERICS" = "yes"; then 
        AC_MSG_WARN([You are running Java $JVERSION, which does not
    support generics.  Thus, ptolemy/backtrack/eclipse will not compile.])
	PTBACKTRACK_DIR=    
    else
        AC_MSG_CHECKING([for Eclipse installation])
        # Use changequote to protect the square brackets in sed

        # We cd to *clipse so that we get the case right in the jar files.
        if test -d "c:/Program Files/Eclipse" -o -d "c:/Program Files/eclipse"; then
        # Remove /cygdrive	
changequote(<<, >>)dnl
           TMP_ECLIPSE_DIR="`cd c:/Program\ Files/*clipse; pwd | sed 's@/cygdrive/\([a-z]\)/@\1:/@'`"
changequote([, ])dnl
        else 
           TMP_ECLIPSE_DIR="c:/Program\ Files/eclipse"
        fi
	if test -d "/Applications/eclipse"; then
	    TMP_ECLIPSE_DIR=/Applications/eclipse
        else
changequote(<<, >>)dnl
            TMP_ECLIPSE_DIR=`ls -1dr /Applications/[Ee]clipse* | head -1`
changequote([, ])dnl
        fi
        AC_ARG_WITH(eclipse, [  --with-eclipse=ECLIPSE_DIR     use Eclipse from ECLIPSE_DIR,
                         defaults to $TMP_ECLIPSE_DIR],
            ECLIPSE_DIR=$withval,
            ECLIPSE_DIR=$TMP_ECLIPSE_DIR)

        if test "$ECLIPSE_DIR" = "no"; then
	    AC_MSG_WARN([configure called with --without-eclipse-plugins,
   not building in ptolemy/apps/eclipse and ptolemy/backtrack.])
           updateExcludes "ptolemy/apps/eclipse/"
        else
	    if test ! -d "$ECLIPSE_DIR"; then
                AC_MSG_WARN([Failed to find Eclipse in $ECLIPSE_DIR])
                AC_MSG_CHECKING([for $PTII/vendors/eclipse])
                if test -d  "$PTII/vendors/eclipse"; then
	            PT_MSG_RESULT([ok])
	            ECLIPSE_DIR="$PTII/vendors/eclipse"
                else
	            AC_MSG_WARN([Failed to find Eclipse in $PTII/vendors/eclipse])
                    AC_PATH_PROG(PTECLIPSE, eclipse)
                    if test "${PTECLIPSE:-none}" != "none"; then
                 # Remove /cygdrive	
changequote(<<, >>)dnl
	                ECLIPSE_DIR=`dirname $PTECLIPSE | sed 's@/cygdrive/\([a-z]\)/@\1:/@'`
changequote([, ])dnl
	             fi
	         fi
             fi
        fi 
        if test -d "$ECLIPSE_DIR"; then
            # Under RHEL 6.2, eclipse is in /usr/bin/eclipse
            if test ! -d "$ECLIPSE_DIR/plugins"; then
	        savedEclipseDir=$ECLIPSE_DIR
	        ECLIPSE_DIR=no
                eclipsedirs="/usr/local /usr/lib /usr/lib64"
                for eclipsedir in $eclipsedirs
                do
                    if test -d "$eclipsedir/eclipse/plugins"; then
                        ECLIPSE_DIR="$eclipsedir/eclipse"
                        break
                    fi
                done
		if test ! -d "$ECLIPSE_DIR"; then
		    AC_MSG_WARN([Eclipse was found in $savedEclipseDir, but $savedEclipseDir/plugins was not found?"])
                fi
            fi
        fi

        if test -d "$ECLIPSE_DIR"; then
	    PT_MSG_RESULT([$ECLIPSE_DIR])
	    AC_MSG_CHECKING([for jars used by backtracking in $ECLIPSE_DIR])

	    case "`uname -s`" in
	    Darwin) ECLIPSE_SWT_JAR=org.eclipse.swt.cocoa.macosx
		;;
	    Linux) ECLIPSE_SWT_JAR=eclipse.swt.gtk.linux
		;;
	    *) ECLIPSE_SWT_JAR=eclipse.swt.win32.win32.x86_
		;; 
	    esac

	    # jars="jdt.core osgi resources runtime" 
	    # jdt.core core.runtime_ are needed to build backtrack
	    # osgi_ and resources_ are needed to run the tests in backtrack
	    jars="eclipse.jdt.core_ eclipse.core.runtime_ eclipse.osgi_ eclipse.core.resources_ eclipse.equinox.common_ eclipse.core.jobs_ eclipse.core.contenttype_ eclipse.equinox.preferences_ eclipse.text_ eclipse.ui.workbench_ eclipse.jface_ $ECLIPSE_SWT_JAR eclipse.jdt.ui_ eclipse.jface.text_ eclipse.ui.workbench.texteditor_ eclipse.ui.editors_ eclipse.core.commands_ org.eclipse.equinox.registry_ eclipse.ui.console_ eclipse.ui.forms_ eclipse.ui.ide_"
	    ANT_ECLIPSE_CLASSPATH=
	    eclipsejarpath=
	    for jar in $jars
	    do
	    	if test "${PTVERBOSE:-none}" = "none"; then
	            $PT_ECHO $ECHO_N "."
	        else
                    $PT_ECHO $ECHO_N "$jar "
                fi
		# In more recent versions of eclipse, the jdt jars are in dropins/, the other jars are in plugins/
	        jarpath=`$FIND "$ECLIPSE_DIR" -name "*${jar}*.jar" | grep -v source_ | head -1`
   	        if test -f "$jarpath"; then
                    # Keep track of the jars so we can use them while building
		    # with make.
	            ANT_ECLIPSE_CLASSPATH="$ANT_ECLIPSE_CLASSPATH <pathelement location=\"$jarpath\"/> "
  	            eclipsejarpath="$eclipsejarpath$CLASSPATHSEPARATOR$jarpath"

		    # NOTE: Eclipse 3.0 has problems if we include these
		    # jars in the .classpath, instead, .classpath.in includes:
		    #  <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
                    updateClasspath "$jarpath"
 	        else   
		    AC_MSG_WARN([Failed to find $jar in $ECLIPSE_DIR: $jarpath])
	            eclipsejarpath=
		    break
	        fi


	    done	

            if test ! -z "$eclipsejarpath"; then 
                PT_MSG_RESULT([ok])

	        # Get the plugin jar files for use with javadoc in $PTII/doc
		case "`uname -s`" in
		Darwin) ECLIPSE_SWT_JAR=org.eclipse.swt.cocoa.macosx
			# Darwin has problems with echo -n?
			PT_ECHO="/bin/echo -n"
			;;
		Linux)	ECLIPSE_SWT_JAR=eclipse.swt.gtk.linux
			;;
		*)	ECLIPSE_SWT_JAR=eclipse.swt.win32.win32.x86_
			PT_ECHO=echo
			;; 
		esac
	        AC_MSG_CHECKING([for Eclipse jars used with javadoc])
		docjars="eclipse.core.commands_ eclipse.equinox.registry_ eclipse.jface_ eclipse.jface.text_ eclipse.ui.workbench_ eclipse.ui.workbench.texteditor_ eclipse.ui.console_ eclipse.ui.editors_ eclipse.text_ eclipse.ui.forms_ eclipse.ui.ide_ eclipse.jdt.ui_ $ECLIPSE_SWT_JAR"
		# eclipse.core.runtime_ org.eclipse.equinox.common_ org.eclipse.core.resources_ org.eclipse.core.jobs_
	        PTBACKTRACK_ECLIPSE_DOC_JARS=
	        for jar in $docjars
	        do
	    	    if test "${PTVERBOSE:-none}" = "none"; then
	                $PT_ECHO $ECHO_N "."
	            else
                        $PT_ECHO $ECHO_N "$jar "
                    fi
		    # In more recent versions of eclipse, the jdt jars are in dropins/, the other jars are in plugins/
	            jarpath=`$FIND "$ECLIPSE_DIR" -name "*${jar}*.jar" | head -1`
   	            if test -f "$jarpath"; then
	                # Keep track of the jars so we can use them while
		        # building with ant and make.
			ANT_ECLIPSE_CLASSPATH="$ANT_ECLIPSE_CLASSPATH <pathelement location=\"$jarpath\"/> "
	                PTBACKTRACK_ECLIPSE_DOC_JARS="$PTBACKTRACK_ECLIPSE_DOC_JARS$CLASSPATHSEPARATOR$jarpath"
#			case "`uname -s`" in
#			Darwin) updateClasspath "$jarpath";;
#	   		esac 
 	            else   
		        AC_MSG_WARN([Failed to find $jar in $ECLIPSE_DIR: $jarpath])
			failedToFindEclipseDocJars=1
		        break
	            fi
	        done	
                if test ! -z "$PTBACKTRACK_ECLIPSE_DOC_JARS" -a -z "$failedToFindEclipseDocJars"; then 
                    PT_MSG_RESULT([ok])
                else 
                    AC_MSG_WARN([Failed to find Eclipse jar file for docs.
    As a result, building the javadoc documentation might show warnings.
    $eclipseMessage])
                fi

	        startdir=$PTII
	        cd "$srcdir/config"
	        AC_MSG_CHECKING([for ITreeSelection from Eclipse])
	        if "$JAVAC" -classpath "$PTBACKTRACK_ECLIPSE_DOC_JARS" EclipseITreeSelection.java ; then
                    PT_MSG_RESULT([ok])
		    ANT_CLASSPATH="$ANT_CLASSPATH $ANT_ECLIPSE_CLASSPATH"
		    # Set to eclipse and used in
		    # $PTII/ptolemy/backtrack/makefile if Eclipse jar
		    # files were found
		    PTBACKTRACK_ECLIPSE_DIR=eclipse
		    # PTBACKTRACK_ECLIPSE_PACKAGES is used in ptII/doc/makefile
		    PTBACKTRACK_ECLIPSE_PACKAGES="ptolemy.backtrack.eclipse.ast ptolemy.backtrack.eclipse.ast.transform ptolemy.backtrack.eclipse.plugin ptolemy.backtrack.eclipse.plugin.actions ptolemy.backtrack.eclipse.plugin.editor ptolemy.backtrack.eclipse.plugin.preferences ptolemy.backtrack.eclipse.plugin.util"
		    PTBACKTRACK_ECLIPSE_JARS=$eclipsejarpath
                else
 	            AC_MSG_WARN([Failed to compile config/EclipseITreeSelection.java with
    (cd "$PTII/config"; "$JAVAC" -classpath $PTBACKTRACK_ECLIPSE_DOC_JARS EclipseITreeSelection.java)
    $eclipseMessage])
                    eclipsejarpath=
                fi
	        cd "$startdir"
             fi
        fi	


        if test "$ECLIPSE_DIR" != "no" -a "$PTBACKTRACK_ECLIPSE_DIR" = ""; then
            AC_MSG_WARN([Failed to find Eclipse
    perhaps Eclipse is not installed?
    $eclipseMessage])
	    PTBACKTRACK_ECLIPSE_JARS=
        fi
    fi
fi

if test -z "$PTBACKTRACK_ECLIPSE_DIR"; then
   updateExcludes "ptolemy/apps/eclipse/awt/"
   updateExcludes "ptolemy/backtrack/"
   updateExcludes "ptolemy/backtrack/ast/"
fi 

#--------------------------------------------------------------------
#       db and dbxml is the Oracle Berkeley XML DB
#	http://www.oracle.com/technology/software/products/berkeley-db/xml/index.html
#	dbxml is used by the ptdb directory.
#       db and dbxml are basically GPL'd, see $PTII/ptdb/lib/db-dbxml-license.htm
#--------------------------------------------------------------------

# PTDB_DIR is set to database and used in
# $PTII/ptdb/makefile if dbxml is found
PTDB_DIR=


PTDBXML_JAR='${PTII}/vendors/oracle/dbxml.jar'
PTDB_JAR='${PTII}/vendors/oracle/db.jar'

# Jar files necessary for compilation
PTDBXML_JARS="${PTDBXML_JAR}${CLASSPATHSEPARATOR}${PTDB_JAR}"

# We only need to look for dbxml if $PTDB_USER_DIR
PTDB_USER_DIR="$PTII/ptdb"
if test ! -d "$PTDB_USER_DIR"; then
    PT_MSG_STATUS([$PTDB_USER_DIR is not present,
    so we need not find the dbxml interface.])
else
    AC_MSG_CHECKING([for dbxml.jar ])
    AC_ARG_WITH(dbxml, [  --with-dbxml=JAR       use dbxml.jar from JAR,
                          defaults to \$PTII/vendors/oracle/dbxml.jar],
	PTDBXML_JAR=$withval,
	PTDBXML_JAR=$PTII/vendors/oracle/dbxml.jar)

    if test  -f "$PTDBXML_JAR"; then
	PT_MSG_RESULT([$PTDBXML_JAR])

        AC_MSG_CHECKING([for db.jar ])
        AC_ARG_WITH(db, [  --with-db=JAR       use db.jar from JAR,
                          defaults to \$PTII/vendors/oracle/db.jar],
	PTDB_JAR=$withval,
	PTDB_JAR=$PTII/vendors/oracle/db.jar)

        if test  -f "$PTDB_JAR"; then
	    PT_MSG_RESULT([$PTDB_JAR])
	    # Set to ptdb and used in
	    # $PTII/makefile

	    # Set to database and used in
	    # $PTII/ptdb/makefile
	    PTDB_DIR=database
            # PTDB_PACKAGES is used in ptII/doc/makefile
	    PTDB_PACKAGES=`$FIND ptdb -name "*.java" | grep -v /test | awk -F / '{printf("%s", $1); for (i = 2; i < NF; i++) printf(".%s", $i); printf("\n")}' | sort | uniq | awk '{printf("%s ", $0)}'`
         fi
    fi	

    # Look for shared libraries necessary at runtime.
    AC_MSG_CHECKING([for dbxml runtime shared libraries])
    AC_ARG_WITH(dbxmllib, [  --with-dbxmllib=DIR    use libdbxml from DIR,
                          defaults to \$PTII/vendors/misc/dbxml-2.5.16/install/lib],
	PTDBXML_LIB=$withval,
	PTDBXML_LIB=$PTII/vendors/misc/dbxml-2.5.16/install/lib)
    if test  -d "$PTDBXML_LIB"; then
	PT_MSG_RESULT([$PTDBXML_LIB])
	libdbxml=`$FIND "$PTDBXML_LIB" -name "*dbxml-*"`
	if test ! -f "$libdbxml"; then
	    AC_MSG_WARN([Failed to find dbxml-X.Y shared library in $PTDBXML_LIB])
        fi
    else
        AC_MSG_WARN([Failed to find dbxml-X.Y shared library in $PTDBXML_LIB.
    This means that the Ptolemy/Android HandSimDroid prototype will not run.])       
    fi

    if test "$PTDB_DIR" = ""; then
        AC_MSG_WARN([Failed to find the Oracle Berkeley XML DB (dbxml) in
    $PTDBXML_JAR and
    $PTDB_JAR
    Perhaps the Oracle Berkeley XML DB is not installed?
    You need not download dbxml unless you
    plan on using the ptdb facility which uses a database to manage actors with Ptolemy II. 
    The dbxml interface can be downloaded from
    http://www.oracle.com/technology/software/products/berkeley-db/xml/index.html
    an untar'd into $PTII/vendors/misc and built.
    For further instructions, see $PTII/ptdb/doc] )
    else
        PTDBXML_JARS="${PTDBXML_JAR}${CLASSPATHSEPARATOR}${PTDB_JAR}"
    fi

    if test ! "$HAS_GENERICS" = "yes"; then 
        #ptdb.gui.GraphPatternSearchEditor import ptalon.gt.PtalonMatcher
        AC_MSG_WARN([You are running Java $JVERSION, which does not
    support generics.  Thus, ptdb, which depends on ptolemy/actor/ptalon will not compile.])
        PTDBXML_JAR=""
	PTDB_JAR=""
    fi
fi

if test -z "$PTDB_DIR"; then
   updateExcludes "ptdb/kernel/database/"
else
   updateClasspath "$PTDBXML_JAR"
   updateClasspath "$PTDB_JAR"
fi 


#--------------------------------------------------------------------
#       Garbage Collector (GC)
#       The C code generator can use the Boehm Garbage Collector
#       See http://www.hpl.hp.com/personal/Hans_Boehm/gc/
#--------------------------------------------------------------------
#
# GC_LD_DIRECTIVE is set to the values to pass to cc or ld if
# GC_malloc() can be found either in the default compiler location
# or in $PTII/lib.
# GC_LD_DIRECTIVE is used in ptolemy/copernicus/c/
GC_LD_DIRECTIVE=

# GC_DIR is set to the directory where GC can be found
GC_DIR=

if test ! -d "$PTII/ptolemy/copernicus/c"; then
    PT_MSG_STATUS([$PTII/ptolemy/copernicus/c is not present,
    so we need not find the Boehm GC.])
else
    AC_PATH_PROG(PTCC, gcc)
    if test "${PTCC:-none}" = "none"; then
        AC_MSG_WARN([Failed to find gcc])
        AC_PATH_PROG(PTCC, cc)
        if test "${PTCC:-none}" != "none"; then
            PT_MSG_RESULT([$PTCC])
        else    
            AC_MSG_WARN([Failed to find gcc or cc, so we will
    not be able use GC in $PTII/ptolemy/copernicus/c]);
        fi
    fi

    if test "${PTCC:-none}" != "none"; then
       AC_MSG_CHECKING([for Garbage Collector])
       AC_CHECK_LIB(gc, GC_malloc, PT_GC=yes, PT_GC=no)
       if test "$PT_GC" = "yes"; then
           PT_MSG_RESULT(yes)
       else
           if test -f "$PTII/lib/libgc.a"; then
	      # FIXME: what about Windows?
	      GC_LD_DIRECTIVE='"-L${PTII}/lib" -lgc'
	      PT_MSG_RESULT(use $GC_LD_DIRECTIVE)
           else 
	      # FIXME: This will not work if $PTII has spaces
	      dirs="$PTII/vendors/gc/gc6.4 $PTII/vendors/gc/gc6.1 $PTII/vendors/gc/gc"
	      for dir in $dirs
	      do
	          if test -d "$dir"; then
                      AC_MSG_WARN([Failed to find GC_malloc(), but 
    $dir exists.  See \$PTII/vendors/gc/README.txt
    if you would like to use the Garbage Collector with the C code generator])
                  fi
	      done
           fi 
       fi
    fi
   AC_MSG_CHECKING([for gc.h])
   AC_ARG_WITH(gc-include, [  --with-gc-include=DIR       use gc.h from DIR
                          defaults to \$PTII/vendors/gc/gc/include],
	GC_INCLUDE_DIR=$withval,
	GC_INCLUDE_DIR=$PTII/vendors/gc/gc/include)

   if test -f "$GC_INCLUDE_DIR/gc.h"; then
       PT_MSG_RESULT([$GC_INCLUDE_DIR/gc.h])
   else 
       # FIXME: This will not work if $PTII has spaces
       dirs="$PTII/vendors/gc/gc6.4 $PTII/vendors/gc/gc6.1 $PTII/vendors/gc/gc"
       for dir in $dirs
       do
           if test -f "$dir/include/gc.h"; then
               GC_INCLUDE_DIR=$PTII/vendors/gc/gc6.4/include
	       PT_MSG_RESULT([$GC_INCLUDE_DIR/gc.h])
           fi
       done
       if test ! -f "$GC_INCLUDE_DIR/gc.h"; then
           AC_MSG_WARN([Failed to find gc.h.
    Checked the following directories:
    $dirs
    The Boehm Garbage Collector can be downloaded from
    http://www.hpl.hp.com/personal/Hans_Boehm/gc/
    if you wish to use it with the the older copernicus C code generator.
    The newer codegenerator in codegen does _not_ require the Boehm GC.])
       fi
   fi
fi



#--------------------------------------------------------------------
#       gcc-arm is a GNU compiler for the Arm processor used by 
#	the mbed code generator in ptolemy/cg/adapter/generic/program/procedural/c/mbed
#--------------------------------------------------------------------

# Set to mbed and used in
# $PTII/ptolemy/cg/adapter/generic/program/procedural/c/makefile
# if vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc was found
PTMBED_DIR= 

# We only need to look for vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc if
# $PTII/ptolemy/cg/adapter/generic/program/procedural/c/mbed exists
MBED_USER_DIR="$PTII/ptolemy/cg/adapter/generic/program/procedural/c/mbed"
if test ! -d "$MBED_USER_DIR"; then
    PT_MSG_STATUS([$MBED_USER_DIR is not present,
    so we need not find $PTII/ptolemy/cg/adapter/generic/program/procedural/c/mbed])
else
    AC_MSG_CHECKING([for arm-none-eabi-gcc])
    AC_ARG_WITH(gcc-arm, [  --with-gcc-arm=GCC_BINARY       use gcc-arm
                          defaults to \$PTII/vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc],
	PTGCC_ARM=$withval,
	PTGCC_ARM=$PTII/vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc)

    if test -f "$PTGCC_ARM"; then
	PT_MSG_RESULT([$PTGCC_ARM])
        # Set to mbed and used in
        # $PTII/ptolemy/cg/adapter/generic/program/procedural/c/makefile
        # if vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc was found
	PTMBED_DIR=mbed
    fi	

    if test "$PTMBED_DIR" = ""; then
        AC_MSG_WARN([Failed to find $PTII/vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc
    so the Mbed CG facility will not be run.])
    fi
fi

if test -z "$PTMBED_DIR"; then
   updateExcludes "ptolemy/cg/adapter/generic/program/procedural/c/mbed"
fi 

#--------------------------------------------------------------------
#       iText PDF is a "a library that allows you to generate PDF files on the fly."
#	http://itextpdf.com/
#	However, itextpdf is GPL'd, so we don't ship it.
#--------------------------------------------------------------------

# Set to itextpdf and used in
# $PTII/ptolemy/vergil/basic/export/makefile if iText.jar was found
PTITEXTPDF_DIR=

# iText PDF jar file.  iText is from
# http://itextpdf.com
PTITEXTPDF_JAR=

# We only need to look for iText.jar if $ITEXTPDF_USER_DIR exists
ITEXTPDF_USER_DIR="$PTII/ptolemy/vergil/basic/export/itextpdf"
if test ! -d "$ITEXTPDF_USER_DIR"; then
    PT_MSG_STATUS([$ITEXT_USER_DIR is not present,
    so we need not find the iText PDF interface.])
else
    AC_MSG_CHECKING([for the iText PDF jar])
    AC_ARG_WITH(itextpdf, [  --with-itextpdf=JARFILE       use iText from JARFILE,
                          defaults to \$PTII/vendors/misc/itext/iText.jar],
	PTITEXTPDF_JAR=$withval,
	PTITEXTPDF_JAR=$PTII/vendors/misc/itext/iText.jar)

    if test -f "$PTITEXTPDF_JAR"; then
	PT_MSG_RESULT([$PTITEXTPDF_JAR])
	# Set to itextpdf and used in
	# $PTII/ptolemy/vergil/basic/export/makefile if iText.jar is found
	PTITEXTPDF_DIR=itextpdf
        # PTITEXTPDF_PACKAGES is used in ptII/doc/makefile
	PTITEXTPDF_PACKAGES=ptolemy.vergil.basic.export.itextpdf
    fi	

    if test "$PTITEXTPDF_DIR" = ""; then
        AC_MSG_WARN([Failed to find iText.jar
    as $PTITEXTPDF_JAR.
    Perhaps the iText is not installed?
    You need not download the iText interface unless you
    would like to export PDF from Vergil.
    Note that the iText jar file has the Affero General Public License (AGPL),
    which is an extension of the GNU Public License.
    To use the iText interface, download iText from http://itextpdf.com
    place iText.jar in $PTII/vendors/misc/itext/ and then rerun configure.])
	# Note that we don't substitute in the ${PTII} here
	PTITEXTPDF_JAR='${PTII}/vendors/misc/itext/iText.jar'
    fi
fi

if test -z "$PTITEXTPDF_DIR"; then
   updateExcludes "ptolemy/vergil/basic/export/itextpdf/"
else
   updateClasspath "$PTITEXTPDF_JAR"
fi 

#--------------------------------------------------------------------
#       g4ltl "G4LTL is a standalone tool and a Java library for
#       automatically generating controllers realizing linear temporal
#       logic (LTL).
#	http://www6.in.tum.de/~chengch/g4ltl
#--------------------------------------------------------------------
# PTG4LTL_DIR is set to g4ltl if the g4ltl jar file was found
# $PTII/ptolemy/vergil/actor/makefile uses PTG4LTL_DIR
PTG4LTL_DIR=

# PTG4LTL_PACKAGES is used in doc/makefile
PTG4LTL_PACKAGES=

# The location of the g4ltl jar file, typically $PTII/lib/g4ltl.jar
PTG4LTL_JAR=

# PTSTRUCTURALCODER_JAR is set if $PTII/lib/StructuralCoder.jar was found
# and used in ptolemy/vergil/actor/g4ltl/makefile
PTSTRUCTURALCODER_JAR=

# We only need look for g4ltl if $PTII/ptolemy/vergil/basic/imprt/g4ltl exists
G4LTL_USER_DIR="$PTII/ptolemy/vergil/basic/imprt/g4ltl"
if test ! -d "$G4LTL_USER_DIR"; then
    PT_MSG_STATUS([$G4LTL_USER_DIR is not present, so we need not find G4LTL.])
else
    AC_MSG_CHECKING([G4LTL])
    if test -f "$PTII/lib/g4ltl.jar" -a -f "$PTII/lib/StructuralCoder.jar"; then
        PT_MSG_RESULT($PTII/lib/g4ltl.jar)
	PTG4LTL_JAR="$PTII/lib/g4ltl.jar"
        updateClasspath "$PTG4LTL_JAR"

	PTG4LTL_DIR=g4ltl
	PTG4LTL_PACKAGES="ptolemy.vergil.basic.imprt.g4ltl"

        PTSTRUCTURALCODER_JAR="$PTII/lib/StructuralCoder.jar"
        updateClasspath "$PTSTRUCTURALCODER_JAR"

    else
        AC_MSG_WARN([Failed to find $PTII/lib/g4ltl.jar or $PTII/lib/StructuralCoder.jar,
	which means that importing an FSMActor using LTL synthesis (G4LTL) will not be supported.]);
        updateExcludes "ptolemy/vergil/actor/g4ltl/"
    fi
fi

#--------------------------------------------------------------------
#       GMP - GNU arbitrary precision arithmetic library, needed only by mescal
#       
#--------------------------------------------------------------------
# We only need to look for GMP if mescal/relsat is present
MESCAL_RELSAT_USER_DIR="$PTII/mescal/relsat"

PTGMP=no
if test ! -d "$MESCAL_RELSAT_USER_DIR"; then
    PT_MSG_STATUS([$MESCAL_RELSAT_USER_DIR is not present,
    so we need not find GMP.])
else
    case "`uname -s`" in
	Linux) ARCH=linux;;
        *) ARCH=unknown;;
    esac

    if test "$PTGMP" = "no"; then
        AC_MSG_CHECKING([for GMP in \$PTII/mescal/include/gmp.h])
	if test -f "$PTII/mescal/include/gmp.h"; then
	    PT_MSG_RESULT([ok])
	    PTGMP_INCLUDE="-I$PTII/mescal/include"
	    PTGMP_LIB="-L$PTII/mescal/lib"
	    PTGMP_LD_FLAGS="-Wl,-R$PTII/mescal/lib"
	    PTGMP=yes
        else
	    PT_MSG_RESULT([not found, keep looking])
	fi    
    fi

    if test "$PTGMP" = "no"; then
        AC_MSG_CHECKING([for GMP in /usr/local/include/gmp.h])
        if test -f "/usr/local/include/gmp.h"; then
            PT_MSG_RESULT([ok])
	    if test "$ARCH" != "linux"; then
	        PTGMP_INCLUDE=-I/usr/local/include
		PTGMP_LIB=-L/usr/local/lib
	        PTGMP_LD_FLAGS="-Wl,-R/usr/local/lib"
            fi
	    PTGMP=yes
        else
	    PT_MSG_RESULT([not found, keep looking])
        fi
    fi    

    if test "$PTGMP" = "no"; then
        AC_MSG_CHECKING([for GMP])
        AC_CHECK_HEADERS(gmp.h, PTGMP=yes, PTGMP=no)
    fi

    if test "$PTGMP" = "yes"; then
        AC_MSG_CHECKING([for gcc])
        AC_PATH_PROG(PTCC, gcc)
        if test "${PTCC:-none}" = "none"; then
            AC_MSG_WARN([Failed to find gcc])
	    AC_PATH_PROG(PTCC, cc)
	    if test "${PTCC:-none}" = "none"; then
	        AC_MSG_WARN([Failed to find gcc or cc, so we will
    not be able to compile the mescal output]);
            fi
	fi

	PTGMP_OK=no
	startdir=$PTII
	# Make sure that we check for CXX before cding in to config
	AC_PROG_CXX
        cd "$srcdir/config"
        AC_MSG_CHECKING([gmp by compiling a C small program])
	if "$PTCC" gmpTest.c $PTGMP_INCLUDE -o gmpTest $PTGMP_LD_FLAGS $PTGMP_LIB -lgmp ; then
	    ./gmpTest
	    PT_MSG_RESULT([ok])
	else    
	    RESULTS=`"$PTCC" gmpTest.c $PTGMP_INCLUDE -o gmpTest $PTGMP_LD_FLAGS$PTGMP_LIB -lgmp`
	    AC_MSG_WARN([Failed to compile config/gmpTest.c, 
    "$PTCC" gmpTest.c $PTGMP_INCLUDE -o gmpTest $PTGMP_LIB -lgmp
    $RESULTS])
	fi

        AC_MSG_CHECKING([gmp by compiling a C++ small program])
	if "$CXX" gmpTest2.cc $PTGMP_INCLUDE -o gmpTest2 $PTGMP_LD_FLAGS $PTGMP_LIB -lgmpxx -lgmp ; then
	    ./gmpTest2
	    PT_MSG_RESULT([ok])
	else    
	    RESULTS=`"$CXX" gmpTest2.cc $PTGMP_INCLUDE -o gmpTest2 $PTGMP_LD_FLAGS $PTGMP_LIB -lgmpcxx -lgmp`
	    AC_MSG_WARN([Failed to compile config/gmpTest2.cc, 
    "$CXX" gmpTest2.cc $PTGMP_INCLUDE -o gmpTest2 $PTGMP_LD_FLAG $PTGMP_LIB -lgmpxx -lgmp
    $RESULTS
    Under Cygwin, perhaps you need to add $PTII/bin/mescal to your PATH,
    Under Linux, perhaps you need to add $PTII/bin/mescal to
    your LD_LIBRARY_PATH])
	fi

        cd "$startdir"
    fi

    if test "$PTGMP" = "no"; then 
            AC_MSG_WARN([Failed to find gmp.h, which is only
    needed to compile $MESCAL_RELSAT_USER_DIR
    gmp can be found at http://www.swox.com/gmp/
    Mescal uses c++, and configure will look in /usr/local
    and $PTII/mescal/include and $PTII/mescal/lib for gmp,
    so gmp should be configured with
       ./configure --enable-cxx --prefix=$PTII/mescal])
    fi
fi

#--------------------------------------------------------------------
#       $PTII/ptolemy/homer is a gui builder used by HandSimDroid
#	to allow complex models to be run on handheld devices
#	http://chess.eecs.berkeley.edu/handsimdroid
#	
#--------------------------------------------------------------------

# PTHOMER_DIR is set to homer and used in
# $PTII/ptolemy/makefile if the netbeans visual gui code is found
PTHOMER_DIR=

# Jar files necessary for compilation of homer
PTHOMER_JARS=

# We only need to look for Hessian if $HOMER_USER_DIR is present
HOMER_USER_DIR="$PTII/ptolemy/homer"
if test ! -d "$HOMER_USER_DIR"; then
    PT_MSG_STATUS([$HOMER_USER_DIR is not present,
    so we need not find the Netbeans visual gui interface.])
else
    AC_MSG_CHECKING([for org-openide-util.jar, used by homer ])
    AC_ARG_WITH(openideutil, [  --with-openideutil=JAR       use org-openide-util.jar from JAR,
                          defaults to \$PTII/lib/org-openide-util.jar],
	PTOPENIDEUTIL_JAR=$withval,
	PTOPENIDEUTIL_JAR=$PTII/lib/org-openide-util.jar)

    if test  -f "$PTOPENIDEUTIL_JAR"; then
	PT_MSG_RESULT([$PTOPENIDEUTIL_JAR])
        AC_MSG_CHECKING([for org-openide-util-lookup.jar, used by homer ])
        AC_ARG_WITH(openideutillookup, [  --with-openideutillookup=JAR       use org-openide-util-lookup.jar from JAR,
                          defaults to \$PTII/lib/org-openide-util-lookup.jar],
	    PTOPENIDEUTILLOOKUP_JAR=$withval,
	    PTOPENIDEUTILLOOKUP_JAR=$PTII/lib/org-openide-util-lookup.jar)
        if test  -f "$PTOPENIDEUTILLOOKUP_JAR"; then
	    PT_MSG_RESULT([$PTOPENIDEUTILLOOKUP_JAR])
            AC_MSG_CHECKING([for org-netbeans-api-visual.jar, used by homer ])
            AC_ARG_WITH(netbeansapivisual, [  --with-netbeansapivisual=JAR       use org-netbeans-api-visual.jar from JAR,
                              defaults to \$PTII/lib/org-netbeans-api-visual.jar],
	        PTNETBEANSAPIVISUAL_JAR=$withval,
	        PTNETBEANSAPIVISUAL_JAR=$PTII/lib/org-netbeans-api-visual.jar)
            if test  -f "$PTNETBEANSAPIVISUAL_JAR"; then
	        PT_MSG_RESULT([$PTNETBEANSAPIVISUAL_JAR])
     
	        # Set to homer and used in $PTII/ptolemy/makefile
	        PTHOMER_DIR=homer
                # PTHOMER_PACKAGES is used in ptII/doc/makefile
		PTHOMER_PACKAGES="ptolemy.homer.events ptolemy.homer.gui ptolemy.homer ptolemy.homer.kernel ptolemy.homer.widgets"
            fi
        fi
    fi

    if test "$PTHOMER_DIR" = ""; then
        AC_MSG_WARN([Failed to find the jar files necessary to compile injection.
    The injection code interface is used to support Ptolemy running on the Android.
    For further instructions, see $PTII/ptolemy/actor/injection/package.html] )
    else
        PTHOMER_JARS="${PTOPENIDEUTIL_JAR}${CLASSPATHSEPARATOR}${PTOPENIDEUTILLOOKUP_JAR}${CLASSPATHSEPARATOR}${PTNETBEANSAPIVISUAL_JAR}"
    fi
fi

if test -z "$PTHOMER_JARS"; then
   updateExcludes "ptolemy/homer/"
else
   updateClasspath "$PTOPENIDEUTIL_JAR"
   updateClasspath "$PTOPENIDEUTILLOOKUP_JAR"
   updateClasspath "$PTNETBEANSAPIVISUAL_JAR"
fi 



#--------------------------------------------------------------------
#       JAI is the Java Advanced Imaging Framework
#	For more information, 
#       see https://jai.dev.java.net/
#       See if there was a command-line option for where JAI is.
#--------------------------------------------------------------------

# PTJAI_DIR is set to jai and used in
# $PTII/ptolemy/actor/makefile if jai was found
PTJAI_DIR=

# Used in ptolemy/actor/lib/jai/makefile
JAI_JARS=

# We only need to look for JAI if the actor/lib/jai directory is present
JAI_USER_DIR="$PTII/ptolemy/actor/lib/jai"

if test ! -d "$JAI_USER_DIR"; then
    PT_MSG_STATUS([$JAI_USER_DIR is not present,
    so we need not find JAI - The Java Advanced Imaging API.])
else
    AC_MSG_CHECKING([for Java Advanced Imaging (JAI) API])
    # We need to run javac in the config directory so that javac from jdk1.1.6
    # under NT and cygwin works properly
    startdir=$PTII
    cd "$srcdir/config"
    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" JAITest.javaxxx ; then
       PT_MSG_RESULT(JAI found in the default classpath)
       PTJAI_OK=1
    else
        TMP_JAI_DIR=`find $PTII/vendors -type d -name "jai*"  | head -1`
        if test -d "$TMP_JAI_DIR/lib/jai_core.jar"; then
            JAI_DIR="$TMP_JAI_DIR"
        fi
        if "$JAVAC" -classpath "$TMP_JAI_DIR/lib" JAITest.java ; then
            PT_MSG_RESULT(JAI found in $TMP_JAI_DIR)
            PTJAI_OK=1
            JAI_DIR="$TMP_JAI_DIR"
        fi
    fi

    if ! test -z "$PTJAI_OK" ; then
        PTJAI_DIR=jai
        # PTJAI_PACKAGES is used in ptII/doc/makefile
        PTJAI_PACKAGES=ptolemy.actor.lib.jai

        AC_MSG_CHECKING([for the jai jar files])
	if "$JAVAC" FindClass.java ; then
	    # Usually jai-core.jar will be in the CLASSPATH
	    JAI_JAR=`"$JAVA" -classpath "$PTII/config${CLASSPATHSEPARATOR}${JAI_DIR}/lib" FindClass javax.media.jai.RenderedOp`
	    if test -f "$JAI_JAR" ; then
	       JAI_JARS_DIR=`dirname "$JAI_JAR"`
	       JAI_JARS="${JAI_JARS_DIR}/jai_core.jar${CLASSPATHSEPARATOR}${JAI_JARS_DIR}/jai_codec.jar"
	       PT_MSG_RESULT($JAI_JARS)
	       # Here, we should not be adding JAI_JAR to Eclipse
	       # if jai.jar was in the jre
               case "`uname -s`" in
	       Darwin) 
  	            AC_MSG_WARN([Not including
   $JAI_JARS_DIR/{jai_core.jar,jai_codec.jar}
   to the Eclipse classpath under Darwin because it is already present.]);;
               *)
	           updateClasspath "$JAI_JARS_DIR/jai_core.jar"
		   updateClasspath "$JAI_JARS_DIR/jai_codec.jar"
		   ;;
               esac
	    else 
       	       AC_MSG_WARN([Either we could not find 
    javax.media.jai.RenderOp or else it was already in the JRE.
    Searching for jai-core.jar returned:
      $JAI_JAR
    If the class cannot be found, then Eclipse might not be able to find
    the JAI files.  
    This is only a problem if you are using Eclipse.
    If the class was in the JRE, then Eclipse should compile the JAI files
    without problems])
	       JAI_JAR=
            fi
	else
	    AC_MSG_WARN(['"$JAVAC" -classpath "$PTII/config${CLASSPATHSEPARATOR}${JAI_DIR}/lib" FindClass javax.media.jai.RenderedOp` 
    failed.            
    This means that Eclipse might not be able to find the JAI files.
    This is only a problem if you are using Eclipse])
        fi
    else
       AC_MSG_WARN(['"$JAVAC" JAITest.java' failed.
    perhaps the Java Advanced Imaging API is not installed?
    You need not download Jai unless you plan on using the video
    actors in $JAI_USER_DIR
    The JAI API can be downloaded from 
    http://www.oracle.com/technetwork/java/javasebusiness/downloads/java-archive-downloads-java-client-419417.html])
    fi
    cd "$startdir"
fi

if test -z "$PTJAI_DIR"; then
   updateExcludes "ptolemy/actor/lib/jai/"
fi

#--------------------------------------------------------------------
#       "CERTI is an Open Source HLA RTI. HLA (High-Level Architecture) is a general purpose architecture for distributed computer simulation systems."
#	See https://savannah.nongnu.org/projects/certi
#       JCerti is used by org/hlacerti
#--------------------------------------------------------------------

# JCERTI jar files used by org/hlacerti
PTJCERTI_JAR=

# We only need to look for JCERTetty if $HLACERT_USER_DIR is present
HLACERTI_USER_DIR="$PTII/org/hlacerti"

if test ! -d "$HLACERTI_USER_DIR" ; then
    PT_MSG_STATUS([$HLACERTI_USER_DIR is not present,
    so we need not find jcerti.jar.])
else
    if test "$PRE_JDK18" = "yes" ; then
        AC_MSG_WARN([org/hlacerti requires Java 1.8 or later])
        updateExcludes "org/hlacerti/"
    else
        AC_MSG_CHECKING([for Jcerti, used by hlacerti ])
        AC_ARG_WITH(jcerti, [  --with-jcerti=JAR       use jcert.jar from JAR,
                          defaults to \$PTII/lib/jcerti.jar],
            PTJCERTI_JAR=$withval,
	    PTJCERTI_JAR=$PTII/lib/jcerti.jar)
        if test  -f "$PTJCERTI_JAR"; then
	    PT_MSG_RESULT([$PTJCERTI_JAR])
	    # Set to mail and used in
	    # $PTII/ptolemy/apps/makefile if jcerti.jar was found.
	    PTHLACERTI_DIR=hlacerti
            # PTHLACERTI_PACKAGES is used in ptII/doc/makefile
	    PTHLACERTI_PACKAGES="org.hlacerti.lib"
	    updateClasspath "$PTJCERTI_JAR"
        else 
            AC_MSG_WARN([Failed to find jcerti.jar necessary to compile org/hlacerti
    hlacerti is optional])	
           updateExcludes "org/hlacerti/"
        fi
    fi
fi

#--------------------------------------------------------------------
#       "Jetty is a pure Java-based HTTP server and Java Servlet container." 
#	See http://www.eclipse.org/jetty/
#       Jetty is used by Ptango and Ptserver 
#--------------------------------------------------------------------

# Jetty jar files used by Ptango and ptserver.
PTJETTY_JAR=

# javax.servlet-api*.jar used by Ptango and ptserver.
PTSERVLET_JAR=

# smack.jar and smackx.jar used by Ptango, implements xmpp
PTSMACK_JAR=
PTSMACKX_JAR=

# We only need to look for Jetty if $PTANGO_USER_DIR is present
# We only need to look for Jetty if $PTSERVER_USER_DIR is present
PTANGO_USER_DIR="$PTII/org/ptolemy/ptango/"
PTSERVER_USER_DIR="$PTII/ptserver/"
PTHOMER_USER_DIR="$PTII/ptolemy/homer/"
if test ! -d "$PTANGO_USER_DIR" -a ! -d "$PTSERVER_USER_DIR" -a ! -d "$PTHOMER_DIR"; then
    PT_MSG_STATUS([$PTANGO_USER_DIR, $PTSERVER_USER_DIR
    and $PTHOMER_DIR are not present,
    so we need not find Jetty, javax.servlet, smack or smackx])
else
    AC_MSG_CHECKING([for Jetty, used by ptango and ptserver ])
    AC_ARG_WITH(jetty, [  --with-jetty=JAR       use jetty.jar from JAR,
                          defaults to \$PTII/lib/jetty-all-8.1.5-v20120716.jar],
        PTJETTY_JAR=$withval,
	PTJETTY_JAR=$PTII/lib/jetty-all-8.1.5-v20120716.jar)
    if test  -f "$PTJETTY_JAR"; then
	PT_MSG_RESULT([$PTJETTY_JAR])
	
        AC_MSG_CHECKING([for Servlet, used by ptango and ptserver])
	AC_ARG_WITH(servlet, [  --with-servlet=JAR       use servlet.jar from JAR,
                          defaults to \$PTII/lib/javax.servlet-api-3.0.1.jar],
	    PTSERVLET_JAR=$withval,
	    PTSERVLET_JAR=$PTII/lib/javax.servlet-api-3.0.1.jar)

        if test  -f "$PTSERVLET_JAR"; then
	    PT_MSG_RESULT([$PTSERVLET_JAR])
        fi
    fi

    AC_MSG_CHECKING([for Smack, used by ptango])
    AC_ARG_WITH(smack, [  --with-smack=JAR       use smack.jar from JAR,
                          defaults to \$PTII/lib/smack.jar],
        PTSMACK_JAR=$withval,
	PTSMACK_JAR=$PTII/lib/smack.jar)
    if test  -f "$PTSMACK_JAR"; then
	PT_MSG_RESULT([$PTSMACKJAR])
       updateClasspath "$PTSMACK_JAR"
    else
        AC_MSG_WARN([Failed to find the Smack jar files necessary to compile ptango.
    Ptango is the Ptolemy Internet of Things project.
    For further instructions, see http://chess.eecs.berkeley.edu/ptango.])
    fi

    AC_MSG_CHECKING([for Smackx, used by ptango])
    AC_ARG_WITH(smackx, [  --with-smackx=JAR       use smackx.jar from JAR,
                          defaults to \$PTII/lib/smackx.jar],
        PTSMACKX_JAR=$withval,
	PTSMACKX_JAR=$PTII/lib/smackx.jar)

    if ! test  -f "$PTSMACKX_JAR"; then
        updateExcludes "$PTANGO_USER_DIR"
        AC_MSG_WARN([Failed to find the Smackx jar files necessary to compile ptango.
    Ptango is the Ptolemy Internet of Things project.
    For further instructions, see http://chess.eecs.berkeley.edu/ptango.])

    else
	PT_MSG_RESULT([$PTSMACKXJAR])
        updateClasspath "$PTSMACKX_JAR"
    fi

    if ! test -f "$PTJETTY_JAR"; then
        updateExcludes "$PTANGO_USER_DIR"
        updateExcludes "$PTSERVER_USER_DIR"
        updateExcludes "$PTHOMER_USER_DIR"
        AC_MSG_WARN([Failed to find the Jetty jar files necessary to compile ptango,
    ptserver and homer.
    Ptango is the Ptolemy Internet of Things project.
    For further instructions, see http://chess.eecs.berkeley.edu/ptango.])

    else 
        updateClasspath "$PTJETTY_JAR"
    fi

    if ! test -f "$PTSERVLET_JAR"; then
        updateExcludes "$PTANGO_USER_DIR"
        updateExcludes "$PTSERVER_USER_DIR"
        updateExcludes "$PTHOMER_USER_DIR"
        AC_MSG_WARN([Failed to find the Servlet jar files necessary to compile ptango,
    ptserver and homer.
    Ptango is the Ptolemy Internet of Things project.
    For further instructions, see http://chess.eecs.berkeley.edu/ptango.])

    else 
       updateClasspath "$PTSERVLET_JAR"
    fi

    # We check that the appropriate jars are available below for Ptango
fi

#--------------------------------------------------------------------
#       JavaMail is a Java interface that sends email
#	https://java.net/projects/javamail/pages/Home
#--------------------------------------------------------------------

# PTJAVAMAIL_DIR is set to mail
# $PTII/ptolemy/domains/makefile if JavaMail was found
PTJAVAMAIL_DIR=

# JavaMail Directory.  JavaMail is available from
# https://java.net/projects/javamail/pages/Home
JAVAMAIL_DIR='${PTII}/lib'

# JavaMail jar files.   Used to compile the mail actors.
PTJAVAMAIL_JARS=

JAVAMAIL_USER_DIR="$PTII/ptolemy/actor/lib/mail"
# We only need to look for JavaMail if $JAVAMAIL_USER_DIR
if test ! -d "$JAVAMAIL_USER_DIR"; then
    PT_MSG_STATUS([$JAVAMAIL_USER_DIR is not present,
    so we need not find the JavaMail interface.])
else
    AC_MSG_CHECKING([for JavaMail directory])
    AC_ARG_WITH(javamail, [  --with-javamail=DIRECTORY       use JavaMail interface from DIRECTORY,
                          defaults to \$PTII/lib],
	JAVAMAIL_DIR=$withval,
	JAVAMAIL_DIR=$PTII/lib)

    if test -f "$JAVAMAIL_DIR/javax.mail.jar"; then
	# Set to mail and used in
	# $PTII/ptolemy/actor/lib/makefile if javax.mail.jar was found.
	PTJAVAMAIL_DIR=mail
        # PTJAVAMAIL_PACKAGES is used in ptII/doc/makefile
	PTJAVAMAIL_PACKAGES="ptolemy.actor.lib.mail"

	PTJAVAMAIL_JARS="${JAVAMAIL_DIR}/javax.mail.jar"
        updateClasspath "$JAVAMAIL_DIR/javax.mail.jar"
	PT_MSG_RESULT([$JAVAMAIL_DIR])
    fi

    if test "$PTJAVAMAIL_DIR" = ""; then
        AC_MSG_WARN([Failed to find javax.mail.jar
    in $JAVAMAIL_DIR
    perhaps the JavaMail interface is not installed?
    You need not download the JavaMail interface unless you
    plan on using the Ptolemy actors that send email.
    The JavaMail interface can be downloaded from
    https://java.net/projects/javamail/pages/Home with
      cd $PTII/lib
      wget --no-check-certificate http://java.net/projects/javamail/downloads/download/javax.mail.jar
      cd $PTII
      ./configure])
	# Note that we don't substitute in the ${PTII} here
	JAVAMAIL_DIR='${PTII}/lib'
    fi
fi

if test -z "$PTJAVAMAIL_DIR"; then
   updateExcludes "ptolemy/actor/lib/mail/"
fi 

#--------------------------------------------------------------------
#       Ptolemy includes one or more FMUs that use JModelica
#       
#--------------------------------------------------------------------

# PTJMODELICA_DIR is set to jmodelica if JModelica was found
# $PTII/ptolemy/actor/lib/fmi/fmus/makefile uses PTJMODELICA_DIR
PTJMODELICA_DIR=

# Directory that contains JModelica.
JMODELICA_HOME=

# PTJMODELICA_PACKAGES is used in doc/makefile
PTJMODELICA_PACKAGES=

# We only beed look for jmf if $PTII/ptolemy/actor/lib/fmi exists
JMODELICA_USER_DIR="$PTII/ptolemy/actor/lib/fmi/fmus/jmodelica"
if test ! -d "$JMODELICA_USER_DIR"; then
    PT_MSG_STATUS([$JMODELICA_USER_DIR is not present,
    so we need not find JModelica.])
else
    AC_MSG_CHECKING([for JModelica])
    if test -f "/usr/local/jmodelica/include/jmi.h"; then
        PT_MSG_RESULT([/usr/local/jmodelica/include/jmi.h])
	JMODELICA_HOME="/usr/local/jmodelica"
	PTJMODELICA_DIR=jmodelica
	PTJMODELICA_PACKAGES=""
    else
        AC_MSG_WARN([Failed to find /usr/local/jmodelica/include/jmi.h
    which is part of JModelica.    	
    Ptolemy optionally includes one or more FMUs that use JModelica.
    To install JModelica, see https://svn.jmodelica.org/trunk/INSTALL])
    fi
fi

#--------------------------------------------------------------------
#       JavaFX is used the the audio ClipPlayer demo under CapeCode
#       
#--------------------------------------------------------------------

# PTJAVAFX_DIR is used in ptolemy/actor/lib/jjs/modules
PTJAVAFX_DIR=

# PTJAVAFX_PACKAGES is used in ptII/doc/makefile
PTJAVAFX_PACKAGES=

# We only need look for JavaFX if this directory exists
JAVAFX_USER_DIR="$PTII/ptolemy/actor/lib/jjs/modules/audio"
if test ! -d "$JAVAFX_USER_DIR"; then
    PT_MSG_STATUS([$JAVAFX_USER_DIR is not present,
    so we need not check for JavaFX.])
else
    AC_MSG_CHECKING([for JavaFX])
    # We need to run javac in the config directory so that javac from jdk1.1.6
    # under NT and cygwin works properly
    startdir=$PTII
    cd "$srcdir/config"
    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" JavaFXTest.java ; then
        PT_MSG_RESULT(JavaFX found in the default classpath)
        # PTJAVAFX_DIR is used in ptolemy/actor/lib/jjs/modules
        PTJAVAFX_DIR=audio
        # PTJAVAFX_PACKAGES is used in ptII/doc/makefile
        PTJAVAFX_PACKAGES=ptolemy.actor.lib.jjs.modules
    else
       AC_MSG_WARN(['"$JAVAC" JavaFXTest.java' failed.
    perhaps you are running an OpenJDK JDK instead of an
    Oracle JDK?
    This means that the audio accessors will not work under CapeCode.])
       updateExcludes "ptolemy/actor/lib/jjs/modules/audio/"
    fi
    cd "$startdir"

fi

#--------------------------------------------------------------------
#       JMF is the Java Media Framework
#	For more information, 
#       see http://www.oracle.com/technetwork/java/javase/tech/index-jsp-140239.html
#       See if there was a command-line option for where JMF is.
#--------------------------------------------------------------------

# PTJMF_DIR is set to jmf and used in
# $PTII/ptolemy/actor/lib/makefile if jmf was found
PTJMF_DIR=

# Used in ptolemy/actor/lib/jmf/makefile
JMF_JARS=

# We only need to look for jmf if $PTII/ptolemy/actor/lib exists
JMF_USER_DIR="$PTII/ptolemy/actor/lib/jmf"
if test ! -d "$JMF_USER_DIR"; then
    PT_MSG_STATUS([$JMF_USER_DIR is not present,
    so we need not find the JMF - The Java Media Framework.])
else
    AC_MSG_CHECKING([for Java Media Framework (JMF)])
    # We need to run javac in the config directory so that javac
    # from jdk1.1.6 under NT and cygwin works properly
    startdir=$PTII
    cd "$srcdir/config"
    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" JMFTest.java ; then
        PT_MSG_RESULT(JMF found in the default classpath.)
        PTJMF_DIR=jmf
	# PTJMF_PACKAGES is used in ptII/doc/makefile
	PTJMF_PACKAGES=ptolemy.actor.lib.jmf
	# Usually, JMF gets installed in C:/Program Files/JMF2.1.1
	# and CLASSPATH gets that C:/Program Files/JMF2.1.1/lib/jmf.jar
	# and C:/Program Files/JMF2.1.1/lib/sound.jar appended to it
	# We need to figure out where it was found so that Eclipse
	# can find it
	AC_MSG_CHECKING([for the JMF directory])
	if "$JAVAC" FindClass.java ; then
	    # Usually jmf.jar will be in the CLASSPATH
	    JMF_JAR=`"$JAVA" -classpath "$PTII/config$CLASSPATHSEPARATOR$CLASSPATH" FindClass javax.media.CaptureDeviceInfo`
	    if test -f "$JMF_JAR" ; then
	       JMF_JARS_DIR=`dirname "$JMF_JAR"`
	       PT_MSG_RESULT($JMF_JARS_DIR)
	       # Here, we should not be adding JMF_JAR to Eclipse
	       # if jmf.jar was in the jre
	       updateClasspath "$JMF_JAR"
	       JMF_JARS="$JMF_JAR"
	       if test -f "$JMF_JARS_DIR/sound.jar" ; then 
	       	    updateClasspath "$JMF_JARS_DIR/sound.jar"
                   JMF_JARS="$JMF_JARS$CLASSPATHSEPARATOR$JMF_JARS_DIR/sound.jar"
               fi
	    else 
       	       AC_MSG_WARN([Either we could not find 
    javax.media.CaptureDeviceInfo or else it was already in the JRE.
    Searching for jmf.jar returned:
      $JMF_JAR
    If the class cannot be found, then Eclipse might not be able to find
    the JMF files.  
    This is only a problem if you are using Eclipse.
    If the class was in the JRE, then Eclipse should compile the JMF files
    without problems])
		JMF_JAR=
            fi
	else
	    AC_MSG_WARN(['"$JAVAC" FindClass.java' failed.
    This means that Eclipse might not be able to find the JMF files.
    This is only a problem if you are using Eclipse])
        fi
    else
        case "`uname -s`" in
            Darwin) JMF_MESSAGE="
    Under Mac OS X, download the Cross-Platform Java version, unzip it,
    run:
        mkdir -p ~/Library/Java/Extensions/
        cp ~yourlogin/src/jmf/JMF-2.1.1e/lib/* ~/Library/Java/Extensions/
    and then rerun ./configure.";;
            *) JMF_MESSAGE="";;
        esac
        AC_MSG_WARN(['"$JAVAC" JMFTest.java' failed.
    perhaps the Java Media Framework (JMF) is not installed?
    You need not download the JMF unless you plan on using the video
    actors in $JMF_USER_DIR
    The JMF SDK can be downloaded from 
    http://www.oracle.com/technetwork/java/javase/download-142937.html $JMF_MESSAGE])
    fi
    cd "$startdir"
fi

if test -z "$PTJMF_DIR"; then
   updateExcludes "ptolemy/actor/lib/jmf/"
fi


#--------------------------------------------------------------------
#       The Java Native Access (JNA) facility is used to call native code without JNI
#	https://github.com/twall/jna
#       
#--------------------------------------------------------------------

# PTFMI_DIR is set to fmi if jna.jar was found
# $PTII/ptolemy/actor/lib/makefile uses PTFMI_DIR
PTFMI_DIR=

# PTFMI_PACKAGES is used in doc/makefile
PTFMI_PACKAGES=

# The location of the jna.jar file, typically $PTII/lib/jna.jar
JNA_JAR=

# The jar file to default to.  FIXME: the ./configure --help message may be wrong.
JNA_DEFAULT_JAR=jna-4.0.0-variadic.jar 
#JNA_DEFAULT_JAR=jna-4.1.0.jar
#JNA_DEFAULT_JAR=jna-4.1.0-variadic.jar 

# We only need look for jmf if $PTII/ptolemy/actor/lib/fmi exists
JNA_USER_DIR_FMI="$PTII/ptolemy/actor/lib/fmi"

if test ! -d "$JNA_USER_DIR_FMI" ;  then
    PT_MSG_STATUS([$JNA_USER_DIR_FMI are not present,
    so we need not find the JNA - The Java Native Access utility.])
else
    AC_MSG_CHECKING([for Java Native Access (JNA) jar])
    AC_ARG_WITH(jna-jar, [  --with-jna-jar=JARFILE       use JNA from JARFILE,
                          defaults to \$PTII/jna-4.0.0-variadic.jar],
	JNA_JAR=$withval,
	JNA_JAR=$PTII/lib/$JNA_DEFAULT_JAR)
    if test -f "$JNA_JAR"; then
        PT_MSG_RESULT($JNA_JAR)
	if test -d "$PTII/ptolemy/actor/lib/fmi"; then
		PTFMI_DIR=fmi
		PTFMI_PACKAGES="ptolemy.actor.lib.fmi org.ptolemy.fmi org.ptolemy.fmi.driver org.ptolemy.fmi.type ptolemy.vergil.basic.imprt.fmu"
        fi		
        updateClasspath "$JNA_JAR"
    else
        AC_MSG_WARN([Failed to find $PTII/lib/jna-4.0.0-variadic.jar,
    JNA is the Java Native Access interfaced, used by the 
    Functional Mock-up Inteface actors in
    ptolemy/actor/lib/fmi
    These actors are optional, but require JNA.
    For more information about JNA, see https://github.com/twall/jna])
        updateExcludes "ptolemy/actor/lib/fmi/"
    fi
fi

#--------------------------------------------------------------------
#       The Joystick interface is a Java interface to Joysticks, see
#	http://sourceforge.net/projects/javajoystick/
#       See if there was a command-line option for where Joystick interface is
#       If not, look for $PTII/vendors/misc/joystick
#--------------------------------------------------------------------

# PTJOYSTICK_DIR is set to joystick and used in
# $PTII/ptolemy/actor/lib/makefile if Joystick.jar was found
PTJOYSTICK_DIR=

# Joystick Jar file
JOYSTICK_JAR='${PTII}/vendors/misc/joystick/Joystick.jar'

# We only need to look for joystick if $PTII/ptolemy/actor/lib/joystick exists
if test ! -d "$PTII/ptolemy/actor/lib/joystick"; then
    PT_MSG_STATUS([$PTII/ptolemy/actor/lib/joystick is not present,
    so we need not find the Joystick interface.])
else
    AC_MSG_CHECKING([for joystick jar file])
    AC_ARG_WITH(joystick-jar, [  --with-joystick-jar=JARFILE       use JOYSTICK from JARFILE,
                          defaults to \$PTII/vendors/misc/joystick/Joystick.jar],
	JOYSTICK_JAR=$withval,
	JOYSTICK_JAR=$PTII/vendors/misc/joystick/Joystick.jar)

    if test -f "$JOYSTICK_JAR"; then
	PT_MSG_RESULT([$JOYSTICK_JAR])
	# Set to joystick and used in
	# $PTII/ptolemy/actor/lib/joystick if joystick was found
	PTJOYSTICK_DIR=joystick
        # PTJOYSTICK_PACKAGES is used in ptII/doc/makefile
	PTJOYSTICK_PACKAGES=ptolemy.actor.lib.joystick
    fi	

    if test "$PTJOYSTICK_DIR" = ""; then
        AC_MSG_WARN([Failed to find $JOYSTICK_JAR
    perhaps the Joystick is not installed?
    You need not download the Joystick interface unless you
    plan on using a Joystick with Ptolemy II. 
    The Joystick interface can be downloaded from
    http://sourceforge.net/projects/javajoystick/])
	# Note that we don't substitute in the ${PTII} here
	JOYSTICK_JAR='${PTII}/vendors/misc/joystick/Joystick.jar'
    fi
fi

if test -z "$PTJOYSTICK_DIR"; then
   updateExcludes "ptolemy/actor/lib/joystick/"
else
   updateClasspath "$JOYSTICK_JAR"
fi 

#--------------------------------------------------------------------
#	See if there was a command-line option for where Jacl is
#       Jacl is a 100% Java implementation of a subset of Tcl.
#       We use Jacl for unit tests.
#--------------------------------------------------------------------

# We only need to find Jacl if $PTII/util/testsuite
# exists.  If we are shipping ptplot, then this directory might not
# exist
PTJACL_JAR=$PTII/lib/ptjacl.jar
# JTCLSH uses JAVAFLAGS for use with the 
# vergil/test/VergilConfiguration.tcl test
# We set the ptolemy.ptII.dir property for use in the 
# actor.lib.test.auto.FileWriter{1,2}.xml tests
# JTCLSHFLAGS gets set to -Dptolemy.ptII.isRunningNightlyBuild=true
# when we are running the nightlybuild
# Codegen uses up lots of memory while running
# Set ptolemy.ptII.batchMode to true so that when $PTII/org/terraswarm/accessor/test/auto/AccessViolation.xml is run, we don't hang with "Overwrite local changes? (yes or no)"
JTCLSH='["$(JAVA)" -Xmx1000M $(JAVAFLAGS) "-Dptolemy.ptII.dir=$(PTII)" -Dptolemy.ptII.batchMode=true $(JTCLSHFLAGS) tcl.lang.Shell]'
# PTJACL_DIR is set to ptjacl and used in $PTII/ptolemy/actor/gui/makefile
# if the ptjacl.jar file was found
PTJACL_DIR= 

if test ! -d "$PTII/util/testsuite"; then
    PT_MSG_STATUS([$PTII/util/testsuite is not present,
    so we need not find Jacl.])
else
    AC_MSG_CHECKING([for ptjacl.jar])
    AC_ARG_WITH(ptjacl_jar, [  --with-ptjacl_jar=PTJACL.JAR  ptjacl.jar file,
                           used for running the test scripts],
	PTJACL_JAR=$withval, PTJACL_JAR=$PTII/lib/ptjacl.jar)

    if test -f "$PTJACL_JAR"; then
	PT_MSG_RESULT([$PTJACL_JAR])
	AC_MSG_CHECKING([for how to run jacl with "$JAVA"])
	# This command starts up Jacl
	if echo "set java::jdkVersion; exit" | "$JAVA" -classpath "$PTJACL_JAR" tcl.lang.Shell; then
		PT_MSG_RESULT($PTJACL_JAR)
		PTJACL_DIR=ptjacl
	else
		PT_MSG_RESULT(["$JAVA" -classpath "$PTJACL_JAR" tcl.lang.Shell failed])
		AC_MSG_CHECKING([for how to run jacl with "$JAVA" "$PTJACL_FLAG]")
		if echo "set java::jdkVersion; exit" | "$JAVA" -classpath "$PTJACL_JAR" tcl.lang.Shell; then
			PT_MSG_RESULT($PTJACL_JAR)
		else
			PT_MSG_RESULT(["$JAVA" -classpath "$PTJACL_JAR" tcl.lang.Shell' failed,
	use '"$JAVA" -classpath "$PTJACL_JAR" tcl.lang.Shell'
	instead. ptjacl is used by the test suite, so you may be able to
	ignore this error.])
		fi
		JTCLSH='["$(JAVA)" $(JAVAFLAGS) "-Dptolemy.ptII.dir=$(PTII)" $(JTCLFLAGS tcl.lang.Shell]'
	fi
    else
	AC_MSG_WARN([The ptjacl.jar file was not found at '$PTJACL_JAR'
    ptjacl.jar is only necessary if you plan on running the test suite.
    You can download ptjacl.jar from
    http://ptolemy.eecs.berkeley.edu/~cxh/java/jacl/ptjacl.html])
    fi
fi

if test -z "$PTJACL_DIR"; then
   updateExcludes "ptolemy/actor/gui/ptjacl/"
else
   updateClasspath "$PTJACL_JAR"
fi 

#--------------------------------------------------------------------
#       "jsoup: Java HTML Parser"
#	See http://www.jsoup.org
#       Jsoup is used by the export html facility
#--------------------------------------------------------------------

# JSoup jar files used by export html facility
PTJSOUP_JAR=

# Set to jsoup if jsoup is found and used in $PTII/ptolemy/vergil/basic/export/makefile
PTJSOUP_DIR=

# We only need to look for Jsoup if $PTJSOUP_USER_DIR is present
PTJSOUP_USER_DIR="$PTII/ptolemy/vergil/basic/export/html"

if test ! -d "$PTJSOUP_USER_DIR"; then
    PT_MSG_STATUS([$PTJSOUP_USER_DIR is not present,
    so we need not find Jsoup.])
else
    AC_MSG_CHECKING([for JSoup, used when exporting html pages. ])
    AC_ARG_WITH(jsoup, [  --with-jsoup=JAR       use jsoup.jar from JAR,
                          defaults to \$PTII/lib/jsoup-1.8.2.jar],
        PTJSOUP_JAR=$withval,
	PTJSOUP_JAR=$PTII/lib/jsoup-1.8.2.jar)

    if test  -f "$PTJSOUP_JAR"; then
	PT_MSG_RESULT([$PTJSOUP_JAR])
        updateClasspath "$PTJSOUP_JAR"
        PTJSOUP_DIR=jsoup
        # PTJSOUP_PACKAGES is used in ptII/doc/makefile
	PTJSOUP_PACKAGES=ptolemy.vergil.basic.export.html.jsoup
    else
        updateExcludes "ptolemy/vergil/basic/export/html/"
        AC_MSG_WARN([Failed to find the JSoup jar files necessary to
    to compile the export html facility.
    Typically, JSoup is found at $PTII/lib/jsoup-1.8.2.jar.])
    fi
fi


#--------------------------------------------------------------------
#       JUnit is the Java Unit testing framework
#--------------------------------------------------------------------

# PTJUNIT_DIR is set to junit and used in
# $PTII/util/testsuite/makefile if junit was found
PTJUNIT_DIR=

# Used in many test/makefiles
JUNITS_JAR=

# We only need to look for JUnit if this directory is present
# and if Jacl is presnt
JUNIT_USER_DIR="$PTII/ptolemy/util/test/junit"

if test ! -d "$JUNIT_USER_DIR" -o ! -f "$PTJACL_JAR"; then
    PT_MSG_STATUS([Either '$JUNIT_USER_DIR' is not present,
    or the Jacl jar file '$PTJACL_JAR' was not found,
    so we need not find JUnit - the Java Unit Testing Framework.])
else
    AC_MSG_CHECKING([for the JUnit - the Java Unit Testing Framework])
    AC_ARG_WITH(junit, [  --with-junit=JARFILE       use JUnit Testing Framework from JARFILE,
                          defaults to \$PTII/lib/junit-4.8.2.jar],
	JUNIT_JAR=$withval,
	JUNIT_JAR=$PTII/lib/junit-4.8.2.jar)

    if test -f "$JUNIT_JAR"; then
	PT_MSG_RESULT([$PTJUNIT_JAR])
	AC_MSG_CHECKING([for the JUnitParams, needed by our JUnit tests])
	AC_ARG_WITH(junitparams, [  --with-junitparams=JARFILE       use JUnitParams Testing Framework from JARFILE,
                          defaults to \$PTII/lib/JUnitParams-0.4.0.jar],
	JUNITPARAMS_JAR=$withval,
	JUNITPARAMS_JAR=$PTII/lib/JUnitParams-0.4.0.jar)
        if test -f "$JUNITPARAMS_JAR"; then
	    PT_MSG_RESULT([$PTJUNITPARAMS_JAR])
            JUNIT_JARS="${JUNIT_JAR}${CLASSPATHSEPARATOR}${JUNITPARAMS_JAR}"
	    PTJUNIT_DIR=junit
            # PTJUNIT_PACKAGES is used in ptII/doc/makefile
	    PTJUNIT_PACKAGES=ptolemy.util.test.junit
        fi
    fi	

    if test "$PTJUNIT_DIR" = ""; then
        AC_MSG_WARN([Failed to find junit-4.8.2.jar and/or JUnitParams-0.4.0.jar
    Perhaps the JUnit Java Unit Testing Framework is not installed?
    You need not download JUnit unless you want to run the unit tests.])
	# Note that we don't substitute in the ${PTII} here
	JUNIT_JARS='${PTII}/lib/junit-4.8.2.jar${CLASSPATHSEPARATOR}${PTII}/lib/JUnitParams-0.4.0.jar'
    fi
fi

if test -z "$PTJUNIT_DIR"; then
   updateExcludes "ptolemy/util/test/junit/"
   updateExcludes "**/junit/"
else
   updateClasspath "$JUNIT_JAR"
   updateClasspath "$JUNITPARAMS_JAR"
fi 

#--------------------------------------------------------------------
#       JXL is the Java Excel library, which is GPL'd.
#	For more information, see 
#       http://jexcelapi.sourceforge.net/
#--------------------------------------------------------------------

# PTEXCEL_DIR is set to excel and used in
# $PTII/ptolemy/actor/lib/makefile if jxl was found
PTEXCEL_DIR=

# Used in ptolemy/actor/lib/excel/makefile
PTJXL_JAR=

# We only need to look for JXL if the actor/lib/excel directory is present
EXCEL_USER_DIR="$PTII/ptolemy/actor/lib/excel"

if test ! -d "$EXCEL_USER_DIR"; then
    PT_MSG_STATUS([$EXCEL_USER_DIR is not present,
    so we need not find JXL - The Java Excel API.])
else
    AC_MSG_CHECKING([for the Java Excel API (JXL)])
    AC_ARG_WITH(jxl, [  --with-jxl=JARFILE       use Java Excel API from JARFILE,
                          defaults to \$PTII/ptolemy/actor/lib/excel/jxl.jar],
	PTJXL_JAR=$withval,
	PTJXL_JAR=$PTII/ptolemy/actor/lib/excel/jxl.jar)

    if test -f "$PTJXL_JAR"; then
	PT_MSG_RESULT([$PTJXL_JAR])
	# Set to excel and used in
	# $PTII/ptolemy/actor/lib/makefile if iText.jar is found
	PTEXCEL_DIR=excel
        # PTJXL_PACKAGES is used in ptII/doc/makefile
	PTEXCEL_PACKAGES=ptolemy.actor.lib.excel
    fi	

    if test "$PTEXCEL_DIR" = ""; then
        AC_MSG_WARN([Failed to find jxl.jar
    as $PTEXCEL_JAR.
    Perhaps the Java Excel API (JXL)  is not installed?
    You need not download the JXL interface unless you
    would like to use the Excel actor.])
	# Note that we don't substitute in the ${PTII} here
	PTJXL_JAR='${PTII}/ptolemy/actor/lib/excel/jxl.jar'
    fi
fi

if test -z "$PTEXCEL_DIR"; then
   updateExcludes "ptolemy/actor/lib/excel/"
else
   updateClasspath "$PTJXL_JAR"
fi 

#--------------------------------------------------------------------
#       Jython is an implementation of Python in Java
#	For more information, 
#       see http://www.jython.org
#       See if there was a command-line option for where Jython is.
#--------------------------------------------------------------------

# PTJYTHON_DIR is set to python (FIXME: should be jython) and used in
# $PTII/ptolemy/actor/lib/makefile if Jython was found.
PTJYTHON_DIR=

# Directory that contains the jython jar files
JYTHON_DIR='${PTII}/lib'

# We only need to look for jython if $PTII/ptolemy/actor/lib/python exists
# FIXME: Note that the package is called jython, but the directory is python
JYTHON_USER_DIR="$PTII/ptolemy/actor/lib/python"
if test ! -d "$JYTHON_USER_DIR"; then
    PT_MSG_STATUS([$JYTHON_USER_DIR is not present,
    so we need not find the Jython, the java implementation of Python.])
else
    AC_PATH_PROG(PTJYTHON, jython)
    if test "${PTJYTHON:-none}" != "none"; then
        JYTHON_PROG_PARENT_DIR=`dirname "$PTJYTHON"`
   	if test -f "$JYTHON_PROG_PARENT_DIR/jython.jar"; then
	    if test "$JYTHON_DIR" != "$JYTHON_PROG_PARENT_DIR"; then 
		# Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
		# Remove /cygdrive so we can compile with MSVC
		JYTHON_TMP_DIR=`echo "$JYTHON_PROG_PARENT_DIR" | sed 's@/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl
		AC_MSG_WARN([Found $PTJYTHON,
    using $JYTHON_TMP_DIR/jython.jar instead of
          $JYTHON_DIR/jython.jar])
		JYTHON_DIR="$JYTHON_TMP_DIR"
	    fi    
        fi
    else
        AC_PATH_PROG(PTJYTHON_BAT, jython.bat)
	if test "${PTJYTHON_BAT:-none}" != "none"; then
	    JYTHON_PROG_PARENT_DIR=`dirname "$PTJYTHON_BAT"`
   	    if test -f "$JYTHON_PROG_PARENT_DIR/jython.jar"; then
	        if test "$JYTHON_DIR" != "$JYTHON_PROG_PARENT_DIR"; then 
		    # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
		    # Remove /cygdrive so we can compile with MSVC
		    JYTHON_TMP_DIR=`echo "$JYTHON_PROG_PARENT_DIR" | sed 's@/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl
		    AC_MSG_WARN([Found $PTJYTHON_BAT,
    using $JYTHON_TMP_DIR/jython.jar instead of
          $JYTHON_DIR/jython.jar])
		    JYTHON_DIR="$JYTHON_TMP_DIR"
                fi
            fi
        fi
    fi	
    AC_MSG_CHECKING([for Jython, the Java implementation of Python])
    AC_ARG_WITH(jython, [  --with-jython=DIR       use jython.jar from DIR,
                          defaults to \$PTII/lib, though the path
			  is searched for jython],
	JYTHON_DIR=$withval,
	JYTHON_DIR=$JYTHON_DIR)

    if test -f "$JYTHON_DIR/jython.jar"; then
	PT_MSG_RESULT([$JYTHON_DIR])
	# FIXME: This is ugly, but we set to python instead of jython
	# $PTII/ptolemy/actor/lib/makefile if jython was found
	PTJYTHON_DIR=python
	# PTJYTHON_PACKAGES is used in ptII/doc/makefile
	PTJYTHON_PACKAGES="ptolemy.actor.lib.python ptolemy.actor.gui.python"
    fi

    if test "$PTJYTHON_DIR" = ""; then
        if test -f "$PTII/vendors/jython/jython.jar"; then
	    JYTHON_DIR="$PTII/vendors/jython"
	    PT_MSG_RESULT([$JYTHON_DIR])
	    # FIXME: This is ugly, but we set to python instead of jython
 	    # $PTII/ptolemy/actor/lib/makefile if jython was found
	    PTJYTHON_DIR=python
	    PTJYTHON_PACKAGES="ptolemy.actor.lib.python ptolemy.actor.gui.python"
	else     
	    if test -f "$PTII/lib/jython.jar"; then
	       JYTHON_DIR="$PTII/lib"
	       PT_MSG_RESULT([$JYTHON_DIR])
	       # FIXME: This is ugly, but we set to python instead of jython
	       # $PTII/ptolemy/actor/lib/makefile if jython was found
	       PTJYTHON_DIR=python
	       PTJYTHON_PACKAGES="ptolemy.actor.lib.python ptolemy.actor.gui.python"
            else 
               AC_MSG_WARN([Failed to find 
    $PTII/lib/jython.jar and
    $PTII/vendors/jython/jython.jar
    perhaps Jython is not installed?
    Jython is a java implementation of Python.
    You need not download Jython unless you plan on using the Jython
    actors in ptolemy/actor/lib/python
    The Jython can be downloaded http://www.jython.org/download.html])
	# Note that we don't substitute in the ${PTII} here
	JYTHON_DIR='${PTII}/vendors/jython'
            fi
        fi
    fi
fi

if test -z "$PTJYTHON_DIR"; then
   updateExcludes "ptolemy/actor/lib/jython/"
else
   updateClasspath "$JYTHON_DIR/jython.jar"
fi 

#--------------------------------------------------------------------
#	Classes used to layout entities and relations in Vergil that use the
#       KIELER layout algorithm.
#	http://www.informatik.uni-kiel.de/rtsys/kieler/
#
#--------------------------------------------------------------------

# We only need to look for kieler if $PTII/ptolemy/vergil/basic/layout/kieler is present
KIELER_USER_DIR="$PTII/ptolemy/vergil/basic/layout/kieler"
# PTKIELER_DIR is set to kieler and used in
# $PTII/ptolemy/vergil/basic/layout/makefile if kieler was found
PTKIELER_DIR=

# Directory that contains the kieler jar files
KIELER_JAR='${PTII}/lib/kieler.jar'

if test ! -d "$KIELER_USER_DIR"; then
    PT_MSG_STATUS([$KIELER_USER_DIR is not present,
    so we need not find KIELER.])
else
    AC_MSG_CHECKING([for kieler jar file used by layout ])
    AC_ARG_WITH(kieler-jar, [  --with-kieler-jar=JARFILE       use JARFILE,
                          defaults to \$PTII/lib/kieler.jar],
	KIELER_JAR=$withval,
	KIELER_JAR=$PTII/lib/kieler.jar)

    if test -f "$KIELER_JAR"; then
	PT_MSG_RESULT([$KIELER_JAR])
        # Set to kieler and used in
	# $PTII/ptolemy/vergil/basic/layout/makefile if kieler was found
	PTKIELER_DIR=kieler
    fi

    if test "$PTKIELER_DIR" = ""; then
        AC_MSG_WARN([Failed to find $KIELER_JAR
    perhaps KIELER is not installed?
    You need not use KIELER unless you plan on using the KIELER layout
    facility in $KIELER_USER_DIR
    The KIELER jar is usually found at $PTII/lib/kieler.jar])
	# Note that we don't substitute in the ${PTII} here
	KIELER_JAR='${PTII}/lib/kieler.jar'
    fi
fi

if test -z "$PTKIELER_DIR"; then
   updateExcludes "ptolemy/vergil/basic/layout/kieler/"
else
   updateClasspath "$KIELER_JAR"
fi 

#--------------------------------------------------------------------
#       npm is the Node.js package manager, which is
#       used by CapeCode.
#       npm5 has a critical bug in that it removed files
#       from node_modules.
#       See https://www.icyphy.org/accessors/wiki/Notes/Npm5
#--------------------------------------------------------------------

# We only need to look for npm if this directory is present
NPM_USER_DIR="$PTII/org/terraswarm/accessor/accessors"

if test ! -d "$NPM_USER_DIR" ; then
    PT_MSG_STATUS([$NPM_USER_DIR is not present,
    so we need not check for npm 5, the Node.js Package Manager])
else
    AC_MSG_CHECKING([for node])
    AC_PATH_PROG(PTNODE, node)
    if test "${PTNODE:-none}" = "none"; then
       if test -f "$PTII/bin/node" ; then
           NODE_VERSION=`"$PTII/bin/node" --version`
           status=$?
           if test "$status" -eq 2; then
               AC_MSG_WARN([Failed to find the node executable in your path, $PTII/bin/node also failed.])
           else
               PTNODE="$PTII/bin/node"
               AC_MSG_WARN([Failed to find the node executable in your path, but $PTII/bin/node worked.  Please add $PTII/bin to your PATH.])
           fi
       fi
    fi

    if test -f "$PTNODE" ; then
        NODE_VERSION=`"$PTNODE" --version`
        status=$?
        if test "$status" -eq 2; then
            AC_MSG_WARN([$PTNODE was found, but "$PTNODE --version" returned 2.]);
            PTNODE="";
        fi
    fi

    if test "${PTNODE:-none}" = "none"; then
           AC_MSG_WARN([Failed to find the node executable, which means that the Node.js Accessor Host
    To install Node.js, see https://nodejs.org/en/download/

    If node is installed in $PTII/vendors/node, for example
    $PTII/vendors/node.bak/node-v7.10.1-darwin-x64/bin/node 
    then $PTII/bin/node will use it.

    Note that npm 5.x has a critical flaw that prevents
    its use, so install Node 7.x, not Node 8.x
    
    Without Node, it is still possible to run the CapeCode Accessor Host,
    but generating Swarmlets and running them using Node
    will only work if the node executable is the path.])

    else
       if test -f "$PTNODE" ; then
           AC_MSG_CHECKING([for npm])
           AC_PATH_PROG(PTNPM, npm)
           if test "${PTNPM:-none}" = "none"; then
               if test -f "$PTII/bin/npm" ; then
                   NODE_VERSION=`"$PTII/bin/npm" --version`
                   status=$?
                   if test "$status" -eq 2; then
                       AC_MSG_WARN([Failed to find the npm executable in your path, $PTII/bin/npm also failed.])
                   else
                       PTNODE="$PTII/bin/node"
                       AC_MSG_WARN([Failed to find the node executable in your path, but $PTII/bin/npm worked.  Please add $PTII/bin to your PATH.])
                   fi
               else
                   if test -f "$PTNPM" ; then
                       NODE_VERSION=`"$PTNPM" --version`
                       status=$?
                       if test "$status" -eq 2; then
                           AC_MSG_WARN([$PTNPM was found in the path, but "$PTNPM --version" returned 2.])
                           PTNPM=""
                       fi
                   fi
               fi
           fi
       fi
       if test "${PTNPM:-none}" = "none"; then
           AC_MSG_WARN([Failed to find npm, which means that the Node.js Accessor Host
    probably won't work.
    To npm is part of Node.js, see https://nodejs.org/en/download/

    If node is installed in $PTII/vendors/node, for example
    $PTII/vendors/node.bak/node-v7.10.1-darwin-x64/bin/node 
    then $PTII/bin/node will use it.

    Note that npm 5.x has a critical flaw that prevents
    its use, so install Node 7.x, not Node 8.x.])
       else
           upgradeNpm=0
           AC_MSG_CHECKING([for npm before 5.x])
           NPM_VERSION=`"$PTNPM" --version`
           status=$?
           if test "$status" -ne 0; then        
              AC_MSG_WARN(["$PTNPM" --version returned $status, which is non-zero.
    Please install Node 7.x, not Node 8.x or later.])
              FINAL_WARNING="$FINAL_WARNING

$PTNPM --version returned $status, which indicates a problem.  Please install Node 7.x from https://nodejs.org/download/release/v7.10.1/.  If npm does not work, then building the JavaScript Documentation will fail."
             upgradeNpm=1
           fi

           echo "$NPM_VERSION" | egrep '^[5-9]\.'
           status=$?
           if test "$status" -eq 1; then
              PT_MSG_RESULT([ok, npm is version $NPM_VERSION])
           else              
              AC_MSG_WARN([npm is version $NPM_VERSION, which is 5.x or greater.
    npm 5.x removes files in node_modules so it should not be used.
    See https://www.icyphy.org/accessors/wiki/Notes/Npm5
    It is still possible to run the CapeCode Accessor Host,
    but generating Swarmlets and running them using Node Accessor Host
    will likely fail in mysterious ways])
             FINAL_WARNING="$FINAL_WARNING

The npm 5.x or greater binary is found in the path, which will cause problems with the Node Accessor host because npm 5.x removes files in node_modules/.  However, the CapeCode accessor host will likely not be affected by npm5.x.  See above for details."
             upgradeNpm=1
           fi

           if test $upgradeNpm -eq 1; then
               case "`uname -s`" in
                   Darwin) npmArch=darwin;;
                   CYGWIN*) npmArch=win;;
                   Linux) npmArch=linux;;
                   *) npmArch=FIXME-Insert-Your-Architecture-Here;;
               esac

               FINAL_WARNING="$FINAL_WARNING

The Node Accessor Host requires Node 7.x.  Node 8.x and later will not
work because npm 5.x removes files from the node_modules directory.
See https://www.icyphy.org/accessors/wiki/Notes/Npm5

The CapeCode Accessor Host does not use Node at runtime.

With Node 8.x and greater, it is still possible to run the Node
Accessor Host, but generating Swarmlets and running them using Node
Accessor Host will likely fail in mysterious ways])

However, node and npm are used to build the JavaScript docs, so you
may want to install Node 7.x if you want to view the CapeCode
JavaScript documentation.  Building the documentation is optional.

To install Node 7.x:
    cd \$PTII/vendors
    mkdir node
    wget https://nodejs.org/download/release/v7.10.1/node-v7.10.1-$npmArch-x64.tar.gz
    tar -zxf node-v7.10.1-$npmArch-x64.tar.gz
    cd \$PTII
    export PATH=$PTII/bin:\${PATH}"
   

          fi

        fi
    fi
fi

#--------------------------------------------------------------------
#       OpenCV is the Computer Vision platform
#	For more information, see http://opencv.org
#       There used to be actors in ptolemy/actor/lib/opencv,
#       but they used an older version of the Java interface to OpenCV
#       and were removed in March, 2016.        
#--------------------------------------------------------------------

# PTOPENCV_DIR is set to opencv.
PTOPENCV_DIR=

# The OpenCV Jar file.
OPENCV_JAR=

# We only need to look for OpenCVif the org/ptolemy/opencv directory is present
OPENCV_USER_DIR="$PTII/org/ptolemy/opencv"


if test ! -d "$OPENCV_USER_DIR" ; then
    PT_MSG_STATUS([$OPENCV_USER_DIR is not present,
    so we need not find OpenCV - The Open Computer Vision API.])
else
    AC_MSG_CHECKING([for OpenCV Java API])
    # We need to run javac in the config directory so that javac from jdk1.1.6
    # under NT and cygwin works properly

    # If you update $PTII/lib/opencv-*.jar, then please update these files
    # .classpath.default
    # adm/gen-11.0/capecode1_0_devel_setup_windows.xml
    # build.default.xml
    # config/OpenCVTest.java

    AC_ARG_WITH(opencv-jar, [  --with-opencv-jar=JARFILE       use OpenCV from JARFILE,
                          defaults to \$PTII/lib/opencv-320.jar],
	OPENCV_JAR=$withval,
	OPENCV_JAR=$PTII/lib/opencv-320.jar)

    OPENCV_CLASSPATH="-classpath $OPENCV_JAR${CLASSPATHSEPARATOR}."
    startdir=$PTII
    cd "$srcdir/config"

    # If we did not find the jar, then look in $PTII/lib
    if test ! -f "$OPENCV_JAR"; then
        TMP_OPENCV_JAR=`find $PTII/lib -name "opencv-*.jar" | head -1`
        if test -e "$TMP_OPENCV_JAR"; then
            AC_MSG_WARN([Did not find $OPENCV_JAR, but $TMP_OPENCV_JAR is present])
            OPENCV_JAR=$TMP_OPENCV_JAR
            OPENCV_CLASSPATH="-classpath $OPENCV_JAR${CLASSPATHSEPARATOR}."
        fi
    fi

    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" $OPENCV_CLASSPATH OpenCVTest.java ; then
        if "$JAVA" $OPENCV_CLASSPATH OpenCVTest; then
            PT_MSG_RESULT(OpenCV found in the default classpath.)
            PTOPENCV_DIR=opencv
            # PTOPENCV_PACKAGES is used in ptII/doc/makefile
            PTOPENCV_PACKAGES="org.ptolemy.opencv"
            if test -z "$OPENCV_JAR"; then
                AC_MSG_CHECKING([for the OpenCV jar files])
                if "$JAVAC" FindClass.java ; then
	            # Usually opencv.jar will be in the CLASSPATH
	            OPENCV_JAR=`"$JAVA" -classpath "$PTII/config$CLASSPATHSEPARATOR$CLASSPATH" FindClass org.opencv.core.Core`
	            if test -f "$OPENCV_JAR" ; then
	                PT_MSG_RESULT($OPENCV_JAR)
  	                updateClasspath "$OPENCV_JAR"
	            else 
       	                AC_MSG_WARN([Either we could not find 
    org.opencv.core.Core or else it was already in the JRE.
    Searching for OpenCV.jar returned:
      $OPENCV_JAR
    If the class cannot be found, then Eclipse might not be able to find
    the OpenCV files.  
    This is only a problem if you are using Eclipse.
    If the class was in the JRE, then Eclipse should compile the OpenCV files
    without problems.
    For details, see $PTII/org/ptolemy/opencv/package.html])
                    fi # -f "$OPENCV_JAR"
	        else
	            AC_MSG_WARN(['"$JAVAC" FindClass.java' failed.
    This means that Eclipse might not be able to find the OpenCV files.
    This is only a problem if you are using Eclipse])
                fi # "$JAVAC" FindClass.java
            else
                PT_MSG_RESULT($OPENCV_JAR)
                updateClasspath "$OPENCV_JAR"
            fi # -z "$OPENCV_JAR"
        else
            AC_MSG_WARN(['"$JAVA" $OPENCV_CLASSPATH OpenCVTest' failed.
    perhaps the OpenCV Computer Vision API is not installed?
    You need not download OpenCV unless you plan on using the video
    actors in $OPENCV_USER_DIR
    The OpenCV API can be downloaded from http://opencv.org.
    Under Mac OS X, try:
       sudo port install opencv +python27 +java
    See org/ptolemy/opencv/package.html for installation help.])
        fi
    else
       AC_MSG_WARN(['"$JAVAC" OpenCVTest.java' failed.
    perhaps the OpenCV Computer Vision API is not installed?
    You need not download OpenCV unless you plan on using the video
    actors in $OPENCV_USER_DIR
    The OpenCV API can be downloaded from http://opencv.org.
    Under Mac OS X, try:
       sudo port install opencv +python27 +java
    See org/ptolemy/opencv/package.html for installation help.])
    fi
    cd "$startdir"
fi

if test -z "$PTOPENCV_DIR"; then
   updateExcludes "org/ptolemy/opencv/"
fi


#--------------------------------------------------------------------
#       oscP5 Open Sound Control/processing.org interface
#	http://www.sojamo.de/libraries/oscP5/
#       oscP5 is used by actors in org/ptolemy/osc
#--------------------------------------------------------------------

# lib/oscp5.jar
PTOSCP5_JAR=

# Set to osc if oscp5.jar is found and used in $PTII/org/ptolemy/makefile
PTOSCP5_DIR=

# Set to org.ptolemy.osc and used int $PTII/doc/makefile if oscp5 is found
PTOSCP5_PACKAGES=

# We only need to look for Jsoup if $PTOSCP5_USER_DIR is present
PTOSCP5_USER_DIR="$PTII/org/ptolemy/osc"

if test ! -d "$PTOSCP5_USER_DIR"; then
    PT_MSG_STATUS([$PTOSCP5_USER_DIR is not present,
    so we need not find the Open Sound Control/Processing.org interface.])
else
    AC_MSG_CHECKING([for Open Sound Control/Processing.org interface (oscP5). ])
    AC_ARG_WITH(oscp5, [  --with-oscp5=JAR       use oscP5.jar from JAR,
                          defaults to \$PTII/lib/oscP5.jar],
        PTOSCP5_JAR=$withval,
	PTOSCP5_JAR=$PTII/lib/oscP5.jar)

    if test  -f "$PTOSCP5_JAR"; then
	PT_MSG_RESULT([$PTOSCP5_JAR])
	updateClasspath "$PTOSCP5_JAR"
	PTOSCP5_DIR=osc
	PTOSCP5_PACKAGES=org.ptolemy.osc
    fi
fi

if test -z "$PTOSCP5_DIR"; then
    updateExcludes "org/ptolemy/osc/"

    # Only print the message if the directory was found.
    if test -d "$PTOSCP5_USER_DIR"; then
        AC_MSG_WARN([Failed to find the Open Sound Control/Processing.org (oscP5) interface necessary
    to compile org/ptolemy/osc.
    Typically, the oscp5.jar file is found at $PTII/lib/oscP5.jar.])
    fi
fi

#--------------------------------------------------------------------
#       RXTX is the Serial Port interface that replaces
#       Sun's commapi.
#       We are using nrjavaserial from https://github.com/NeuronRobotics/nrjavaserial/
#--------------------------------------------------------------------
# We only need to look for rxtx if $PTII/ptolemy/actor/lib/io/comm is present
RXTX_USER_DIR="$PTII/ptolemy/actor/lib/io/comm"
RXTX_JAR_DEFAULT='${PTII}/lib/nrjavaserial-3.11.0.devel.jar'
RXTX_PRESENT=no
# PTLEGO_DIR is set to lego
# $PTII/ptolemy/apps/makefile if the Java Communications API was found
#
PTLEGO_DIR=
# PTCOMM_DIR is set to comm and used in 
# $PTII/ptolemy/actor/lib/io/makefile if the Java Communications API was found
#
PTCOMM_DIR=

# PTSERIAL_DIR is set to serial and used in
# $PTII ptolemy/actor/lib/jjs/modules/makefile if the Java Communications API was found
PTSERIAL_DIR=

# PTIMUSENSOR_DIR is set to IMUSensor and used in ptolemy/actor/lib/jjs/modules/makefile if the Java Communications API was found
PTIMUSENSOR_DIR=

if test ! -d "$RXTX_USER_DIR"; then
    PT_MSG_STATUS([$RXTX_USER_DIR is not present,
    so we need not find rxtx.])
    # Use curly brackets around PTII so that if rxtx is not present
    # then ${PTII} will appear in ptinvoke.
else
    AC_MSG_CHECKING([for rxtx directory])
    AC_ARG_WITH(rxtx, [  --with-rxtx=DIR       use Java Serial Port Interface rxtx from DIR,
                          defaults to $RXTX_JAR_DEFAULT],
	RXTX_JAR=$withval,
	RXTX_JAR=$PTII/lib/nrjavaserial-3.11.0.devel.jar)

    if test -f "$RXTX_JAR"; then
        PT_MSG_RESULT($RXTX_JAR)
	RXTX_PRESENT=yes
	updateClasspath "$RXTX_JAR"
    else 
	AC_MSG_RESULT([Did not find 
	'$RXTX_JAR'])
        AC_MSG_CHECKING([for rxtx classes in CLASSPATH])
        startdir=$PTII
        cd "$srcdir/config"

        if "$JAVAC" FindClass.java ; then
	    # Usually RXTXcomm.jar will be in the CLASSPATH
	    RXTX_JAR=`"$JAVA" -classpath "$PTII/config$CLASSPATHSEPARATOR$CLASSPATH" FindClass gnu.io.SerialPort`
	    if test -f "$RXTX_JAR" ; then
	       PT_MSG_RESULT($RXTC_JAR)
	       RXTX_PRESENT=yes
	       # Here, we should not be adding RXTX_JAR to Eclipse
	       # if RXTXcomm.jar was in the jre
               case "`uname -s`" in
	       Darwin) 
  	            AC_MSG_WARN([Not including
   $RXTX_JAR
   to the Eclipse classpath under Darwin because it is already present.]);;
               *)
		   updateClasspath "$RXTX_JAR"
		   ;;
               esac
            else
	       # RXTX_JAR might contain a warning message from FindClass
	       RXTX_JAR="" 
	       "$JAVA" -classpath "$PTII/config$CLASSPATHSEPARATOR$CLASSPATH" FindClass gnu.io.SerialPort > /dev/null
	       retval=$?
	       if test "$retval" = "0"; then
	       	       PT_MSG_RESULT([ok, RXTX is probably in the jre directory])
		       RXTX_PRESENT=yes
	       fi
	    fi
        cd "$startdir"
        fi
    fi
    if test "$RXTX_PRESENT" = "no"; then
        AC_MSG_WARN([Perhaps rxtx is not installed?
    You need not download rxtx unless you plan the actors in actor.lib.comm.
    The rxtx package can be found at
    https://github.com/NeuronRobotics/nrjavaserial/releases and the jar
    file placed at $PTII/lib/nrjavaserial-3.11.0.devel.jar and configure rerun.])
    fi
fi

if test "$RXTX_PRESENT" = "yes"; then
    # Subdirectories that contains Java Communications API specific code
    PTLEGO_DIR=lego
    PTCOMM_DIR=comm
    PTSERIAL_DIR=serial
    PTIMUSENSOR_DIR=IMUSensor
    # PTRXTX_PACKAGES is used in ptII/doc/makefile
    PTRXTX_PACKAGES="ptolemy.actor.lib.io.comm ptolemy.actor.lib.jjs.modules.IMUSensor ptolemy.actor.lib.jjs.modules.serial"
else
    RXTX_JAR="$RXTX_JAR_DEFAULT"
    updateExcludes "ptolemy/actor/lib/io/comm/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/IMUSensor/"
fi 

#--------------------------------------------------------------------
#       Lejos is a Java Virtual machine that runs on the Lego Mindstorm
#	For more information, see http://lejos.sourceforge.net
#	See if there was a command-line option for rxtxi is
#       If not, check to see if $PTII/vendors/lejos/lejos/lejosBeta3
#--------------------------------------------------------------------

# We only need to look for rxtx if $PTII/ptolemy/apps/lejos
LEJOS_USER_DIR="$PTII/ptolemy/apps/lejos"
LEJOS_PRESENT=no
# PTLEJOS_DIR is set to lejos
# $PTII/ptolemy/apps/makefile if the Java Communications API was found
PTLEJOS_DIR=
if test ! -d "$LEJOS_USER_DIR"; then
    PT_MSG_STATUS([$LEJOS_USER_DIR is not present,
    so we need not find lejos.])
    # Use curly brackets around PTII so that if lejos is not present
    # then ${PTII} will appear in ptinvoke.
    LEJOS_DIR='${PTII}/vendors/lejos/lejosBeta3'
else
    if test "$RXTX_PRESENT" = "no"; then
        AC_MSG_WARN([Lejos requires rxtx, which was not found.])
    else 
	AC_MSG_CHECKING([for lejos directory])
	AC_ARG_WITH(lejos, [  --with-lejos=DIR       use Java lejos from DIR,
                          defaults to \$PTII/vendors/lejos/lejosBeta3],
		LEJOS_DIR=$withval,
		LEJOS_DIR=$PTII/vendors/lejos/lejosBeta3)

	if test -d "$LEJOS_DIR/classes/josx"; then
	    PT_MSG_RESULT([$LEJOS_DIR])
	    # Subdirectory that contains Java Communications API specific code
	    PTLEJOS_DIR=lejos
	    LEJOS_PRESENT=yes
	else
	    AC_MSG_WARN([Failed to find $LEJOS_DIR/classes/josx/])
	    LEJOS_DIR='${PTII}/vendors/lejos'
	fi
    fi	
    if test "$LEJOS_PRESENT" = "no"; then
	AC_MSG_WARN([Perhaps Lejos is not installed?
	You need not download Lejos unless you plan on use the Lego Mindstorm
	demos in \$PTII/ptolemy/apps/lejos. Lejos can be downloaded from
	http://lejos.sourceforge.net
	and placed  in \$PTII/vendors/lejos/lejosBeta3])
    fi
fi


#--------------------------------------------------------------------
#	See if there was a command-line option for where javacc is;  if
#	not, check to see if $PTII/vendors/sun/JavaCC exists
#       if it is does not, look for javacc on the path.
#  Note that JavaCC-4.2 will not work, there are problems with
#  ReInit() being static or not static
#--------------------------------------------------------------------

# We only need to look for JavaCC if $PTII/ptolemy/data/expr exists
if test ! -d "$PTII/ptolemy/data/expr"; then
    PT_MSG_STATUS([$PTII/ptolemy/data/expr is not present,
    so we need not find JavaCC.])
    JAVACC_DIR=$PTII/vendors/sun/javacc-5.0
    JAVACC=javacc
    JJTREE=jjtree
else
    AC_MSG_CHECKING([for JavaCC])
    AC_ARG_WITH(javacc, [  --with-javacc=DIR       use JavaCC.zip from DIR,
                           defaults to \$PTII/vendors/sun/javacc-5.0],
	JAVACC_DIR=$withval, JAVACC_DIR=$PTII/vendors/sun/javacc-5.0)

    if test "`uname -s`" = "CYGWIN_NT-4.0" -o \
		"`uname -s`" = "CYGWIN_NT-5.0" ; then
	JJTREE='"$(JAVA)" COM.sun.labs.jjtree.Main'
	JAVACC='"$(JAVA)" COM.sun.labs.javacc.Main'
	AC_MSG_WARN([
Be sure that your CLASSPATH includes JavaCC.zip, which is located in]);
    else
	if test ! -d "$JAVACC_DIR"; then
	    AC_MSG_WARN([Could not find directory
    '${JAVACC_DIR}'
    so we search for the jjtree command.])
	    AC_PATH_PROG(JJTREE, jjtree)
	    if test -x "$JJTREE"; then
		PT_MSG_RESULT([$JJTREE]);
		JAVACCBIN=`dirname $JJTREE`
		JAVACC_DIR=`dirname $JAVACCBIN`
	    else
		AC_MSG_WARN([Failed to find jjtree]);
	    fi
	fi
	if test -d "$JAVACC_DIR"; then
	    PT_MSG_RESULT([$JAVACC_DIR])
	    AC_MSG_CHECKING([for jjtree])
	    if test -x "$JAVACC_DIR/bin/jjtree"; then
		# Note that we don't substitute in the $(JAVACC_DIR) here
		JJTREE='$(JAVACC_DIR)/bin/jjtree'
		PT_MSG_RESULT([$JJTREE])
		JJTREE_OPTIONS=-STATIC=false
	    else
		AC_MSG_WARN([Failed to find jjtree in '$JAVACC_DIR/bin']);
	    fi
	    AC_MSG_CHECKING([for javacc])
	    if test -x "$JAVACC_DIR/bin/javacc"; then
		# Note that we don't substitute in the $(JAVACC_DIR) here
		JAVACC='$(JAVACC_DIR)/bin/javacc'
		PT_MSG_RESULT([$JAVACC])
		JAVACC_OPTIONS=-STATIC=false
	    else
		AC_MSG_WARN([Failed to find javacc in '$JAVACC_DIR/bin']);
	    fi
	fi
    fi

    if test ! -d "$JAVACC_DIR"; then
        AC_MSG_WARN([Failed to find javacc, perhaps JavaCC is not installed?
    You need not download JavaCC unless you plan on modifying .jjt files
    in ptolemy/data/expr.
    JavaCC is available from	
    http://javacc.dev.java.net/

    Note that the zip file that gets downloaded is actually an installer
    that must be run to install the JavaCC.zip file that contains the classes.

    Note that JavaCC-4.1 and 4.2 will not work, there are problems with
    ReInit() being static or not static.

    JavaCC-6.0 seems to not include the jjtree and javacc scripts, so
    we recommend JavaCC-5.0.

    Try:
    cd $PTII/vendors/sun
    wget https://java.net/projects/javacc/downloads/download/javacc-5.0.tar.gz
    tar -zxf javacc-5.0.tar.gz
    cd $PTII
    ./configure

    Configure looks for JavaCC in $PTII/vendors/sun/javacc-5.0
    so either install JavaCC in that location or use the --with-javacc= flag
    and then rerun configure.'])
	JJTREE=touch
	JAVACC=touch
    fi
fi

#--------------------------------------------------------------------
#	Test for javax.media.j3d (Java 3D)
#       https://java3d.dev.java.net/
#--------------------------------------------------------------------
# PTJAVA3D_DIR is set to gr and used in
# $PTII/ptolemy/actor/lib/makefile if Java 3D was found
PTJAVA3D_DIR=

# Name of the jar file that includes the GR domain if Java 3D was found
# Used in domains/makefile
PTGRDOMAIN_JAR=

# We only need to look for Java3D if the gr domain is present
JAVA3D_USER_DIR="$PTII/ptolemy/domains/gr"

if test ! -d "$JAVA3D_USER_DIR"; then
    PT_MSG_STATUS([$JAVA3D_USER_DIR is not present,
    so we need not find Java 3D.])
else
    AC_MSG_CHECKING([for Java 3D])
    AC_ARG_WITH(java3D, [  --with-java3D=DIR       use j3dcore.jar, j3dutils.jar,
                          and vecmath.jar from DIR.  Usually Java 3D is
			  installed in the JDK in jre/lib/ext or $PTII/vendors/j3d],
	JAVA3D_DIR=$withval,
	JAVA3D_DIR=)

    # We want to use -classpath, which overrides $CLASSPATH
    if test -z "$CLASSPATH"; then
        tmpClasspath="."
    else
        tmpClasspath="$CLASSPATH"
    fi

    if test -z "$JAVA3D_DIR" ; then
       # Special version of Java3D for Mac OS X, see http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Java3D
       if test "`uname -s`" = "Darwin"; then 
           directory=`ls -d $PTII/vendors/j3d/Darwin/*/lib/ext`
       else
           directory=`ls -d $PTII/vendors/j3d/*/lib/ext`
       fi
       if test -d "$directory"; then
       	  JAVA3D_DIR="$directory"
       fi
    fi
    if test -f "$JAVA3D_DIR/j3dcore.jar" -a -f "$JAVA3D_DIR/j3dutils.jar" -a -f "$JAVA3D_DIR/vecmath.jar"; then
        JAVA3D_JARS="$JAVA3D_DIR/j3dcore.jar$CLASSPATHSEPARATOR$JAVA3D_DIR/j3dutils.jar$CLASSPATHSEPARATOR$JAVA3D_DIR/vecmath.jar$CLASSPATHSEPARATOR"
	Java3DClasspath="$JAVA3D_JARS"
	updateClasspath "$JAVA3D_DIR/j3dcore.jar"
	updateClasspath "$JAVA3D_DIR/j3dutils.jar"
	updateClasspath "$JAVA3D_DIR/vecmath.jar"
    else
	Java3DClasspath="$tmpClasspath"
    fi

    # We need to run javac in the config directory so that javac from jdk1.1.6
    # under NT and cygwin works properly
    startdir=$PTII
    cd "$srcdir/config"
    # Don't use 'env $JAVAC . . .' here, it will not work under Cygwin
    if "$JAVAC" -classpath "$Java3DClasspath" java3dTest.java ; then
        PT_MSG_RESULT($Java3DClasspath)

	if test "`uname -s`" = "Darwin"; then 
 	    AC_MSG_CHECKING([for Jogl])
            AC_ARG_WITH(jogl, [  --with-jogl=DIR       use jogl-all.jar and gluegen.jar from DIR,
			  Java3D under Mac OS with JDK 1.7 and later requires Jogl.
			  Usually Jogl is installed in $PTII/vendors/jogl],
	        JOGL_DIR=$withval,
	        JOGL_DIR=)

            if test -f /System/Library/Java/Extensions/j3dcore.jar; then
               AC_MSG_WARN([/System/Library/Java/Extensions/j3dcore.jar exists.

    Under Mac OS X 10.9 (Mavericks) and later with Java 1.8, Java 3D
    will probably not work if
    /System/Library/Java/Extensions/j3dcore.jar and other files exist.
    Instead, Ptolemy II uses a version of Java 3D in
    $PTII/vendors/j3d.  If you run Ptolemy with the version of Java3D
    installed in /System/Library/Java/Extensions, the the demo will
    fail to render the 3D viewer and you may see messages like:
       JavaVM WARNING: JAWT_GetAWT must be called after loading a JVM
       AWT not found
    The fix is to remove the files from /System/Library/Java/Extensions:
       sudo rm /System/Library/Java/Extensions/{*J3D*,*j3d*}
    WARNING: Sadly, El Capitan has a new feature called
    System Integrity Protection (SIP), that prevents root from removing files.
    So to remove these files, you will need to reboot into recovery mode,
    disable SIP, reboot, remove the files and reboot again to enable SIP:

    1. Reboot by restarting and holding down Command+R until the Apple logo appears
    2. Click on Utilities -> Terminals and run:
          csrutil disable
    3. Reboot
    4. Login, start a terminal, run:
          sudo rm /System/Library/Java/Extensions/{*J3D*,*j3d*}
    5. Reconfigure and build: (cd $PTII;./configure; ant build build-bin)
       Note that you have not yet done so, you will need to install Jogl.
    6. Verify that Java3D runs:
          $PTII/bin/vergil ptolemy/domains/gr/demo/Pendulum/Pendulum.xml
    7. Reboot by restarting and holding down Command+R until the Apple logo appears
    8. Click on Utilities -> Terminals and run:
          csrutil enable
    9. Reboot

    For details, see
    https://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Java3D])
            fi
	    if test -z "$JOGL_DIR" ; then
                directory=`ls -d $PTII/vendors/jogl/*/jar`
                if test -d "$directory"; then
       	            JOGL_JAR_DIR="$directory"
		    PTJOGL_DIR=`dirname $JOGL_JAR_DIR`
                fi
		if test -f "$JOGL_JAR_DIR/gluegen.jar" -a -f "$JOGL_JAR_DIR/jogl-all.jar" -a -f "$JOGL_JAR_DIR/gluegen-rt-natives-macosx-universal.jar"; then
		     PT_MSG_RESULT($JOGL_JAR_DIR)
		    JAVA3D_JARS="$JAVA3D_JARS${CLASSPATH}$JOGL_JAR_DIR/gluegen.jar$CLASSPATHSEPARATOR$JOGL_JAR_DIR/jogl-all.jar$CLASSPATHSEPARATOR$JOGL_JAR_DIR/gluegen-rt-natives-macosx-universal.jar"
		    updateClasspath "$JOGL_JAR_DIR/gluegen.jar"
		    updateClasspath "$JOGL_JAR_DIR/jogl-all.jar"
		    updateClasspath "$JOGL_JAR_DIR/gluegen-rt-natives-macosx-universal.jar"
		else
		    AC_MSG_WARN([Could not find the Jogl directory.
   This could be problem at runtime for Mac OS X with Java 3D.
   We don't include Jogl in the ptII source code repository because it is so large.
   To install, do
       mkdir -p $PTII/vendors/jogl
       cd $PTI/vendors/jogl
       wget http://jogamp.org/deployment/v2.2.4/archive/jogamp-all-platforms.7z
       7z x jogamp-all-platforms.7z
       cd $PTII
       ./configure
   If you don't have 7z, the on the Mac install Mac Ports from https://www.macports.org/
   and then do
       sudo port install p7zip
   and then proceed with:
       7z x jogamp-all-platforms.7z
       cd $PTII
       ./configure
])
		fi
            fi
       fi

       PTJAVA3D_DIR=gr
       PTGRDOMAIN_JAR=gr/gr.jar
       # PTGR_PACKAGES is used in ptII/doc/makefile
       PTGR_PACKAGES="ptolemy.domains.gr.kernel ptolemy.domains.gr.lib"
    else
       AC_MSG_WARN(['"$JAVAC" -classpath "$Java3DClasspath" java3dTest.java' failed.
    Java 3D may be found at https://java3d.java.net/
    Java 3D is only needed if you want to build in
    $JAVA3D_USER_DIR,
    otherwise the build will proceed fine without Java 3D.
    Configure looks for jar files in $PTII/vendors/j3d/*/lib/ext/.
    If your Java 3D installation is in a non-standard place, use  --with-java3d=DIR
    where DIR contains j3dcore.jar, j3dutils.jar and vecmath.jar, for example:
    ./configure --with-java3D=/usr/java/j3d-1_5_2-linux-amd64/lib/ext]
    Under Mac OS X, a special version of Java 3D is present in $PTII/vendors/j3d/Darwin.
    See http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Java3D
    Under Mac OS X, Jogl must also be installed.  Configure looks for Jogl
    in $PTII/vendors/jogl/*/jar.  Jogl may be found at http://jogamp.org/jogl/www/.
    Try:
       cd $PTII/vendors; mkdir jogl; cd jogl
       wget http://jogamp.org/deployment/jogamp-current/archive/jogamp-all-platforms.7z
       7z x  jogamp-all-platforms.7z
    If you don't have 7z, get it from http://www.7-zip.org/download.html
    Then rerun ./configure ])
    fi
    cd "$startdir"
fi

if test -z "$PTJAVA3D_DIR"; then
    updateExcludes "ptolemy/domains/gr/"
fi 

#--------------------------------------------------------------------
#       Jini is connection technology from Sun, see http://www.jini.org
#       See if there was a command-line option for where Jini is
#       If not, look in $PTII/lib
#--------------------------------------------------------------------

# We only need to look for jini if the distributed directory is present
JINI_USER_DIR="$PTII/ptolemy/distributed"
JINI_PRESENT=no
# PTDISTRIBUTED_DIR is set to distributed and used in
# $PTII/ptolemy/makefile if jini was found.
PTDISTRIBUTED_DIR=
if test ! -d "$JINI_USER_DIR"; then
    PT_MSG_STATUS([$JINI_USER_DIR is not present,
    so we need not find Jini.])
    # We don't use JINI_VERSION here so that we don't expand PTII
    # in the makefile
    JINI_DIR='$PTII/ptolemy/distributed/jini'
else
    AC_MSG_CHECKING([for jini directory])
    AC_ARG_WITH(jini, [  --with-jini=DIR       use Jini jars from DIR,
                          defaults to \$PTII/ptolemy/distributed/jini],
	JINI_DIR=$withval,
	JINI_DIR=$PTII/ptolemy/distributed/jini)

    JINI_JARS="jini-core.jar jini-ext.jar sun-util.jar"

    if test -d "$JINI_DIR"; then
	PT_MSG_RESULT([$JINI_DIR])
	AC_MSG_CHECKING([for jars used by jini])
	JINI_PRESENT=yes
	jinijarpath=
	for jar in $JINI_JARS
	do 
	    if test "${PTVERBOSE:-none}" = "none"; then
	        $PT_ECHO $ECHO_N "."
	    else
                $PT_ECHO $ECHO_N "$jar "
            fi
	    jarpath=`$FIND "$JINI_DIR" -name $jar | head -1`
   	    if test -f "$jarpath"; then
  	        jinijarpath="$jinijarpath$CLASSPATHSEPARATOR$jarpath"
		# FIXME: we should not be adding to ECLIPSE_CLASSPATHENTRY_LIBS
		# unless we are sure that we can find all the jars
                updateClasspath "$jarpath"
 	    else   
		AC_MSG_WARN([Failed to find $jar in $JINI_DIR: $jarpath])
	        jinijarpath=
		break
	    fi
        done 
	if test ! -z "$jinijarpath"; then 
	    PT_MSG_RESULT([ok])
	    JINI_PRESENT="yes"
	    # PTDISTRIBUTED_DIR is set to distributed and used in
	    # $PTII/ptolemy/makefile if jini was found
	    PTDISTRIBUTED_DIR=distributed
   	    # PTDISTRIBUTED_PACKAGES is used in ptII/doc/makefile
	    PTDISTRIBUTED_PACKAGES="ptolemy.distributed.actor.lib ptolemy.distributed.actor ptolemy.distributed.client ptolemy.distributed.common ptolemy.distributed.domains.sdf.kernel ptolemy.distributed.rmi ptolemy.distributed.util"
	    PTDISTRIBUTED_JARS=$jinijarpath
        fi
    else
	JINI_DIR='$PTII/vendors/sun/jini/$JINI_VERSION'
    fi

    if test "$JINI_PRESENT" = "no"; then
        AC_MSG_WARN([Perhaps Jini is not installed?
    You need not download Jini unless you plan on use the
    distributed Ptolemy feature in ptolemy/distributed.
    Jini can be downloaded from http://www.jini.org, the
    $JINI_JARS copied to 
    \$PTII/ptolemy/distributed/jini/jars
    and configure rerun.])
    fi

fi



#--------------------------------------------------------------------
#       Java Native Interface (JNI)
#       Ptolemy II can interface to user provided native code using JNI
#	Ptolemy II can interface to Matlab using JNI
#--------------------------------------------------------------------
# Set to jni if we can compile Java Native Interface code and used in ptolemy/actor/lib/fmi/makefile
PTJNI_DIR=

if test ! -d "$PTII/ptolemy/matlab/" -a ! -d "$PTII/lbnl/lib/matlab/" ; then
    PT_MSG_STATUS([$PTII/ptolemy/matlab and $PTII/lbnl/lib/matlab are not present,
    so we need not find gcc or cc.])
else
    AC_MSG_CHECKING([for the proper JNI architecture])
    case "`uname -s`" in
        CYGWIN_*) PTJNI_ARCHITECTURE=win32;;
	Linux) PTJNI_ARCHITECTURE=linux;;
	SunOS) PTJNI_ARCHITECTURE=solaris;;
	Darwin) PTJNI_ARCHITECTURE=darwin;;
	*) PTJNI_ARCHITECTURE=unknown;;
    esac

    case "`uname -s`" in    	
        CYGWIN_*)
            AC_PATH_PROGS(PTCCJNI, mingw32-gcc i686-pc-mingw32-gcc x86_64-w64-mingw32-gcc.exe,)
	    if test "${PTCCJNI:-none}" = "none"; then
                AC_MSG_WARN([Failed to find mingw32-gcc, i686-pc-mingw32-gcc or x86_64-w64-mingw32-gcc.exe.
    Under Windows, Mingw or VisualStudio are required to create shared
    libraries that work with Java.
    Cygwin gcc will compile the dll, but it will not run.  To install
    Mingw, see http://www.mingw.org or 
    http://ptolemy.org/ptolemyII/ptIIlatest/cygwin.htm])
            fi;;
        *) AC_PATH_PROG(PTCCJNI, gcc)
	   if test "${PTCCJNI:-none}" != "none"; then
               AC_PATH_PROG(PTCCJNI, cc)
           else    
               AC_MSG_WARN([Failed to find gcc or cc, so we will
    not be able to compile the JNI interface in $PTII/jni]);
           fi
           ;;
    esac

    AC_PATH_PROG(JAVAH, javah)
    # Under MacOS X, JAVAH might be a link
    if test ! -e "$JAVAH"; then
        AC_MSG_WARN([ Failed to find javah at '$JAVAH', perhaps Java is not installed?])
    fi
	
    AC_MSG_CHECKING([for the cc for JNI])
    if test "${PTCCJNI:-none}" != "none"; then
        # PT_MSG_RESULT([$PTJNICC])
        PTJNI_DIR=jni

        AC_MSG_CHECKING([for that the pieces for JNI have been found])
        if test ! -z $PTJNI_DIR; then 
            PT_MSG_RESULT(['$PTJNI_ARCHITECTURE'])

            AC_MSG_CHECKING([for the proper JNI architecture include directory])
       	    if test $PTJNI_ARCHITECTURE = "darwin"; then
	        if test -f "$PTJAVA_HOME/../Headers/jni.h"; then
		    PTJNI_INCLUDE="$PTJAVA_HOME/../Headers"
                else
		    if test -f "$PTJAVA_HOME/../include/jni.h"; then
		       # Java 1.7.0_04-ea
		       PTJNI_INCLUDE="$PTJAVA_HOME/../include"
                    else 
	                if test -f "/System/Library/Frameworks/JavaVM.framework/Headers/jni.h"; then
		            PTJNI_INCLUDE="/System/Library/Frameworks/JavaVM.framework/Headers"
                        else
		            APPLE_JNI_PROBLEM="$PTJAVA_HOME/{Headers,include}/jni.h not found.
    Apple made a poor decision when shipping Java 1.6 
    and decided to *not* to include jni.h in the 1.6 installation, even though they
    include javah, which generates a .h that includes jni.h.  
    http://developer.apple.com/library/mac/#releasenotes/Java/JavaSnowLeopardUpdate3LeopardUpdate8RN/Introduction/Introduction.html says:
       If you do JNI development, you must install the Java Developer
       package, since it contains updated headers for the native
       JavaVM.framework and its sub-frameworks (8421130). The Java
       Developer package is available from http://connect.apple.com."
		            AC_MSG_WARN([$APPLE_JNI_PROBLEM])
                        fi
                     fi
                fi
	    else
		PTJNI_INCLUDE="$PTJAVA_HOME/../include"
	    fi

	    if test ! -d "$PTJNI_INCLUDE"; then 
	    	AC_MSG_WARN([$PTJNI_INCLUDE was not found.  As a result, compilation of JNI actors will fail.])
	    else 
	    	PT_MSG_RESULT([$PTJNI_INCLUDE])
            fi

            AC_MSG_CHECKING([for the proper JNI library architecture])
            case "`uname -p`" in
	        *86) PTJNI_LIB_ARCHITECTURE=i386;;
	        sparc) PTJNI_LIB_ARCHITECTURE=sparc;;
	        unknown) # Some platforms do not properly implement uname -p
                     if test $PTJNI_ARCHITECTURE = "win32" -o $PTJNI_ARCHITECTURE = "linux"; then
		         PTJNI_LIB_ARCHITECTURE=i386
		     else    
		         PTJNI_LIB_ARCHITECTURE=unknown
		     fi    
                     ;;
	        x86_64) PTJNI_LIB_ARCHITECTURE=amd64;;
	        *) PTJNI_LIB_ARCHITECTURE=unknown;;
            esac

            PT_MSG_RESULT(['$PTJNI_LIB_ARCHITECTURE'])

dnl             AC_MSG_CHECKING([for the proper JNI architecture lib directory])

dnl 	    if test $PTJNI_ARCHITECTURE = "darwin"; then
dnl 	        if test -d "$PTJAVA_HOME/../Libraries"; then
dnl 		    # Probably Apple Java 1.6 under Mac OS X 10.7
dnl 		    PTJNI_LIB="$PTJAVA_HOME/../Libraries"
dnl                 else
dnl 		    if test -d "$PTJAVA_HOME/lib"; then
dnl 		        # Probably Oracle Java 1.7
dnl 			# Why Oracle did not put the libs in
dnl 			# an arch directory like ALL THE OTHER
dnl 			# RELEASES is beyond me.  So much for write
dnl 			# once, run everywhere. -cxh
dnl 		        PTJNI_LIB="$PTJAVA_HOME/lib"
dnl 	            fi
dnl                 fi 
dnl 	    else
dnl 		PTJNI_LIB="$PTJAVA_HOME/lib/$PTJNI_LIB_ARCHITECTURE"
dnl 	    fi

dnl             if test ! -d "$PTJNI_LIB"; then 
dnl 	        AC_MSG_WARN([$PTJNI_LIB was not found.
dnl     As a result, $PTII/jni/launcher/launcher might not work.])
dnl             else 
dnl 	        PT_MSG_RESULT([$PTJNI_LIB])
dnl             fi

            AC_MSG_CHECKING([for if the -mno-cygwin flag is available])
            case "`uname -s`" in
                CYGWIN_ME-*) PTJNI_NO_CYGWIN=-mno-cygwin;;
	        CYGWIN_NT-*) PTJNI_NO_CYGWIN=-mno-cygwin;;
	        CYGWIN_98-*) PTJNI_NO_CYGWIN=-mno-cygwin;;
	        *) PTJNI_NO_CYGWIN=;;
            esac
            PT_MSG_RESULT(['$PTJNI_NO_CYGWIN'])

            AC_MSG_CHECKING([for the proper shared library gcc flag])
            case "`uname -s`" in
	        Darwin) PTJNI_GCC_SHARED_FLAG=-dynamiclib;;
	        *) PTJNI_GCC_SHARED_FLAG=-shared;
            esac
            PT_MSG_RESULT(['$PTJNI_GCC_SHARED_FLAG'])

            AC_MSG_CHECKING([for the proper shared library cc flag])
	    # Under Cygwin with gcc, we need -D__int64="long long"
	    # FIXME: we should have a test for this instead of setting it explictly
            case "`uname -s`" in
                CYGWIN_*) PTJNI_SHAREDLIBRARY_CFLAG="-D__int64=\"long long\"";;
	        Linux)	 PTJNI_SHAREDLIBRARY_CFLAG=-fPIC;;
	        SunOS)	 PTJNI_SHAREDLIBRARY_CFLAG=-fPIC;;
	        *) PTJNI_SHAREDLIBRARY_CFLAG=;;
            esac
            PT_MSG_RESULT(['$PTJNI_SHAREDLIBRARY_CFLAG'])

            AC_MSG_CHECKING([for the proper shared library link flag])
            case "`uname -s`" in
                CYGWIN_*) PTJNI_SHAREDLIBRARY_LDFLAG=-Wl,--add-stdcall-alias;;
		Darwin)  if test "`uname -m`" = "x86_64"; then
		             PTJNI_SHAREDLIBRARY_LDFLAG=-m64
			 fi;;    
	        Linux)	 PTJNI_SHAREDLIBRARY_LDFLAG=-fPIC;;
	        SunOS)	 PTJNI_SHAREDLIBRARY_LDFLAG=-fPIC;;
	        *) PTJNI_SHAREDLIBRARY_LDFLAG=;;
            esac
            PT_MSG_RESULT(['$PTJNI_SHAREDLIBRARY_LDFLAG'])

            AC_MSG_CHECKING([for the proper shared library prefix])
            case "`uname -s`" in
                CYGWIN_ME-*) PTJNI_SHAREDLIBRARY_PREFIX=;;
	        CYGWIN_NT-*) PTJNI_SHAREDLIBRARY_PREFIX=;;
	        CYGWIN_98-*) PTJNI_SHAREDLIBRARY_PREFIX=;;
	        SunOS)	 PTJNI_SHAREDLIBRARY_PREFIX=lib;;
	        *) PTJNI_SHAREDLIBRARY_PREFIX=lib;;
            esac
            PT_MSG_RESULT(['$PTJNI_SHAREDLIBRARY_PREFIX'])

            AC_MSG_CHECKING([for the proper shared library suffix])
	    # PTJNI_SHAREDLIBRARY_SUFFIX2 can use glob wildcards like *
	    PTJNI_SHAREDLIBRARY_SUFFIX2=""
            case "`uname -s`" in
                CYGWIN_*)    PTJNI_SHAREDLIBRARY_SUFFIX=dll
	    		     PTJNI_SHAREDLIBRARY_SUFFIX2=dll.a;;
	        SunOS)	     PTJNI_SHAREDLIBRARY_SUFFIX=so;;
	        Linux)       PTJNI_SHAREDLIBRARY_SUFFIX=so
			     PTJNI_SHAREDLIBRARY_SUFFIX2=so.*;;
	        Darwin)      PTJNI_SHAREDLIBRARY_SUFFIX=jnilib
	    	  	     PTJNI_SHAREDLIBRARY_SUFFIX2=dylib;;
	        *) PTJNI_SHAREDLIBRARY_SUFFIX=unknown
            esac
            PT_MSG_RESULT(['$PTJNI_SHAREDLIBRARY_SUFFIX'])

            AC_MSG_CHECKING([for JNI libraries needed to link JNI])
            PTJNI_DL_LIBRARY=
            case "`uname -s`" in
	        CYGWIN_*) PTJNI_LIBRARIES=-lcygwin;;
	        Linux)    PTJNI_LIBRARIES=
	                  PTJNI_DL_LIBRARY=-ldl;;
	        *)        PTJNI_LIBRARIES=;;
            esac
            PT_MSG_RESULT(['$PTJNI_LIBRARIES'])
        fi
    fi
fi

#--------------------------------------------------------------------
#      	Jode is a java decompiler.  It is useful for looking at the contents
#       of class files.  It can be downloaded from 
#	http://jode.sourceforge.net/download.php
#	Jode is full GPL, so we can't distribute it without making Ptolemy
#	GPL'd as well.
#--------------------------------------------------------------------

# PTJODE_DIR is set to jode and used in
# $PTII/ptolemy/apps/makefile if jode was found
#PTJODE_DIR=

# Note that we don't substitute in the ${PTII} or $(JODE_DIR) here
# Defaults for ptII.mk and bin/ptinvoke.in
# Use {} here instead of () because bin/ptinvoke uses JODE_DIR and JODE_CLASSES
# and under /bin/sh $(FOO) does not work, but ${FOO} does
JODE_DIR='${PTII}/vendors/jode/1.1.2-pre1'
JODE_CLASSES='${JODE_DIR}/jode.jar'

# We only need to look for jode if $PTII/ptolemy/apps/jode exists
if test ! -d "$PTII/vendors/jode"; then
    PT_MSG_STATUS([$PTII/vendors/jode is not present,
    so we need not find Jode, which is a java disassembler.])
else
    AC_MSG_CHECKING([for jode directory])
    AC_ARG_WITH(jode, [  --with-jode=DIR       use JODE from DIR,
                          defaults to \$PTII/vendors/jode/1.1.2-pre1],
	JODE_DIR=$withval,
	JODE_DIR=$PTII/vendors/jode/1.1.2-pre1)

    if test -d "$JODE_DIR"; then
	PT_MSG_RESULT([$JODE_DIR])
        AC_MSG_CHECKING([for \$JODE_DIR/jode.jar])
	if test -f "$JODE_DIR/jode.jar"; then
	    PT_MSG_RESULT([$JODE_DIR/jode.jar])
	    JODE_CLASSES=$JODE_DIR/jode.jar
        else
	    JODE_CLASSES=no
        fi
    fi
    	
    if test "$JODE_CLASSES" = "no"; then
        AC_MSG_WARN([Failed to find jode/jode.jar
    perhaps Jode is not installed?
    Jode is used to disassemble Java .class files and is only necessary
    if you plan on debugging the byte code based code generator.
    Jode can be downloaded from http://jode.sourceforge.net/download.php])
	# Note that we don't substitute in the ${PTII} or $(JODE_DIR) here
	JODE_DIR='${PTII}/vendors/jode/1.1.2-pre1'
   	JODE_CLASSES='${JODE_DIR}/jode.jar'
    #else
	# Set to jode and used in
	# $PTII/ptolemy/apps/makefile if jode was found
	#PTJODE_DIR=jode
    fi
fi

#--------------------------------------------------------------------
#      	The JavaScript Object Notation (JSON) package.
#	JSON can be downloaded from http://www.json.org
#	JSON is used by ptolemy/actor/lib/conversions/json/ and ptolemy/cg/syntactic
#--------------------------------------------------------------------

# PTJSON_DIR is set to json and used in
# ptolemy/actor/lib/conversions/json/ and $PTII/ptolemy/cg/lib/syntatic if json was found
PTJSON_DIR=

# Note that we don't substitute in the ${PTII} or $(JSON_DIR) here
# Defaults for ptII.mk and bin/ptinvoke.in
# Use {} here instead of () because bin/ptinvoke uses JSON_DIR and JSON_CLASSES
# and under /bin/sh $(FOO) does not work, but ${FOO} does
#JSON_DIR='${PTII}/vendors/jode/1.1.2-pre1'
#JSON_CLASSES='${JSON_DIR}/jode.jar'

# We only need to look for jode if either of these directories exists:
JSON_USER_DIR1="$PTII/ptolemy/actor/lib/conversions/json"
JSON_USER_DIR2="$PTII/ptolemy/actor/lib/jjs"

if test ! -d "$JSON_USER_DIR1" -a ! -d "$JSON_USER_DIR2"; then
    PT_MSG_STATUS([$JSON_USER_DIR1 and $JSON_USER_DIR2 are not present,
    so we need not find JSON, the JavaScript Object Notation package.])
else
    AC_MSG_CHECKING([for json directory])
    AC_ARG_WITH(jode, [  --with-json=DIR       use JSON from DIR,
                          defaults to \$PTII/org/json],
	JSON_DIR=$withval,
	JSON_DIR=$PTII/org/json)

    if test -d "$JSON_DIR"; then
	PT_MSG_RESULT([$JSON_DIR])
	# Used in org/makefile
	PTJSON_DIR=json
	PTJSON_JAR=actor/lib/conversions/json/json.jar
        if test "$PRE_JDK18" = "yes" ; then
            AC_MSG_WARN([ptolemy.vergil.basic.imprt.accessor requires Java 1.8 or later])
            updateExcludes "ptolemy.vergil.basic.imprt.accessor"
	    # Used in doc/makefile
	    PTJSON_PACKAGES="org.json ptolemy.actor.lib.conversions.json"
        else
	    # Used in doc/makefile
	    PTJSON_PACKAGES="org.json ptolemy.actor.lib.conversions.json ptolemy.vergil.basic.imprt.accessor"
        fi
    else
        AC_MSG_WARN([Failed to find $PTII/org/json/
    perhaps JSON is not installed?
    JSON is the JavaScript Object Notation package used by the accessors
    work.  You need only have JSON if you plan on using Accessors.])
        updateExcludes "org.json"
        updateExcludes "ptolemy.actor.lib.conversions.json"

	# JavaScript imports
	# ptolemy.actor.lib.conversions.TokenToJSON, so if we don't
	# have org.json, we don't have accessors.

	updateExcludes "ptolemy.actor.lib.jjs"
	updateExcludes" org.terraswarm.accessor"
        updateExcludes "ptolemy.vergil.basic.imprt.accessor"
    fi
fi

#--------------------------------------------------------------------
#       KVM is the JDK for PalmOS
#	See if there was a command-line option for where
#       j2me_cldc/bin/api/classes is;  if not,
#       check to see if $PTII/vendors/sun/j2me_cldc exists
#--------------------------------------------------------------------

# PTKVM_DIR is set to kvm and used in
# $PTII/ptolemy/makefile if kvm was found
PTKVM_DIR=
#
# We only need to look for kvm if $PTII/ptolemy/apps/kvm exists
if test ! -d "$PTII/ptolemy/apps/kvm"; then
    PT_MSG_STATUS([$PTII/ptolemy/apps/kvm is not present,
    so we need not find the PalmOS kvm.])
    KVM_DIR='${PTII}/vendors/sun/j2me_cldc'
    # Unfortunately, j2me_cldc does not ship with a jar of zip file
    # It needs to be built
    KVM_CLASSES='$(KVM_DIR)/bin/api/classes'
else
    AC_MSG_CHECKING([for kvm directory])
    AC_ARG_WITH(kvm, [  --with-kvm=DIR       use PalmOS KVM from DIR,
                          defaults to \$PTII/vendors/sun/j2me_cldc],
	KVM_DIR=$withval,
	KVM_DIR=$PTII/vendors/sun/j2me_cldc)

    if test -d "$KVM_DIR"; then
	PT_MSG_RESULT([$KVM_DIR])
        AC_MSG_CHECKING([for \$KVM_DIR/bin/api/classes])
	if test -d "$KVM_DIR/bin/api/classes"; then
	    KVM_CLASSES='$(KVM_DIR)/bin/api/classes'
	    PT_MSG_RESULT([$KVM_CLASSES])
        else
	    KVM_CLASSES=no
        fi
    else
	PT_MSG_RESULT([Not found in $KVM_DIR])
	AC_MSG_CHECKING([for kvm directory in /j2me_cldc])
	# Likely place for kvm under windows
	KVM_DIR=/j2me_cldc
        if test -d "$KVM_DIR"; then
	    PT_MSG_RESULT([$KVM_DIR])
            AC_MSG_CHECKING([for \$KVM_DIR/bin/api/classes])
	    if test -d "$KVM_DIR/bin/api/classes"; then
	        KVM_CLASSES='$(KVM_DIR)/bin/api/classes'
	        PT_MSG_RESULT([$KVM_CLASSES])
            else
	        KVM_CLASSES=no
            fi
        else
		KVM_CLASSES=no
        fi

    fi
    if test "$KVM_CLASSES" = "no"; then
        AC_MSG_WARN([Failed to find j2me_cldc/bin/api/classes,
    perhaps Kvm is not installed?
    You need not download Kvm unless you plan on building applications
    for the Palm Pilot or Handspring Visor.
    Kvm can be downloaded from http://java.sun.com/products/cldc])
	# Note that we don't substitute in the ${PTII} or $(KVM_DIR) here
	KVM_DIR='${PTII}/vendors/sun/kvm'
   	KVM_CLASSES='$(KVM_DIR)/bin/api/classes'
    else
	# Set to kvm and used in
	# $PTII/ptolemy/makefile if kvm was found
	PTKVM_DIR=kvm
    fi
fi

#--------------------------------------------------------------------
#       MATLAB Interface
#       check to see if matlab is in the user's path
#--------------------------------------------------------------------
# PTMATLAB_DIR is set to matlab and used in $PTII/ptolemy/makefile
# if matlab and gcc are found; PTMATLAB_LIBDIR is then also set to
# the platform-dependent directory containg Matlab's engine libraries
PTMATLAB_DIR=
PTMATLAB_LIBDIR=

# Extension for matlab .mex files, for example "mexmaci64"
PTMATLAB_MEXEXT=

PTMATLAB_SUPPORTED=no

case "`uname -s`" in
Darwin)
	if test -f "$PTJNI_INCLUDE/jni.h"; then
	    PTMATLAB_SUPPORTED=yes
        else 
	    if test  -d "$PTII/ptolemy/matlab/" -o -d "$PTII/lbnl/lib/matlab/" ; then
	        AC_MSG_WARN([$APPLE_JNI_PROBLEM])
            fi
        fi	    
	;;
Linux)
	PTMATLAB_SUPPORTED=yes
	;;
CYGWIN*)
	PTMATLAB_SUPPORTED=yes
	;;
SunOS*)
	PTMATLAB_SUPPORTED=yes
	;;
esac


if test "$PTMATLAB_SUPPORTED" = "no"; then
    if test ! -d "$PTII/ptolemy/matlab/" -a ! -d "$PTII/lbnl/lib/matlab/" ; then
        PT_MSG_STATUS([$PTII/ptolemy/matlab and $PTII/lbnl/lib/matlab are not present,
    so we need not find matlab.])
    else 
        AC_MSG_WARN([The Matlab interface is not supported on this platform (you are running `uname -s`).])
    fi
else
    # We only need to look for matlab if $PTII/ptolemy/matlab exists
    if test ! -d "$PTII/ptolemy/matlab"; then
	PT_MSG_STATUS([$PTII/ptolemy/matlab is not present,
    so we need not find matlab and gcc.])
	MATLAB_DIR=/matlab
	#PTCC=gcc
    else
	AC_PATH_PROG(MATLAB, matlab)
	if test "${MATLAB:-none}" = "none"; then
	    AC_MSG_WARN([Failed to find matlab executable in the path.
    Perhaps Matlab is not installed?
    If Matlab is not present, then the Ptolemy II/Matlab interface in
    \$PTII/ptolemy/matlab will not be usable.]);
	else 
	    startdir=$PTII
	    cd "$srcdir/config"
	    if "$JAVAC" RootDirectory.java ; then
		AC_MSG_CHECKING([the value of the Matlab root directory ])
		if env "$JAVA" -classpath "$PTII/config" RootDirectory "$MATLAB"> /dev/null; then

		    MATLAB_DIR_TMP=`"$JAVA" -classpath "$PTII/config" RootDirectory "$MATLAB"`

		    # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
		    # Remove /cygdrive so we can compile with MSVC
		    MATLAB_DIR=`echo "$MATLAB_DIR_TMP" | sed 's@/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl

		    PT_MSG_RESULT('$MATLAB_DIR')
		else	
		    AC_MSG_WARN(['"$JAVA" -classpath "$PTII/config" RootDirectory "$MATLAB"' failed.
    We will not be able to compile the Matlab interface in ptolemy/matlab/]);
		fi
	    else
		AC_MSG_WARN(['cd "$PTII/config"; $JAVAC RootDirectory.java' failed.
    We will not be able to compile the Matlab interface in ptolemy/matlab]);
	    fi
	    cd "$startdir"

	    if test ! -d "$MATLAB_DIR"; then
		    AC_MSG_WARN([Failed to find '${MATLAB_DIR}'
	    If Matlab is not present, then the Ptolemy II/Matlab interface in
    \$PTII/ptolemy/matlab will not be usable.]);
	    else


            AC_MSG_CHECKING([for gcc])
	    case "`uname -s`" in    	
	        CYGWIN_*) MATLAB_LIBDIR=${MATLAB_DIR}/bin/win32
		        # We test for MATLAB_LIBDIR here to determine 32-bit vs. 64-bit.
			# We set MATLAB_LIBDIR again below.
			# FIXME: Running a 32-bit JVM requires a 32-bit Matlab etc.  We could check that here.
			if test  -d "${MATLAB_LIBDIR}"; then
			    # 32-bit
			    AC_PATH_PROGS(PTMATLAB_CC, mingw32-gcc i686-pc-mingw32-gcc)
			    progs="mingw32-gcc i686-pc-mingw32-gcc"
                        else 
			    MATLAB_LIBDIR=${MATLAB_DIR}/bin/win64
			    if test  ! -d "${MATLAB_LIBDIR}"; then
			        $AC_MSG_WARN([Failed to find ${MATLAB_DIR}/bin/win32 and ${MATLAB_LIBDIR}?])
                            fi
			    # 64-bit
			    AC_PATH_PROGS(PTMATLAB_CC, x86_64-w64-mingw32-gcc)
			    progs="x86_64-w64-mingw32-gcc"
			fi	
		         if test "${PTMATLAB_CC:-none}" = "none"; then
			     AC_MSG_WARN([Failed to find $progs
    Under Windows, Mingw or VisualStudio are required to compile the
    Ptolemy/Matlab dll.
    Cygwin gcc will compile the dll, but it will not run.  To install
    Mingw, see http://www.mingw.org or 
    http://ptolemy.org/ptolemyII/ptIIlatest/cygwin.htm])
			  else
                              OLDCC="$CC"
			      CC="$PTMATLAB_CC"
                              PTJNI_LIBC="" 
			  fi;;
		       *) AC_PATH_PROG(PTMATLAB_CC, gcc)
 		          if test "${PTMATLAB_CC:-none}" != "none"; then
                              OLDCC="$CC"
			      CC="$PTMATLAB_CC"
                              PTJNI_LIBC="-lc" 
			  else    
			      AC_MSG_WARN([Failed to find gcc])
			      AC_PATH_PROG(PTMATLAB_CC, cc)
			      if test "${PTMATLAB_CC:-none}" != "none"; then
                                  OLDCC="$CC"
			          CC="$PTMATLAB_CC"
                                  PTJNI_LIBC="-lc" 
			      else	
			          AC_MSG_WARN([Failed to find gcc or cc, so we will
    not be able to compile the Matlab interface in ptolemy/matlab]);
                               fi
                          fi;;
            esac

            if test "${PTMATLAB_CC:-none}" != "none"; then

	    AC_CHECK_FUNCS(malloc_size, MALLOC_SIZE_FLAG=-DHAVE_MALLOC_SIZE)
	    CC="$OLDCC"

	    # Extension for matlab .mex files, for example "mexmaci64"
	    case "`uname -s`" in    	
	        CYGWIN_*)  # Can't run mexext.bat here, so we guess.  This is wrong for 32-bit? We adjust below
		   PTMATLAB_MEXEXT=mexmaci684;;
		*) AC_MSG_CHECKING([the extension for Matlab .mex files])
                   PTMATLAB_MEXEXT=`"${MATLAB_DIR}/bin/mexext"`
		   PT_MSG_RESULT($PTMATLAB_MEXEXT);;
            esac 

	    cd "$srcdir/config"
	    if "$JAVAC" MajorOSName.java ; then
	        AC_MSG_CHECKING([which major type of OS we are running under])
		# Older versions of cygwin might not have env, but 1.1 does
		if env "$JAVA" -classpath "$PTII/config" MajorOSName > /dev/null; then
		    # Run it again and get the results.  We get just the first word: Windows, Linux, Mac etc.
		    MAJOR_OS_NAME=`"$JAVA" -classpath "$PTII/config" MajorOSName | awk '{print $1}'`
		    PT_MSG_RESULT($MAJOR_OS_NAME)
		else   
		    AC_MSG_WARN(['"$JAVA" -classpath "$PTII/config" MajorOSName' failed.
    The Matlab interface will build fine, but not being able to determine
    the major operating system name could cause problems with running 
    (cd "$PTII/ptolemy/matlab"; make install)]);		    
		fi
	    fi

	    cd "$startdir"
		MATLAB_USE_MSVC="no"
		# These flags work for MacOSX r2009a, Linux r2008a, Windows r2008a
		PTMATLAB_CC_FLAGS="-DPT_NO_ENGGETARRAY -DPT_NO_ENGPUTARRAY -DPT_NO_MXGETNAME $MALLOC_SIZE_FLAG" 
		case "`uname -s`" in
		Linux)
		    if test "`uname -m`" = "x86_64"; then
			    MATLAB_LIBDIR=${MATLAB_DIR}/bin/glnxa64
		    else
			    MATLAB_LIBDIR=${MATLAB_DIR}/bin/glnx86
			    if ! test -d ${MATLAB_DIR}; then
				    MATLAB_LIBDIR=${MATLAB_DIR}/extern/lib/glnx86
			    fi
		    fi
			;;
		CYGWIN*)
                        # As of 5/2007, we no longer use MSVC cl for Matlab
			MATLAB_USE_MSVC="no"
			MATLAB_LIBDIR=${MATLAB_DIR}/bin/win32
			PTMATLAB_MEXEXT=mexmaci
			if test ! -d "${MATLAB_LIBDIR}"; then
				MATLAB_LIBDIR=${MATLAB_DIR}/bin/win64
				PTMATLAB_MEXEXT=mexmaci64
			fi	
			;;
		SunOS*)
			MATLAB_LIBDIR=${MATLAB_DIR}/extern/lib/sol2
			if test ! -d "$MATLAB_LIBDIR"; then
			    # Why, under Unix, are the libs in the bin dir? 
			    MATLAB_LIBDIR=${MATLAB_DIR}/bin
			    if test ! -f "$MATLAB_LIBDIR/libmx.so"; then
			        MATLAB_LIBDIR=${MATLAB_DIR}/bin/sol64
				PTMATLAB_CC_FLAGS="-m64 $PTMATLAB_CC_FLAGS"
                            fi
			else     
			    if test ! -f "$MATLAB_LIBDIR/libmx.so"; then
			        # Why, under Unix, are the libs in the bin dir? 
			        # matlab r2006a
			        MATLAB_LIBDIR=${MATLAB_DIR}/bin
			    fi				
                        fi  
			;;
		Darwin)
			MATLAB_LIBDIR=${MATLAB_DIR}/bin/maci
			MATLAB_64LIBDIR=${MATLAB_DIR}/bin/maci64
			;;
		*)
			MATLAB_LIBDIR=${MATLAB_DIR}/extern/lib
			;;
		esac
		PT_MSG_STATUS([using '${MATLAB_LIBDIR}' for Matlab's engine libraries])
		if test $MATLAB_USE_MSVC = "yes"; then
		    AC_MSG_CHECKING([for Microsoft Visual C cl])
		    AC_PATH_PROG(PTMATLAB_CC, cl)
		    if test "${PTMATLAB_CC:-none}" != "none"; then
		        PTMATLAB_DIR=matlab
			MATLAB_LIBPATH_DIR="${MATLAB_DIR}/extern/lib/win32/microsoft"
			MATLAB_LIBPATH=`echo "$MATLAB_LIBPATH_DIR" | sed 's/ /\\\\\ /'`
			PTMATLAB_LD_ARGS="/Tpptmatlab.cc /Feptmatlab.dll /link /dll /libpath:\\\"${MATLAB_LIBPATH}\\\" libeng.lib libmx.lib"

	            else    
			AC_MSG_WARN([Failed to find cl])
			AC_PATH_PROG(PTMATLAB_CC, gcc)
			if test "${PTMATLAB_CC:-none}" != "none"; then
			    PTMATLAB_DIR=matlab
			else	
			    AC_MSG_WARN([Failed to find MSVC cl or GNU gcc, so we will
    not be able to compile the Matlab interface in ptolemy/matlab.
    Note that the Matlab interface does not work under Windows with gcc-3.3,
    you must use the Microsoft Visual C 'cl' compiler.]);
			fi
		    fi
                else 
		    if test $PTJNI_ARCHITECTURE = "darwin"; then
		        PTMATLAB_LD_ARGS="ptmatlab.cc -fno-exceptions -dynamiclib -o ${PTJNI_SHAREDLIBRARY_PREFIX}ptmatlab32.${PTJNI_SHAREDLIBRARY_SUFFIX}	-L\"${MATLAB_LIBDIR}\" \"-Wl,-rpath,${MATLAB_64LIBDIR}\" ${PTJNI_SHAREDLIBRARY_LDFLAG} -leng -lmx -lmex"
		        PTMATLAB_64LD_ARGS="ptmatlab.cc -fno-exceptions -dynamiclib -o ${PTJNI_SHAREDLIBRARY_PREFIX}ptmatlab64.${PTJNI_SHAREDLIBRARY_SUFFIX}	-L\"${MATLAB_64LIBDIR}\" \"-Wl,-rpath,${MATLAB_64LIBDIR}\" ${PTJNI_SHAREDLIBRARY_LDFLAG} -leng -lmx -lmex"
		    else
		        PTMATLAB_LD_ARGS="-shared ptmatlab.cc -fno-exceptions -o ${PTJNI_SHAREDLIBRARY_PREFIX}ptmatlab.${PTJNI_SHAREDLIBRARY_SUFFIX}	-L\"${MATLAB_LIBDIR}\" ${PTJNI_SHAREDLIBRARY_LDFLAG} ${PTJNI_LIBC} -leng -lmx -lmex"
		        if test "`uname -m`" = "x86_64"; then
		            PTMATLAB_LD_ARGS="$PTMATLAB_LD_ARGS -fPIC"
		        fi
		    fi

		    # Under MacOS X, JAVAH might be a link
		    if test ! -e "$JAVAH"; then
		        AC_MSG_WARN([Failed to find javah at '$JAVAH',
    perhaps the JDK is not installed?
    We will not be able to compile the Matlab interface in ptolemy/matlab]);
                    else
		        PTMATLAB_DIR=matlab
		    fi
                fi
	    fi
	    fi
	fi
    fi	
fi

if test -z "$PTMATLAB_DIR"; then
    updateExcludes "ptolemy/matlab/"
else
    # Set to the matlab jars that need to be signed if matlab was found.
    # Used in jnlp.mk
    PTMATLAB_JARS="ptolemy/matlab/matlab.jar ptolemy/matlab/demo/demo.jar lib/matlab.jar"
    # Used in $PTII/doc/makefile
    PTMATLAB_PACKAGES=ptolemy.matlab
fi 


#--------------------------------------------------------------------
#       Mescal - 
#       
#--------------------------------------------------------------------
# PTMESCAL_DIR is set to mescal and used in $PTII/makefile 
# if $PTII/mescal was found
PTMESCAL_DIR=

MESCAL_USER_DIR="$PTII/mescal"
if test -d "$MESCAL_USER_DIR"; then
   PTMESCAL_DIR=mescal
   updateExcludes "**/devel/"
   updateExcludes "mescal/apps/"
   updateExcludes "mescal/totem/domains/meta/codegen/"
   updateExcludes "mescal/views/memory/registerfile/"
   updateExcludes "mescal/views/simulation/model/probe/"
   updateExcludes "mescal/xml2hmdes/"
fi

#--------------------------------------------------------------------
#       OpenModelica is an implementation of Modelica.
#       At compile time, it is used in $PTII/ptolemy/actor/lib/fmi/fmus/omc
#       At runtime, it is used in $PTII/ptolemy/domains/openmodelica        
#	See https://openmodelica.org
#--------------------------------------------------------------------

# We only enable OpenModelical if either of these two directories are present
PTOMC_USER_DIR="$PTII/ptolemy/actor/lib/fmi/fmus/omc"
PTOPENMODELICA_USER_DIR="$PTII/ptolemy/domains/openmodelica"


if test ! -d "$PTOMC_USER_DIR" -a ! -d "$PTOPENMODELICA_USER_DIR"; then
    PT_MSG_STATUS([$PTOMC_USER_DIR and $PTOPENMODELICA_USER_DIR are not present])
else
    AC_PATH_PROG(PTOMC, omc)
    if test "${PTOMC:-none}" = "none"; then
        AC_MSG_WARN([Failed to find omc, the OpenModelicaCompiler.
    Rebuilding the OpenModelica fmus will not be possible.
    Running the OpenModelica models will not be possible.
    This is only a concern if you are interested in OpenModelica])
        updateExcludes "ptolemy/actor/lib/fmi/fmus/omc"
        updateExcludes "ptolemy/domains/openmodelica"
    else
        if test -d "$PTOMC_USER_DIR";  then
                PTOMC_DIR=omc
        fi
        if test -d "$PTOPENMODELICA_USER_DIR";  then
                PTOPENMODELICA_DIR=openmodelica
                PTOPENMODELICA_PACKAGES="ptolemy.domains.openmodelica.kernel ptolemy.domains.openmodelica.lib ptolemy.domains.openmodelica.lib.omc ptolemy.domains.openmodelica.lib.omc.corba"
		PTOPENMODELICADOMAIN_JAR=openmodelica/openmodelica.jar
        fi
    fi
fi


#--------------------------------------------------------------------
#       ProtoBuf - "Protocol Buffers are a way of encoding structured data in an efficient yet extensible format."
#	https://code.google.com/p/protobuf/#       
#--------------------------------------------------------------------

# PTMETROII_DIR is set to metroII if the ProtoBuf jar file was found
# $PTII/ptolemy/domains/makefile uses PTMETROII_DIR
PTMETROII_DIR=

# PTMETROII_PACKAGES is used in doc/makefile
PTMETROII_PACKAGES=

# The location of the protobuf jar file, typically $PTII/lib/protobuf-java-2.4.1.jar 
PTPROTOBUF_JAR=

# We only need look for protobuf if $PTII/ptolemy/domains/metro exists.
PROTOBUF_USER_DIR="$PTII/ptolemy/domains/metroII"
if test ! -d "$PROTOBUF_USER_DIR"; then
    PT_MSG_STATUS([$PROTOBUF_USER_DIR is not present, so we need not find ProtoBuf.])
else
    AC_MSG_CHECKING([for Protocol Buffers (ProtoBuf)])
    if test -f "$PTII/lib/protobuf-java-2.4.1.jar"; then
        PT_MSG_RESULT($PTII/lib/protobuf-java-2.4.1.jar)
	PTPROTOBUF_JAR="$PTII/lib/protobuf-java-2.4.1.jar"
	PTMETROII_DIR=metroII
	PTMETROII_PACKAGES="net.jimblackler.Utils ptolemy.domains.metroII.gui ptolemy.domains.metroII.kernel ptolemy.domains.metroII.kernel.util.ProtoBuf"
        updateClasspath "$PTPROTOBUF_JAR"
    else
        AC_MSG_WARN([Failed to find $PTII/lib/protobuf-java-2.4.1.jar. 
    The Google page at https://code.google.com/p/protobuf fo Protobuf says:
      Protocol Buffers are a way of encoding structured data in an efficient
      yet extensible format.
    Protobuf is needed at runtime for the MetroII director.])
        updateExcludes "ptolemy/domains/metroII/"
    fi
fi

#--------------------------------------------------------------------
#       Paho "The Paho Java Client is an MQTT client library written
#       in Java for developing applications that run on the JVM or
#       other Java compatible platforms such as Android"
#	See https://eclipse.org/paho/clients/java/
#--------------------------------------------------------------------

# We only enable Ptango if $PTPAHO_USER_DIR is present
PTPAHO_USER_DIR="$PTII/ptolemy/actor/lib/jjs/modules/localStorage"

# PTPAHO_MQTT_DIRS is set to localStorage and mqtt if Paho MQTT is found and used in ptII/ptolemy/actor/lib/jjs/modules/
PTPAHO_MQTT_DIRS=

# The Paho MQTT Client Library, defaults to $PTII/lib/org.eclipse.paho.client.mqttv3.jar.
PTPAHO_MQTT_JAR=

# PTPAHO_MQTT_PACKAGES is used in doc/makefile
PTPAHO_MQTT_PACKAGES=

if test ! -d "$PTPAHO_USER_DIR"; then
    PT_MSG_STATUS([$PTPAHO_USER_DIR is not present])
else
    if test "$PRE_JDK18" = "yes" ; then
        AC_MSG_WARN([ptolemy/actor/lib/jjs/modules/localStorage requires Java 1.8 or later])
    else
        AC_MSG_CHECKING([for the Paho MQTT jar])
        AC_ARG_WITH(pahoMqtt, [  --with-paho-mqtt-jar=Jar       use Paho MQTT from JAR,
                                  defaults to \$PTII/lib/org.eclipse.paho.client.mqttv3.jar],
	                          PTPAHO_MQTT_JAR=$withval,
                                  PTPAHO_MQTT_JAR=$PTII/lib/org.eclipse.paho.client.mqttv3.jar)

        if test -f "$PTPAHO_MQTT_JAR"; then
            PT_MSG_RESULT([$PTPAHO_MQTT_JAR])
        else
            AC_MSG_WARN([Failed to find the PTPAHO_MQTT Jar file.
    The default location is $PTII/lib/
    Paho MQTT is used by $PTII/ptolemy/actor/lib/jjs/modules/localStorage])
        fi
    fi
fi

if test -z "$PTPAHO_MQTT_JAR"; then
   updateExcludes "ptolemy/actor/lib/jjs/modules/localStorage/"
else 
   updateClasspath "$PTPAHO_MQTT_JAR"
   PTPAHO_MQTT_DIRS="localStorage mqtt"
   PTPAHO_MQTT_PACKAGES="ptolemy.actor.lib.jjs.modules.localStorage ptolemy.actor.lib.jjs.modules.mqtt"
fi 

#--------------------------------------------------------------------
#       Ptango is the Ptolemy Internet of Things project
#	See http://chess.eecs.berkeley.edu/ptango
#--------------------------------------------------------------------

# PTANGO_DIR is set to ptango if ptango is found.
PTANGO_DIR=

# PTXMPP_DIR is set to xmpp if smack.jar and smackx.jar are found.  See org/ptolemy/ptango/makefile
PTXMPP_DIR=

# We only enable Ptango if $PTANGO_USER_DIR is present
PTANGO_USER_DIR="org/ptolemy/ptango"
if test ! -d "$PTANGO_USER_DIR"; then
    PT_MSG_STATUS([$PTANGO_USER_DIR is not present])
else
    # We checked for Jetty above.	
    if test  -f "$PTJETTY_JAR"; then
	# We checked for Servlet above.
        if test  -f "$PTSERVLET_JAR" -a -f "$PTSMACK_JAR" -a -f "$PTSMACKX_JAR"; then
	    PTANGO_DIR=ptango
	    PTXMPP_DIR=xmpp
            # PTANGO_PACKAGES is used in ptII/doc/makefile
	    PTANGO_PACKAGES=`find $PTANGO_USER_DIR -name "*.java" | grep -v /test | awk -F / '{printf("%s", $1); for (i = 2; i < NF; i++) printf(".%s", $i); printf("\n")}' | sort | uniq | awk '{printf("%s ", $0)}'`
        fi
    fi

    if test "$PTANGO_DIR" = ""; then
        AC_MSG_WARN([Failed to find the Jetty, Servlet, Smack or SmackX jar files necessary to compile ptango.
    Ptango is the Ptolemy Internet of Things project.
    For further instructions, see http://chess.eecs.berkeley.edu/ptango.])
    else
        PTANGO_JARS="${CLASSPATHSEPARATOR}${PTJETTY_JAR}${CLASSPATHSEPARATOR}${PTSERVLET_JAR}${CLASSPATHSEPARATOR}${PTSMACK_JAR}${CLASSPATHSEPARATOR}${PTSMACKX_JAR}"
    fi
fi

if test -z "$PTANGO_JARS"; then
   updateExcludes "org/ptolemy/ptango/"
fi 


#--------------------------------------------------------------------
#       ptserver is the Ptolemy server interface to the Android client
#	http://chess.eecs.berkeley.edu
#	
#--------------------------------------------------------------------

# PTSERVER_DIR is set to ptserver and used in
# $PTII/makefile if ptserver is found
PTSERVER_DIR=

# Jar files used by ptserver.
PTHESSIAN_JAR=
PTWMQTT_JAR=

# Jar files necessary for compilation of ptserver.
PTSERVER_JARS=

# We only need to look for Hessian if $PTSERVER_USER_DIR is present
PTSERVER_USER_DIR="$PTII/ptserver"
PTSERVER_USER_DIR2="$PTII/ptolemy/homer"
if test ! -d "$PTSERVER_USER_DIR" -o ! -d "$PTSERVER_USER_DIR2" -o -z "$PTHOMER_DIR"; then
    PT_MSG_STATUS([$PTSERVER_USER_DIR or
    $PTSERVER_USER_DIR2 are not present or
    Homer was not found
    so we need not find the Hessian, Jetty, Servlet and WMQTT interfaces for ptserver.])
else
    # We checked for Jetty above.	
    if test  -f "$PTJETTY_JAR"; then
	# We checked for Servlet above.
        if test  -f "$PTSERVLET_JAR"; then
	    AC_MSG_CHECKING([for Hessian, used by ptserver ])
	    AC_ARG_WITH(hessian, [  --with-hessian=JAR       use Hessian.jar from JAR,
                          defaults to \$PTII/ptserver/lib/hessian-4.0.7.jar],
  	    PTHESSIAN_JAR=$withval,
	    PTHESSIAN_JAR=$PTII/ptserver/lib/hessian-4.0.7.jar)
            if test  -f "$PTHESSIAN_JAR"; then
   	        PT_MSG_RESULT([$PTHESSIAN_JAR])

		AC_MSG_CHECKING([for WMQTT, used by ptserver ])
		AC_ARG_WITH(wmqtt, [  --with-wmqtt=JAR       use wmqtt.jar from JAR,
                          defaults to \$PTII/ptserver/lib/wmqtt.jar],
	  	PTWMQTT_JAR=$withval,
		PTWMQTT_JAR=$PTII/ptserver/lib/wmqtt.jar)

		if test  -f "$PTWMQTT_JAR"; then
	     	    PT_MSG_RESULT([$PTWMQTT_JAR])

	            # Set to ptserver and used in
	            # $PTII/makefile
	            PTSERVER_DIR=ptserver
                    # PTSERVER_PACKAGES is used in ptII/doc/makefile
	            PTSERVER_PACKAGES=`find ptserver -name "*.java" | grep -v /test | awk -F / '{printf("%s", $1); for (i = 2; i < NF; i++) printf(".%s", $i); printf("\n")}' | sort | uniq | awk '{printf("%s ", $0)}'`
                fi
             fi
         fi
    fi

    if test "$PTSERVER_DIR" = ""; then
        AC_MSG_WARN([Failed to find the jar files necessary to compile ptserver.
    The ptserver interface is used to support Ptolemy running on the Android.
    For further instructions, see $PTII/ptserver/package.html] )
    else
        PTSERVER_JARS="${CLASSPATHSEPARATOR}${PTHESSIAN_JAR}${CLASSPATHSEPARATOR}${PTJETTY_JAR}${CLASSPATHSEPARATOR}${PTSERVLET_JAR}${CLASSPATHSEPARATOR}${PTWMQTT_JAR}"
    fi
fi

if test -z "$PTSERVER_JARS"; then
   updateExcludes "ptserver/"
   updateExcludes "ptolemy/homer/"
else
   updateClasspath "$PTHESSIAN_JAR"
   updateClasspath "$PTWMQTT_JAR"
fi 

#--------------------------------------------------------------------
#       PSDF is the Parameterized Synchronous Data Flow domain
#--------------------------------------------------------------------

# PTPSDF_DIR is set to PSDF and used in
# $PTII/ptolemy/domains/makefile if mapss.jar was found.
PTPSDF_DIR=

# Directory that contains the mapss.jar file
PSDF_DIR='${PTII}/lib'

# We only need to look for on if $PTII/ptolemy/domains/psdf exists
PSDF_USER_DIR="$PTII/ptolemy/domains/psdf"
if test ! -d "$PSDF_USER_DIR"; then
    PT_MSG_STATUS([$PSDF_USER_DIR is not present,
    so we need not find the mapss.jar.])
else
    AC_MSG_CHECKING([for mapss.jar, used by the PSDF domain])
    AC_ARG_WITH(mapss, [  --with-mapss=DIR       use mapss.jar from DIR,
                          defaults to \$PTII/lib],
	PSDF_DIR=$withval,
	PSDF_DIR=$PTII/lib)

    if test -f "$PSDF_DIR/mapss.jar"; then
	PT_MSG_RESULT([$PSDF_DIR])
	PTPSDF_DIR=psdf
    else  
        AC_MSG_WARN([Failed to find PTII/lib/mapss.jar
    If it is not present, you will not be able to use the 
    Parameterized Synchronous Data Flow domain.])
	# Note that we don't substitute in the ${PTII} here
	PSDF_DIR='${PTII}/lib/'
    fi
fi

if test -z "$PTPSDF_DIR"; then
   updateExcludes "ptolemy/domains/psdf/"
else
   updateClasspath "$PSDF_DIR/mapss.jar"
fi 

#--------------------------------------------------------------------
#       PowerMock is used for testing and is CPL'd.
#       PowerMock includes JUnit and EasyMock. 
#--------------------------------------------------------------------

# PTPOWERMOCK_DIR is set to test and used in
# $PTII/ptdb/makefile
PTPOWERMOCK_DIR= 

# PowerMock, used for testing, see http://code.google.com/p/powermock/
# Used in ptolemy/ptdb/test/makefile
PTPOWERMOCK_JARS=

# We only need to look for PowerMock if the ptdb/test directory is present
POWERMOCK_USER_DIR="$PTII/ptdb/test"
if test ! -d "$POWERMOCK_USER_DIR"; then
    PT_MSG_STATUS([$POWERMOCK_USER_DIR is not present,
    so we need not find PowerMock])
else
    AC_MSG_CHECKING([for PowerMock test harness])
    AC_ARG_WITH(ptpowermock, [  --with-powermock=DIR       use PowerMock test harness from DIR,
                          defaults to \$PTII/vendors/misc/powermock-easymock-junit-1.3.8],
	POWERMOCK_DIR=$withval,
	POWERMOCK_DIR=$PTII/vendors/misc/powermock-easymock-junit-1.3.8)

    if test -d "$POWERMOCK_DIR"; then
	PT_MSG_RESULT([$POWERMOCK_DIR])
	AC_MSG_CHECKING([for PowerMock jars])
        jars="cglib-nodep- easymock- easymockclassextension- javassist- junit- objenesis- powermock-easymock-"
	powermockjarpath=
	for jar in $jars
	do
	    if test "${PTVERBOSE:-none}" = "none"; then
	        $PT_ECHO $ECHO_N "."
	    else
                $PT_ECHO $ECHO_N "$jar "
            fi
	    # Do not use a leading * before ${jar}.  If we do, then we don't find the easymock jar file.
	    jarpath=`$FIND "$POWERMOCK_DIR" -name "${jar}*.jar" | head -1`
   	    if test -f "$jarpath"; then
                # Keep track of the jars so we can use them while building
	        # with make.
  	        powermockjarpath="$powermockjarpath$CLASSPATHSEPARATOR$jarpath"

                updateClasspath "$jarpath"
            else   
	        AC_MSG_WARN([Failed to find $jar in $POWERMOCK_DIR: $jarpath])
	        powermockjarpath=
	        break
	   fi
	done	
	if test ! -z eclipsejarpath; then
	   PT_MSG_RESULT( ok)
	   PTPOWERMOCK_JARS=$powermockjarpath
	   PTPOWERMOCK_DIR=test
        fi
	
    fi	

    if test "$PTPOWERMOCK_DIR" = ""; then
        AC_MSG_WARN([Failed to find PowerMock.
    Perhaps PowerMock was not installed?
    You need not download these packages if you would like
    to run the tests.  To install PowerMock, go to
    http://code.google.com/p/powermock/ and download
    http://powermock.googlecode.com/files/powermock-easymock-junit-1.3.8.zip
    (which contains PowerMock for EasyMock and JUnit) and unzip it in
    $PTII/vendors/misc so that 
    $PTII/vendors/misc/powermock-easymock-junit-1.3.8 is created,
    then rerun configure.
    Other versions of PowerMock _may_ work, but are untested.])
    fi
fi

if test -z "$PTPOWERMOCK_DIR"; then
    if test -d ptdb; then
        ptdbTestDirectories=`$FIND ptdb -name test`
        for ptdbTestDirectory in $ptdbTestDirectories
        do 
            updateExcludes "$ptdbTestDirectory/"
        done   
    fi
fi 


#--------------------------------------------------------------------
#       Ptalon 
#--------------------------------------------------------------------

# PTPTALON_DIR is set to ptalon and used in
# $PTII/ptolemy/actor/makefile if antlr.jar was found.
PTPTALON_DIR=

# Directory that contains the antlr.jar file
ANTLR_DIR='${PTII}/ptolemy/actor/ptalon/antlr'

# We only need to look for on if $PTII/ptolemy/actor/ptalon exists
PTALON_USER_DIR="$PTII/ptolemy/actor/ptalon"
if test ! -d "$PTALON_USER_DIR"; then
    PT_MSG_STATUS([$PTALON_USER_DIR is not present,
    so we need not find anltr.jar.])
else
    AC_MSG_CHECKING([for anltr.jar, used by the Ptalon])
    AC_ARG_WITH(antlr, [  --with-antlr=DIR       use antlr.jar from DIR,
                          defaults to \$PTII/ptolemy/actor/ptalon/antlr'],
	ANTLR_DIR=$withval,
	ANTLR_DIR=$PTII/ptolemy/actor/ptalon/antlr)

    if test -f "$ANTLR_DIR/antlr.jar"; then
	PT_MSG_RESULT([$ANTLR_DIR])
	PTPTALON_DIR=ptalon
	# PTALON_PACKAGES is used in $PTII/doc/makefile
	PTPTALON_PACKAGES="ptolemy.actor.ptalon ptolemy.actor.ptalon.lib ptolemy.actor.ptalon.gt"
    else  
        AC_MSG_WARN([Failed to find PTII/ptolemy/actor/ptalon/antlr/antlr.jar
    If it is not present, you will not be able to use the 
    Ptalon.])
	# Note that we don't substitute in the ${PTII} here
	PTPTALON_DIR='${PTII}/ptolemy/actor/ptalon/antlr'
    fi

    if test ! "$HAS_GENERICS" = "yes"; then 
        AC_MSG_WARN([You are running Java $JVERSION, which does not
    support generics.  Thus, ptolemy/actor/ptalon will not compile.])
        PTPTALON_DIR=
	PTPTALON_PACKAGES=
    fi
fi

if test -z "$PTPTALON_DIR"; then
   updateExcludes "ptolemy/actor/ptalon/"
else
   updateClasspath "$ANTLR_DIR/antlr.jar"
fi 

#--------------------------------------------------------------------
#       R is a statistical computing language
#	See https://www.r-project.org/
#--------------------------------------------------------------------

# PTRTOOL_DIR is set to r if r is found
PTRTOOL_DIR=

# Used in mk/jnlp.jar 
PTRTOOL_JNLP_JARS=

# We only enable RPtango if $PTRTOOL_USER_DIR is present
PTRTOOL_USER_DIR="ptolemy/actor/lib/r"
if test ! -d "$PTRTOOL_USER_DIR"; then
    PT_MSG_STATUS([$PTRTOOL_USER_DIR is not present])
else
    PTJRI_JAR="$PTII/lib/JRI.jar"
    PTCOMMONS_LANG_JAR="$PTII/lib/commons-lang-2.6.jar"
    PTCOMMONS_LOGGING_JAR="$PTII/lib/commons-logging-1.1.1.jar"
    if test  -f "$PTJRI_JAR" -a -f "$PTCOMMONS_LANG_JAR" -a -f "$PTCOMMONS_LOGGING_JAR"; then
        PTRTOOL_DIR=r
        # PTRTOOL_PACKAGES is used in ptII/doc/makefile
	PTRTOOL_PACKAGES=ptolemy.actor.lib.r
    fi

    if test "$PTRTOOL_DIR" = ""; then
        AC_MSG_WARN([Failed to find $PTJRI_JAR,
    $PTCOMMONS_LANG_JAR
    or $PTCOMMONS_LOGGING_JAR
    so the R statistical computing language interface will not be compiled.])
    else
        PTRTOOL_JARS="${CLASSPATHSEPARATOR}${PTJRI_JAR}${CLASSPATHSEPARATOR}${PTCOMMONS_LANG_JAR}${CLASSPATHSEPARATOR}${PTCOMMONS_LOGGING_JAR}"

	PTRTOOL_JNLP_JARS="ptolemy/actor/lib/r/r.jar ptolemy/actor/lib/r/demo/demo.jar"
	updateClasspath "$PTJRI_JAR"
	updateClasspath "$PTCOMMONS_LANG_JAR"
	updateClasspath "$PTCOMMONS_LOGGING_JAR"
    fi
fi

if test -z "$PTRTOOL_JARS"; then
   updateExcludes "ptolemy/actor/lib/r"
fi

#--------------------------------------------------------------------
#       Scala is a programming language that creates .class files
#--------------------------------------------------------------------

# PTSCALA_DIR is set to scala if scala is found
PTSCALA_DIR=

# We only enable scala if $PTSCALA_USER_DIR is present
PTSCALA_USER_DIR="org/ptolemy/scala"

if test ! -d "$PTSCALA_USER_DIR"; then
    PT_MSG_STATUS([$PTSCALA_USER_DIR is not present])
else
    AC_PATH_PROG(SCALAC, scalac)
    if test -x "$SCALAC"; then
        AC_PATH_PROG(SCALA, scala)
        if test -x "$SCALA"; then
            PTSCALA_DIR=scala
        else
            AC_MSG_WARN([Failed to find the scala binary,
    so org/ptolemy/scala will be excluded])

            updateExcludes "org/ptolemy/scala/"        
        fi
    else
       AC_MSG_WARN([Failed to find the scalac binary,
    so org/ptolemy/scala will be excluded])

        updateExcludes "org/ptolemy/scala/"
    fi
fi


#--------------------------------------------------------------------
#       Soot is a Java Optimization Framework, see
#	http://www.sable.mcgill.ca/soot/
#       See if there was a command-line option for where Soot is
#       If not, look in $PTII/vendors/sun/soot
#--------------------------------------------------------------------

# PTCOPERNICUS_DIR is set to copernicus and used in
# $PTII/ptolemy/makefile if soot was found
PTCOPERNICUS_DIR=

# Directory that contains the soot jar files
SOOT_DIR='${PTII}/lib'

# Soot needs to find java.lang.Object	
# Use {} here instead of () because bin/ptinvoke uses JAVA_SYSTEM_JAR
# and under /bin/sh $(FOO) does not work, but ${FOO} does
JAVA_SYSTEM_JAR='${PTJAVA_HOME}/lib/rt.jar'

# Java 1.5 has javax.crypto.Cipher in jce.jar
JAVAX_CRYPTO_JAR='${PTJAVA_HOME}/lib/jce.jar'

# We don't bother overriding this below so that something close
# to the right default is in ptII.mk and the user can just change
# SOOT_DIR or JAVA_SYSTEM_JAR	
# Use {} here instead of () because bin/ptinvoke uses SOOT_CLASSES
SOOT_CLASSES='${SOOT_DIR}/sootclasses.jar${CLASSPATHSEPARATOR}${CLASSPATHSEPARATOR}${JAVA_SYSTEM_JAR}${CLASSPATHSEPARATOR}${JAVAX_CRYPTO_JAR}'

# We only need to look for soot if $PTII/ptolemy/copernicus exists
if test ! -d "$PTII/ptolemy/copernicus"; then
    PT_MSG_STATUS([$PTII/ptolemy/copernicus is not present,
    so we need not find the Soot - a Java Optimization Framework.])
    SOOT_DIR='${PTII}/lib'
else
    AC_MSG_CHECKING([for soot directory])
    AC_ARG_WITH(soot, [  --with-soot=DIR       use SOOT from DIR,
                          defaults to \$PTII/lib],
	SOOT_DIR=$withval,
	SOOT_DIR=$PTII/lib)

    if test -d "$SOOT_DIR"; then
	PT_MSG_RESULT([$SOOT_DIR])
        AC_MSG_CHECKING([for \$SOOT_DIR/sootclasses.jar])
	if test -f "$SOOT_DIR/sootclasses.jar"; then
	    PT_MSG_RESULT([ok])
	    PT_MSG_STATUS([$SOOT_CLASSES])
        else
	    SOOT_CLASSES_FOUND=no
        fi
    # else
    # We could look in other places . . .
    fi
    	
    if test "$SOOT_CLASSES_FOUND" = "no"; then
        AC_MSG_WARN([Failed to find soot/sootclasses.jar
    perhaps Soot is not installed?
    You need not download Soot unless you plan on using code generation
    The Soot SDK can be downloaded from http://www.sable.mcgill.ca/soot/])
	# Note that we don't substitute in the ${PTII} or $(SOOT_DIR) here
	SOOT_DIR='${PTII}/lib'
    else
	# Set to copernicus and used in
	# $PTII/ptolemy/makefile if soot was found
	PTCOPERNICUS_DIR=copernicus
    fi

    AC_MSG_CHECKING([for rt.jar by compiling config/SystemJar.java])
    AC_ARG_WITH(javasystemjar, [  --with-javasystemjar=DIR       use rt.lib from DIR,
                          defaults to JRE java.home property with lib/rt.jar appended ],
	JAVA_SYSTEM_JAR=$withval,
	JAVA_SYSTEM_JAR='$(PTJAVA_HOME)/lib/rt.jar')

    startdir=$PTII
    cd "$srcdir/config"
    if "$JAVAC" SystemJar.java ; then
	PT_MSG_RESULT(SystemJar.java compiled)
	AC_MSG_CHECKING([the location or rt.jar])
	if env "$JAVA" -classpath "$PTII/config" SystemJar > /dev/null; then
	    # Run it again and get the results
	    JAVA_SYSTEM_JAR=`"$JAVA" -classpath "$PTII/config" SystemJar`
   	    PT_MSG_RESULT('$JAVA_SYSTEM_JAR')
	else	
	    AC_MSG_WARN(['"$JAVA" -classpath "$PTII/config" SystemJar failed.
    Classes that use Soot will compile, but will fail to run.'])
        fi
    else
	AC_MSG_WARN(['cd "$srcdir/config"; "$JAVAC" SystemJar.java failed.
    Classes that use Soot will compile, but will fail to run.'])
    fi
    cd "$startdir"
fi

if test -z "$PTCOPERNICUS_DIR"; then
   updateExcludes "ptolemy/copernicus/"
else
   # Note that kieler.jar should be before sootclasses.jar
   # both jars have a Maps class.
   updateClasspath "$SOOT_DIR/sootclasses.jar"
    # What about JAVA_SYSTEM_JAR?
fi 

#--------------------------------------------------------------------
#       Space - domains/space uses ojdbc6.jar 
#--------------------------------------------------------------------


# PTDATABASE_DIR is set to database and used in
# $PTII/ptolemy/actor/lib/makefile if ojdbc6.jar was found.
PTDATABASE_DIR=

# PTDATABASE_JNLP_JARS is set to the database jars that need to be signed
# and used in mk/jnlp.mk
PTDATABASE_JNLP_JARS=

# PTDATABASE_PACKAGES is used in ptII/doc/makefile
PTDATABASE_PACKAGES=

# PTSPACE_DIR is set to space and used in
# $PTII/ptolemy/domains/makefile if ojdbc6.jar was found.
PTSPACE_DIR=

# PTSPACEDOMAIN_PACKAGES is used in ptII/doc/makefile
PTSPACEDOMAIN_PACKAGES=

# MySQL Jar mysql-connector-java-5.1.6-bin.jar
MYSQL_JAR=

# Oracle Java Database jar (ojdbc5.jar or ojdbc6.jar)
# ojdbc5.jar and ojdbc6.jar are not shipped because of restrictive licenses
# http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5565
ORACLE_OJDBC_JAR=

# PTSPACEDOMAIN_JAR is the name of the jar file that includes the space
# domain if ojdbc6.jar was found.  PTSPACEDOMAIN_JAR used in domains/makefile
PTSPACEDOMAIN_JAR=

# We only need to look for on if $PTII/ptolemy/domains/space exists
SPACE_USER_DIR="$PTII/ptolemy/domains/space"

DATABASE_USER_DIR="$PTII/ptolemy/actor/lib/database"

if test ! -d "$SPACE_USER_DIR" -a ! -d "$DATABASE_USER_DIR"; then
    PT_MSG_STATUS([$SPACE_USER_DIR and $DATABASE_USER_DIR
    are not present,  so we need not find the Mysql jar and Oracle ojdbc6.jar.])
    MYSQL_JAR=
    ORACLE_OJDBC_JAR=
else
    MYSQL_TARGET_JAR=mysql-connector-java-5.1.6-bin.jar
    AC_MSG_CHECKING([for mysql jar, used by the database actors])
    AC_ARG_WITH(mysql, [  --with-mysql=/path/to/mysql.jar  path to mysql.jar
                          defaults to \$PTII/ptolemy/actor/lib/database/$MYSQL_TARGET_JAR],
	MYSQL_JAR=$withval,
	MYSQL_JAR=$PTII/ptolemy/actor/lib/database/$MYSQL_TARGET_JAR)
    if test -f "$MYSQL_JAR"; then
       PT_MSG_RESULT([$MYSQL_JAR])
    fi    
    OJDBC_TARGET_JAR=ojdbc6.jar
    if test "$JAVA1_6_OR_LATER" != "yes"; then
        OJDBC_TARGET_JAR=ojdbc5.jar
    fi
    AC_MSG_CHECKING([for ojdbc.jar])
    AC_ARG_WITH(ojdbc, [  --with-ojdbc=/path/to/ojdbcN.jar  path to ojdbc.jar
                          defaults to \$PTII/ptolemy/actor/lib/database/ojdbc6.jar or ojdbc5.jar $OJDBC_TARGET_JAR],
	    ORACLE_OJDBC_JAR=$withval,
	    ORACLE_OJDBC_JAR=$PTII/ptolemy/actor/lib/database/$OJDBC_TARGET_JAR)

    if test -f "$ORACLE_OJDBC_JAR"; then
	PT_MSG_RESULT([$ORACLE_OJDBC_JAR])
    else
	AC_MSG_WARN([$OJDBC_TARGET_JAR not found,
    but only necessary to use database actors with Oracle.])
    fi

    if test -f "$MYSQL_JAR" -o -f "$ORACLE_OJDBC_JAR"; then
	PTDATABASE_DIR=database
	PTDATABASE_PACKAGES=ptolemy.actor.lib.database
	PTSPACE_DIR=space
	PTSPACEDOMAIN_JAR=space/space.jar
	PTSPACEDOMAIN_PACKAGES=ptolemy.domains.space

	# Update PTDATABASE_JNLP_JARS, used to sign jar files in mk/jnlp.mk
	# The sed commands remove $PTII/
	PTDATABASE_JNLP_JARS="ptolemy/actor/lib/database/database.jar ptolemy/domains/space/space.jar"
	if test -f "$ORACLE_OJDBC_JAR"; then
	    PTDATABASE_JNLP_JARS="$PTDATABASE_JNLP_JARS `echo "$ORACLE_OJDBC_JAR" | sed "s@$PTII/@@"`"
	fi
	if test -f "$MYSQL_JAR"; then
	    PTDATABASE_JNLP_JARS="$PTDATABASE_JNLP_JARS `echo "$MYSQL_JAR" | sed "s@$PTII/@@"`"
	fi
    else  
        AC_MSG_WARN([Failed to find 
    PTII/actor/lib/database/$MYSQL_TARGET_JAR and/or 
    PTII/actor/lib/database/$OJDBC_TARGET_JAR
    If neither Java Database Connection jar is present,
    you will not be able to use the space domain or the database actors.])
	    ORACLE_OJDBC_JAR=
	    MYSQL_JAR=
    fi	    
fi

if test -z "$MYSQL_JAR" -a -z "$ORACLE_OJDBC_JAR"; then
   updateExcludes "ptolemy/actor/lib/database/|ptolemy/domains/space/"
else
   if test -f "$MYSQL_JAR"; then 
       updateClasspath "$MYSQL_JAR"
   fi 
   if test -f "$ORACLE_OJDBC_JAR"; then 
      updateClasspath "$ORACLE_OJDBC_JAR"
   fi 

fi 

#--------------------------------------------------------------------
#       Sphinx4 is a speech recognition engine developed at Carnegie Mellon University.
#       PtolemyII includes an Accessor for speech recognition using sphinx4 at
#       ptolemy/actor/lib/jjs/modules/speechRecognition
#--------------------------------------------------------------------

# PTSPHINX4_DIR is set to sphinx.
PTSPHINX4_DIR=

# The Sphinx4 core Jar file.
PTSPHINX4_CORE_JAR=

PTSPHINX4_DATA_JAR=

PTSPHINX4_PACKAGES=
# We only need to look for Sphinx if this directory is present:
SPHINX4_USER_DIR="$PTII/ptolemy/actor/lib/jjs/modules/speechRecognition"

if test ! -d "$SPHINX4_USER_DIR" ; then
    PT_MSG_STATUS([$SPHINX4_USER_DIR is not present,
    so we need not find Sphinx4 - Speech recognition engine API.])
else
    AC_MSG_CHECKING([for Sphinx4 Speech recognition data jar API])
    AC_ARG_WITH(sphinx-data, [  --with-sphinx-data-jar=/path/to/sphinx4-data-5prealpha.jar  path to 
                          defaults to \$PTII/vendors/misc/sphinx4/sphinx4-data-5prealpha.jar],
	PTSPHINX4_DATA_JAR=$withval,
	PTSPHINX4_DATA_JAR=$PTII/vendors/misc/sphinx4/sphinx4-data-5prealpha.jar)
    if test -f "$PTSPHINX4_DATA_JAR"; then
       PT_MSG_RESULT([$PTSPHINX4_DATA_JAR])
       AC_MSG_CHECKING([for Sphinx4 Speech recognition core jar API])
       AC_ARG_WITH(sphinx-core, [  --with-sphinx-core-jar=/path/to/sphinx4-core-5prealpha.jar path to 
                          defaults to \$PTII/vendors/misc/sphinx4/sphinx4-core-5prealpha.jar],
	  PTSPHINX4_CORE_JAR=$withval,
	  PTSPHINX4_CORE_JAR=$PTII/vendors/misc/sphinx4/sphinx4-core-5prealpha.jar)
       if test -f "$PTSPHINX4_CORE_JAR"; then
           PT_MSG_RESULT([$PTSPHINX4_CORE_JAR])
           PTSPHINX4_DIR="$PTII/ptolemy/actor/lib/jjs/modules/speechRecognition"
	   PTSPHINX4_PACKAGES=ptolemy.actor.lib.jjs.modules.speechRecognition
           updateClasspath "$PTSPHINX4_DATA_JAR"
           updateClasspath "$PTSPHINX4_CORE_JAR"
       fi    
    fi    
fi

if test -z "$PTSPHINX4_DIR"; then
    AC_MSG_WARN([Could not find the sphinx4 jar files.
    These files are only necessary for the accessor in 
    ptolemy/actor/lib/jjs/modules/speechRecognition.
    To install Sphinx4:
    1. mkdir $PTII/vendors/misc/sphinx4
    2. Download these .jar files and place in ptolemy/vendors/misc/sphinx:

      wget -O $PTII/vendors/misc/sphinx4/sphinx4-core-5prealpha.jar 'https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=net.sf.phat&a=sphinx4-core&v=5prealpha&e=jar'

      wget -O $PTII/vendors/misc/sphinx4/sphinx4-data-5prealpha.jar 'https://oss.sonatype.org/service/local/artifact/maven/redirect?r=releases&g=net.sf.phat&a=sphinx4-data&v=5prealpha&e=jar'

    3. Rerun
      (cd $PTII; ./configure)])

    updateExcludes "ptolemy/actor/lib/jjs/modules/speechRecognition/"
fi

#--------------------------------------------------------------------
#       PDFRenderer used to display PDF in vergil.
#	Source may be found at https://pdf-renderer.dev.java.net/
#--------------------------------------------------------------------

# PTPDFRENDERER_DIR is set to pdf and used in
# $PTII/ptolemy/vergil/makefile if PDFRenderer is found
PTPDFRENDERER_DIR=

# Jar file used by ptolemy/vergil/pdfrenderer
PTPDFRENDERER_JAR=

PDFRENDERER_USER_DIR=$PTII/ptolemy/vergil/pdfrenderer
# We only need to look for PDFRender.jar if the directory that uses it exists.
if test ! -d "$PDFRENDERER_USER_DIR"; then
    PT_MSG_STATUS([$PDFRENDERER_USER_DIR is not present,
    so we need not find PDFRenderer.])
else
    AC_MSG_CHECKING([for PDFRenderer])
    AC_ARG_WITH(pdfrenderer, [  --with-pdfrenderer=PDFRENDERER_JAR     use PDFRenderer PDFRENDERER_JAR
                          defaults to \$PTII/lib/PDFRenderer.jar],
	PTPDFRENDERER_JAR=$withval,
	PTPDFRENDERER_JAR=$PTII/lib/PDFRenderer.jar)

    if test -f "$PTPDFRENDERER_JAR"; then
	PT_MSG_RESULT([$PTPDFRENDERER_JAR])
	PTPDFRENDERER_DIR=pdfrenderer
        updateClasspath "$PTPDFRENDERER_JAR"
    fi	
    if test "$PTPDFRENDERER_DIR" = ""; then
        AC_MSG_WARN([Failed to find the PDFRenderer Jar file
    You need only have PDFRenderer if you want to render PDF files in Vergil.
    PDFRenderer may be downloaded from https://pdf-renderer.dev.java.net/])
	PTPDFRENDERER_JAR=
    fi
fi

if test -z "$PTPDFRENDERER_DIR"; then
   updateExcludes "ptolemy/vergil/pdfrenderer/"
fi 

#--------------------------------------------------------------------
#       The Batik SVG toolkit is used by Kepler so we include Batik
#	support in Diva.  See
#	http://xmlgraphics.apache.org/batik/
#       See if there was a command-line option for where Batikc
#       is
#       If not, look for for $PTII/vendors/eclipse
#--------------------------------------------------------------------

# PTSVG_DIR is set to svg and used in
# $PTII/diva/util/java2d/makefile if Batik SVG jar files were found
PTSVG_DIR=

# Jar file used by diva/util/java2d/svg/makefile
PTSVG_JAR=

# We only need to look for Batik if $PTII/diva/util/java2d/svg exists
if test ! -d "$PTII/diva/util/java2d/svg"; then
    PT_MSG_STATUS([$PTII/diva/util/java2d/svg is not present,
    so we need not find Batik SVG.])
else
    AC_MSG_CHECKING([for Batik SVG])
    AC_ARG_WITH(batikjar, [  --with-batikjar=BATIK_JAR     use Batik jar BATIK_JAR,
                          defaults to \$KEPLER/lib/jar/batik-all-1.6.jar],
	PTSVG_JAR=$withval,
	PTSVG_JAR=$KEPLER/lib/jar/batik-all-1.6.jar)

    if test -f "$PTSVG_JAR"; then
	PT_MSG_RESULT([$PTSVG_JAR])
	PTSVG_DIR=svg
        updateClasspath "$PTSVG_JAR"
    fi	
    if test "$PTSVG_DIR" = ""; then
        AC_MSG_WARN([Failed to find Batik Jar file
    You need only have Batik if you are planning on rebuilding diva.jar
    for use with Kepler.
    Batik can be downloaded from http://xmlgraphics.apache.org/batik/])
    fi
fi

if test -z "$PTSVG_DIR"; then
   updateExcludes "diva/util/java2d/svg/"
fi

#--------------------------------------------------------------------
#       svgSalamander is used by FIXME.
#	See https://svgsalamander.java.net/
#--------------------------------------------------------------------

# PTSVGSALAMANDER_DIR is set to svg and used in com/jhlabs/image/svg/makefile
# if the svgSalamander jar file is found.
PTSVGSALAMANDER_DIR=

# svgSalamander Jar file.
PTSVGSALAMANDER_JAR=

# PTSVGSALAMANDER_PACKAGES is used in ptII/doc/makefile
PTSVGSALAMANDER_PACKAGES=

# We only need to look for svgSalamander if com/jhlabs/image/svg is present.
if test ! -d "$PTII/com/jhlabs/image/svg"; then
    PT_MSG_STATUS([$PTII/org/terraswarm/accessors is not present,
    so we need not find svgSalamander.])
else
    AC_MSG_CHECKING([for svgSalamander])
    AC_ARG_WITH(svgsalamanderjar, [  --with-svgsalamanderjar=SVGSALAMANDER_JAR     use svgSalamander jar file,
                                  defaults to \$PTT/lib/svgSalamander.jar],
                          PTSVGSALAMANDER_JAR=$withval,
                          PTSVGSALAMANDER_JAR=$PTII/lib/svgSalamander.jar)

    if test -f "$PTSVGSALAMANDER_JAR"; then
	PT_MSG_RESULT([$PTSVGSALAMANDER_JAR])
	PTSVGSALAMANDER_DIR=svg
        PTSVGSALAMANDER_PACKAGES=com.jhlabs.image.svg
        updateClasspath "$PTSVGSALAMANDER_JAR"
    fi	

    if test "$PTSVGSALAMANDER_DIR" = ""; then
        AC_MSG_WARN([Failed to find the svgSalamander.jar file.
    You need only have find this if com/jhlabs/image/svg is present.
    The svgSalamander facility is used by Cape Code to render icons.
    svgSalamander.jar can be downloaded from http://xmlgraphics.apache.org/batik/])
    fi
fi

if test -z "$PTSVGSALAMANDER_DIR"; then
   updateExcludes "com.jhlabs.image.svg"
fi

#--------------------------------------------------------------------
#       The JavaScript Editor in ptolemy.actor.gui.syntax uses RSyntaxEditor
#       from https://github.com/bobbylight/RSyntaxTextArea
#--------------------------------------------------------------------

# PTRSYNTAXTEXTAREA_DIR is set to syntax and used in
# $PTII/ptolemy/actor/gui/makefile if lib/rsyntaxtextarea-*.jar is found
PTRSYNTAXTEXTAREA_DIR=

# RSyntaxTextArea jar file, typically downloaded from Maven.
PTRSYNTAXTEXTAREA_JAR=

# Java packages that use RSyntaxTextArea, typically ptolemy.actor.gui.syntax.
PTRSYNTAXTEXTAREA_PACKAGES=
# We only need to look for RSyntaxEditor $PTII/ptolemy/actor/gui/syntax exists
if test ! -d "$PTII/ptolemy/actor/gui/syntax"; then
    PT_MSG_STATUS([$PTII/ptolemy/actor/gui/syntax is not present,
    so we need not find RSyntaxEditor.])
else
    AC_MSG_CHECKING([for RSyntaxEditor])
    AC_ARG_WITH(batikjar, [  --with-rsyntaxeditor=RSYNTAXTEXTAREA_JAR     use RSyntaxEditor jar,
                          defaults to \$PTII/lib/rsyntaxtextarea-2.6.0-SNAPSHOT.jar],
	PTRSYNTAXTEXTAREA_JAR=$withval,
	PTRSYNTAXTEXTAREA_JAR=$PTII/lib/rsyntaxtextarea-2.6.0-SNAPSHOT.jar)

    if test -f "$PTRSYNTAXTEXTAREA_JAR"; then
	PT_MSG_RESULT([$PTRSYNTAXTEXTAREA_JAR])
	PTRSYNTAXTEXTAREA_DIR=syntax
        PTRSYNTAXTEXTAREA_PACKAGES=ptolemy.actor.gui.syntax
        updateClasspath "$PTRSYNTAXTEXTAREA_JAR"
    fi	
    if test "$PTRSYNTAXTEXTAREA_DIR" = ""; then
        AC_MSG_WARN([Failed to find the RSyntaxTextArea jar file
    You need only have this jar if you are using the JavaScript syntax editors
    in $PTII/ptolemy/actor/gui/syntax.
    RSyntaxTextArea https://github.com/bobbylight/RSyntaxTextArea])
	PTRSYNTAXTEXTAREA_JAR=
    fi
fi

if test -z "$PTRSYNTAXTEXTAREA_DIR"; then
   updateExcludes "ptolemy/actor/gui/syntax"
fi 


#--------------------------------------------------------------------
#       TINI is the JDK for Dallas Tini board, see
#	www.ibutton.com
#	See if there was a command-line option for where
#       tinisk is;  if not,
#       check to see if $PTII/vendors/dalsemi/tini/bin/tiniclasses.jar exists
#--------------------------------------------------------------------

# PTTINI_DIR is set to tini and used in
# $PTII/ptolemy/apps/makefile if tini was found
PTTINI_DIR=
#
# We only need to look for tini if $PTII/ptolemy/apps/tini exists
if test ! -d "$PTII/ptolemy/apps/tini"; then
    PT_MSG_STATUS([$PTII/ptolemy/apps/tini is not present,
    so we need not find the Dallas Semiconductor tini.])
    TINI_DIR='${PTII}/vendors/dalsemi/tini'
    TINI_CLASSES='${TINI_DIR}/bin/tini.jar'
else
    AC_MSG_CHECKING([for tini directory])
    AC_ARG_WITH(tini, [  --with-tini=DIR       use TINI from DIR,
                          defaults to \$PTII/vendors/dalsemi/tini],
	TINI_DIR=$withval,
	TINI_DIR=$PTII/vendors/dalsemi/tini)

    if test -d "$TINI_DIR"; then
    	PT_MSG_RESULT([$TINI_DIR])
      	AC_MSG_CHECKING([for \$TINI_DIR/bin/tini.jar])
	if test -f "$TINI_DIR/bin/tini.jar"; then
	   PT_MSG_RESULT([$TINI_DIR/bin/tini.jar])
	   TINI_CLASSES='${TINI_DIR}/bin/tini.jar'
	else
	   TINI_CLASSES=no
        fi
	PT_MSG_RESULT([$TINI_CLASSES])
    fi
    if test "$TINI_CLASSES" = "no"; then
        AC_MSG_WARN([Failed to find tini/bin/tiniclasses.jar
    perhaps Tini is not installed?
    You need not download Tini unless you plan on building applications
    for the Dallas Semiconductor Tini board.
    The Tini SDK can be downloaded from http://www.ibutton.com])
	# Note that we don't substitute in the ${PTII} or $(TINI_DIR) here
	TINI_DIR='${PTII}/vendors/dalsemi/tini'
   	TINI_CLASSES='${TINI_DIR}/bin/tini.jar'
    else
	# Set to tini and used in
	# $PTII/ptolemy/apps/makefile if tini was found
	PTTINI_DIR=tini
    fi
fi

#--------------------------------------------------------------------
#	TinyOS	
#--------------------------------------------------------------------
# PTTINYOS_DIR is set to ptinyos and used in
# $PTII/ptolemy/domains/makefile if TinyOS is found
PTTINYOS_DIR=

# The problem is that the nesc/configure script does not understand
# "c:/" style syntax, it works with "/cygdrive/c/", yet Java
# does not understand /cygdrive/c syntax, so we hack
PTINYOS_DIR=$PTII/ptolemy/domains/ptinyos

if test ! -d "$PTINYOS_DIR"; then
    PT_MSG_STATUS([$PTINYOS_DIR is not present
    so we need not set up for TinyOS.])

    # Nothing to exclude
    # updateExcludes "ptolemy/domains/nc/"
else
    AC_MSG_CHECKING([the for TinyOS])
    if test -z "$TOSROOT"; then
        AC_MSG_WARN([\$TOSROOT is not set.  It must be set to use PtinyOS.])
    fi
    if test ! -d "$TOSROOT"; then
        AC_MSG_WARN([\$TOSROOT is set to '$TOSROOT',
     but there is no directory by that name, so we will not set up for PtinyOS.
     For details, see $PTII/ptolemy/domains/ptinyos/README.txt.])
    else
        PT_MSG_RESULT([$TOSROOT])
        # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
        TOSROOT_NO_CYGDRIVE=`echo "$TOSROOT" | sed 's@^/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl

        AC_MSG_CHECKING([for TOSDIR directory])
        if test ! -d "$TOSDIR"; then
	    AC_MSG_WARN([\$TOSDIR is set to '$TOSDIR',
     but there is no directory by that name.
     For details, see $PTII/ptolemy/domains/ptinyos/README.txt.])
        else 
	    PT_MSG_RESULT([$TOSDIR])
        # Use changequote to protect the square brackets in sed
changequote(<<, >>)dnl
        TOSDIR_NO_CYGDRIVE=`echo "$TOSDIR" | sed 's@^/cygdrive/\([a-zA-Z]\)/@\1:/@'`
changequote([, ])dnl

        fi

        AC_MSG_CHECKING([for PTINYOS_MOMLROOT])
	if test -z "$PTINYOS_MOMLROOT"; then
	    AC_MSG_WARN([\$PTINYOS_MOMLROOT is not set.
    For details, see $PTII/ptolemy/domains/ptinyos/README.txt.])
        else 
            PT_MSG_RESULT($PTINYOS_MOMLROOT)
            if test ! -d "$PTINYOS_MOMLROOT"; then
                # Try to make the directory
	        mkdir -p "$PTINYOS_MOMLROOT"
            fi
            AC_MSG_CHECKING([for PTINYOS_MOMLROOT directory])
            if test ! -d "$PTINYOS_MOMLROOT"; then
	        AC_MSG_WARN([\$PTINYOS_MOMLROOT is set to '$PTINYOS_MOMLROOT',
     but there is no directory by that name.
     For details, see $PTII/ptolemy/domains/ptinyos/README.txt.])
            else 
	        PTINYOS_MOMLROOT_NO_CYGDRIVE=`echo "$PTINYOS_MOMLROOT" | sed 's@^/cygdrive/\([a-zA-Z]\)/@\1:/@'`
		if test -d "$PTINYOS_MOMLROOT_NO_CYGDRIVE"; then 

		    # If MOMLROOT is under $PTII, then add it to the classpath
		    echo "$PTINYOS_MOMLROOT_NO_CYGDRIVE" | grep "$PTII" > /dev/null
		    retval=$?
		    if test "$retval" = "0"; then  
		        SHORT_PTINYOS_MOMLROOT_NO_CYGDRIVE=`echo "$PTINYOS_MOMLROOT_NO_CYGDRIVE" | sed "s@$PTII/@@"` 
                        updateClasspath "$SHORT_PTINYOS_MOMLROOT_NO_CYGDRIVE"
	            else 
		        AC_MSG_WARN([\$PTINYOS_MOMLROOT ($PTINYOS_MOMLROOT)
    is not under \$PTII ($PTII) so we are not
    appending \$PTINYOS_MOMLROOT to the Eclipse classpath.
    This is only a problem for Viptos users, who will not be able
    to view .nc files when running under Eclipse.])
	            fi 
                else			
	            AC_MSG_WARN([\$PTINYOS_MOMLROOT_NO_CYGDRIVE does not exist])
                fi			
	        PT_MSG_RESULT([$PTINYOS_MOMLROOT])
            fi
        fi
        # The jars to the classpath
        updateClasspath "$PTINYOS_DIR/lib/nesc.jar"
        updateClasspath "$PTINYOS_DIR/lib/jdom.jar"

	# If TOSROOT is under $PTII, then add it to the classpat
	echo "$TOSROOT_NO_CYGDRIVE" | grep "$PTII" > /dev/null
	retval=$?
	if test "$retval" = "0"; then
		SHORT_TOSROOT_NO_CYGDRIVE=`echo "$TOSROOT_NO_CYGDRIVE" | sed "s@$PTII/@@"` 
	        updateClasspath "$SHORT_TOSROOT_NO_CYGDRIVE"
        else 
	    AC_MSG_WARN([\$TOSROOT ($TOSROOT)is not
    under \$PTII ($PTII) so we are not
    appending \$TOSROOT to the Eclipse classpath.
    This is only a problem for Viptos users, who will not be able
    to view .nc files when running under Eclipse.])
        fi 
    fi
fi 

if test ! -d "$TOSROOT"; then
       updateExcludes "ptolemy/domains/ptinyos/" 
else
       PTTINYOS_DIR=ptinyos
fi

#--------------------------------------------------------------------
#       GiottoSDK is an embedded implementation of the Giotto language
#	www.eecs.berkeley.edu/~fresco/giotto
#
#       check to see if $PTII/vendors/giotto/giotto.jar exists
#--------------------------------------------------------------------

# PTGIOTTO_DIR is set to Giotto and used in
# $PTII/ptolemy/apps/makefile if giotto was found
PTGIOTTO_DIR=
#
if test ! -d "$PTII/ptolemy/domains/giotto"; then
    PT_MSG_STATUS([$PTII/ptolemy/domains/giotto is not present,
    so we need not find the Giotto SDK.])
    GIOTTO_DIR='${PTII}/vendors/giotto'
    GIOTTO_CLASSES='${GIOTTO_DIR}/gdk.jar'
else
    AC_MSG_CHECKING([for giotto directory])
    AC_ARG_WITH(giotto, [  --with-giotto=DIR       use GiottoSDF from DIR,
                          defaults to \$PTII/vendors/giotto],
	GIOTTO_DIR=$withval,
	GIOTTO_DIR=$PTII/vendors/giotto)

    GIOTTO_CLASSES=no
    if test -d "$GIOTTO_DIR"; then
    	PT_MSG_RESULT([$GIOTTO_DIR])
      	AC_MSG_CHECKING([for \$GIOTTO_DIR/gdk.jar])
	if test -f "$GIOTTO_DIR/gdk.jar"; then
	   PT_MSG_RESULT([$GIOTTO_DIR/gdk.jar])
	   GIOTTO_CLASSES='${GIOTTO_DIR}/gdk.jar'
	else
	   GIOTTO_CLASSES=no
        fi
    fi
    if test "$GIOTTO_CLASSES" = "no"; then
        AC_MSG_WARN([Failed to find giotto/gdk.jar
    perhaps Giotto is not installed?
    You need not download Giotto unless you plan on generating code for 
    Giotto models.
    The Giotto SDK can be
    downloaded from https://embedded.eecs.berkeley.edu/giotto/
    Copy gdk.jar to $PTII/vendors/giotto, for example:
        mkdir -p $PTII/vendors/giotto
        cp C:/Program\ Files/Giotto*/gdk.jar $PTII/vendors/giotto/])
	# Note that we don't substitute in the ${PTII} or $(GIOTTO_DIR) here
	GIOTTO_DIR='${PTII}/vendors/giotto'
   	GIOTTO_CLASSES='${GIOTTO_DIR}/gdk.jar'
    else
	# Set to giotto and used in
	# $PTII/ptolemy/copernicus/java/ if giotto was found
	PTGIOTTO_DIR=giotto
    fi
fi

#--------------------------------------------------------------------
#       Vertx
#	http://vertx.io/
#       Vert.x is a lightweight, high performance application platform
#       for the JVM that's designed for modern mobile, web, and
#       enterprise applications.
#--------------------------------------------------------------------

# Vertx jars used by Vert.x modules in ptolemy/actor/lib/jjs
PTVERTX_JARS=

# Set to vertx if the Vertx jars are found
PTVERTX_DIR=

# Set to eventbus if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTEVENTBUS_DIR=

# Set to httpClient if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTHTTPCLIENT_DIR=

# Set to userInterface if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTUSERINTERFACE_DIR=

# Set to textDisplay if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTTEXTDISPLAY_DIR=

# Set to socket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTVERTX_SOCKET_DIR=

# Set to udpSocket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTUDPSOCKET_DIR=

# Set to webSocket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
PTWEBSOCKET_DIR=

# Set to packages that use Vert.x and used in $PTII/doc/makefile if the Vert.x jars are found
PTVERTX_PACKAGES=

# We only need to look for the Vertx jar files if PTWEBSOCKET_USER_DIR are present.
PTWEBSOCKET_USER_DIR="$PTII/ptolemy/actor/lib/jjs/modules/webSocket"

if test ! -d "$PTWEBSOCKET_USER_DIR"; then
    PT_MSG_STATUS([$PTWEBSOCKET_USER_DIR is not present,
    so we need not find the Vertx application platform interface.])
else
    # PRE_JDK18 is set above.
    if test "$PRE_JDK18" = "yes"; then
        AC_MSG_WARN([Vertx requires Java 1.8 or later, you are running $JVERSION.
    Vertx is the application platform interface used in Accessor modules in ptolemy/actor/lib/jjs/modules.
    To use Vertx, choose a Java 1.8 or later JVM and rerun configure.])

    else

        AC_MSG_CHECKING([for the Vertx application platform interface. ])
        AC_ARG_WITH(oscp5, [  --with-vertx=LIB       use vertx jars from JAR,
                              defaults to \$PTII/lib],
            PTVERTX_JAR_DIR=$withval,
        PTVERTX_JAR_DIR=$PTII/lib)
            if test -d "$PTVERTX_JAR_DIR"; then
	    PTEVENTBUS_DIR=eventbus
            PTHTTPCLIENT_DIR=httpClient
            PTHTTPSERVER_DIR=httpServer
            PTTEXTDISPLAY_DIR=textDisplay
            PTUDPSOCKET_DIR=udpSocket
            PTUSERINTERFACE_DIR=userInterface
            PTVERTX_SOCKET_DIR=socket
    	    PTVERTX_DIR=vertx
	    PTWEBSOCKET_DIR=webSocket
	    # Keep these alphabetic

# Use changequote here to preserve square brackets
changequote(<<, >>)dnl
            # Vert.x 3.x jars:
            jars="hazelcast-*.jar jackson-annotations-*.jar jackson-core-*.jar jackson-databind-*.jar netty-buffer-*.jar netty-codec-[^dh]*.jar netty-codec-dns-*.jar netty-codec-http-*.jar netty-codec-http2-*.jar netty-common-*.jar netty-handler-*.jar netty-resolver-[0-9]*.jar netty-resolver-dns-*.jar netty-transport-*.jar vertx-codegen-*.jar vertx-core-*.jar vertx-hazelcast-*.jar vertx-lang-groovy-*.jar vertx-lang-js-*jar vertx-lang-ruby-*.jar vertx-service-proxy-*.jar vertx-web-*jar"
changequote([, ])dnl

            for jar in $jars
    	    do
# Use changequote here to preserve square brackets
changequote(<<, >>)dnl
	        file=`find "$PTVERTX_JAR_DIR" -name "$jar"`
changequote([, ])dnl
                if test -z $file; then
                    AC_MSG_WARN([Hmm, while searching for Vert.x jar files, could not find $jar?]);
                fi
	        if test -e $file -a -f $file; then
	            PTVERTX_JARS="$PTVERTX_JARS\${CLASSPATHSEPARATOR}$file"
		    # If we don't find all the jars, then the classpath will have some of them.
		    # However, it is better to do this here in case the paths have spaces in them.
		    updateClasspath "$file"
	         else
	            AC_MSG_WARN([Failed to the Vertx file $jar in $PTVERTX_JAR_DIR.])
	            PTEVENTBUS_DIR=
                    PTHTTPCLIENT_DIR=
                    PTHTTPSERVER_DIR=
                    PTTEXTDISPLAY_DIR=
                    PTUDPSOCKET_DIR=
                    PTUSERINTERFACE_DIR=
                    PTVERTX_SOCKET_DIR=
    	            PTVERTX_DIR=
	            PTWEBSOCKET_DIR=
	            break;
                 fi
            done
        fi

        if test ! -z "$PTVERTX_DIR"; then
	    PT_MSG_RESULT([$PTVERTX_JARS])
            # org.terraswarm.accessor depends on jjs/JavaScript.java so we
            # list org.terraswarm.accessor with jjs/JavaScript
	    PTVERTX_PACKAGES="org.terraswarm.accessor ptolemy.actor.lib.jjs.modules.eventbus ptolemy.actor.lib.jjs.modules.httpClient ptolemy.actor.lib.jjs.modules.httpServer ptolemy.actor.lib.jjs.modules.socket ptolemy.actor.lib.jjs.modules.textDisplay ptolemy.actor.lib.jjs.modules.udpSocket ptolemy.actor.lib.jjs.modules.userInterface ptolemy.actor.lib.jjs.modules.webSocket"
        fi
    fi
fi

if test -z "$PTVERTX_DIR"; then
    updateExcludes "ptolemy/actor/lib/jjs/modules/eventbus/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/httpClient/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/httpServer/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/socket/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/udpSocket/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/userInterface/"
    updateExcludes "ptolemy/actor/lib/jjs/modules/webSocket/"
    if test -d "$PTVERTX_USER_DIR" -o -d "$PTWEBSOCKET_USER_DIR"; then
        AC_MSG_WARN([Failed to find the the Vertx application platform interface jar files,
    or a version of Java before 1.8 was found
    so ptolemy.actor.lib.jjs.modules.{browser,eventbus,httpClient,httpServersocket,udpSocket,webSocket}
    will not be compiled.
    Vertx consists of a number of jar files that are typically in $PTII/lib.])
    fi
fi

#--------------------------------------------------------------------
#       WABA is the JDK for PalmOS
#	See if there was a command-line option for where
#       wabask is;  if not,
#       check to see if $PTII/vendors/misc/waba/wabasdk exists
#--------------------------------------------------------------------

# PTWABA_DIR is set to waba and used in
# $PTII/ptolemy/makefile if waba was found
PTWABA_DIR=
#
# We only need to look for waba if $PTII/ptolemy/apps/kvm exists
if test ! -d "$PTII/ptolemy/apps/kvm"; then
    PT_MSG_STATUS([$PTII/ptolemy/apps/kvm is not present,
    so we need not find the PalmOS waba.])
    WABA_DIR='${PTII}/vendors/misc/waba/wabasdk'
    # Unfortunately, j2me_cldc does not ship with a jar of zip file
    # It needs to be built
    WABA_CLASSES='$(WABA_DIR)/classes'
else
    AC_MSG_CHECKING([for waba directory])
    AC_ARG_WITH(waba, [  --with-waba=DIR       use PalmOS WABA from DIR,
                          defaults to \$PTII/vendors/misc/waba/wabasdk],
	WABA_DIR=$withval,
	WABA_DIR=$PTII/vendors/misc/waba/wabasdk)

    if test -d "$WABA_DIR"; then
	PT_MSG_RESULT([$WABA_DIR])
        AC_MSG_CHECKING([for \$WABA_DIR/classes])
	if test -d "$WABA_DIR/classes"; then
	    WABA_CLASSES='$(WABA_DIR)/classes'
	    PT_MSG_RESULT([$WABA_CLASSES])
        else
	    WABA_CLASSES=no
        fi
    else
	PT_MSG_RESULT([Not found in $WABA_DIR])
	AC_MSG_CHECKING([for waba directory in /waba])
	# Likely place for waba under windows
	WABA_DIR=/waba/wabasdk
        if test -d "$WABA_DIR"; then
	    PT_MSG_RESULT([$WABA_DIR])
            AC_MSG_CHECKING([for \$WABA_DIR/classes])
	    if test -d "$WABA_DIR/classes"; then
	        WABA_CLASSES='$(WABA_DIR)/classes'
	        PT_MSG_RESULT([$WABA_CLASSES])
            else
	        WABA_CLASSES=no
            fi
        else
		WABA_CLASSES=no
        fi

    fi
    if test "$WABA_CLASSES" = "no"; then
        AC_MSG_WARN([Failed to find waba/wabasdk
    perhaps Waba is not installed?
    You need not download Waba unless you plan on building applications
    for the Palm Pilot or Handspring Visor.
    Waba can be downloaded from http://www.wabasoft.com])
	# Note that we don't substitute in the ${PTII} or $(WABA_DIR) here
	WABA_DIR='${PTII}/vendors/misc/waba/wabasdk'
   	WABA_CLASSES='$(WABA_DIR)/classes'
    else
	# Set to waba and used in
	# $PTII/ptolemy/makefile if waba was found
	PTWABA_DIR=waba
    fi
fi

#--------------------------------------------------------------------
#       webcam-capture is used by the webcam accessor
#	Source may be found at 
#--------------------------------------------------------------------

# Set to cameras and used in ptolemy/actor/lib/jjs/modules/makefile
# if webcam-capture*.jar and other jar files are found.
PTCAMERAS_DIR=

# Jar files used in ptolemy/actor/lib/jjs/modules/webcam/makefile
PTWEBCAMCAPTURE_JARS=

# PTWEBCAMCAPTURE_PACKAGES is used in doc/makefile
PTWEBCAMCAPTURE_PACKAGES=

# We only need to look for webcam-capture if $PTII/ptolemy/actor/lib/jjs/modules/cameras is present
WEBCAMCAPTURE_USER_DIR=$PTII/ptolemy/actor/lib/jjs/modules/cameras

# We only need to look for xbjlib if $PTII/ptolemy/actor/lib/jjs/modules/xbee is present.
# XBJLIB is here because both xbjlib and webcam-capture use slf4j-api and sl4j-nop.
XBJLIB_USER_DIR="$PTII/ptolemy/actor/lib/jjs/modules/xbee"

# Look for slf4j-api and slf4j-simple jar files
PTSLF4J_API_JAR=""
PTSLF4J_SIMPLE_JAR=""
if test -d "$WEBCAMCAPTURE_USER_DIR" -o -d "$XBJLIB_USER_DIR"; then
    AC_MSG_CHECKING([for slf4-api])
    AC_ARG_WITH(slf4j-api, [  --with-slf4j-api=SLF4J_API_JAR     use slf4j-api SLF4J_API_JAR
                          defaults to \$PTII/lib/slf4j-api-1.7.13.jar],
	PTSLF4J_API_JAR=$withval,
	PTSLF4J_API_JAR=$PTII/lib/slf4j-api-1.7.13.jar)
    if test -f "$PTSLF4J_API_JAR"; then
        PT_MSG_RESULT([$PTSLF4J_API_JAR])
        updateClasspath "$PTSLF4J_API_JAR"
        AC_MSG_CHECKING([for slf4-simple])
        AC_ARG_WITH(slf4j-simple, [  --with-slf4j-simple=SLF4J_SIMPLE_JAR     use slf4j-simple SLF4J_SIMPLE_JAR
                              defaults to \$PTII/lib/slf4j-simple-1.7.13.jar],
	    PTSLF4J_SIMPLE_JAR=$withval,
	    PTSLF4J_SIMPLE_JAR=$PTII/lib/slf4j-simple-1.7.13.jar)
        if test -f "$PTSLF4J_SIMPLE_JAR"; then
            PT_MSG_RESULT([$PTSLF4J_SIMPLE_JAR])
            updateClasspath "$PTSLF4J_SIMPLE_JAR"
        else
            AC_MSG_WARN([Failed to find $PTSLF4J_SIMPLE_JAR, so the accessors in
    $WEBCAMCAPTURE_USER_DIR and $XBJLIB_USER_DIR will not work.])
        fi
    else
        AC_MSG_WARN([Failed to find $PTSLF4J_API_JAR, so the accessors in
    $WEBCAMCAPTURE_USER_DIR and $XBJLIB_USER_DIR will not work.])
    fi

fi

# We only need to look for webcam-capture*.jar if the directory that uses it exists.
if test ! -d "$WEBCAMCAPTURE_USER_DIR"; then
    PT_MSG_STATUS([$WEBCAMCAPTURE_USER_DIR is not present,
    so we need not find webcam-capture.])
else
    if test ! -z "$PTSLF4J_API_JAR" -a ! -z "$PTSLF4J_SIMPLE_JAR"; then
        AC_MSG_CHECKING([for webcam-capture])
        AC_ARG_WITH(webcam-capture, [  --with-webcam-capture=WEBCAMCAPTURE_JAR     use webcam-capture WEBCAMCAPTURE_JAR
                          defaults to \$PTII/lib/webcam-capture-0.3.12.jar],
	    PTWEBCAMCAPTURE_JAR=$withval,
	    PTWEBCAMCAPTURE_JAR=$PTII/lib/webcam-capture-0.3.12.jar)

        if test -f "$PTWEBCAMCAPTURE_JAR"; then
            PTBRIDG_JAR="$PTII/lib/bridj-0.7.0.jar"
            if test -f "$PTBRIDG_JAR"; then
                PT_MSG_RESULT([$PTWEBCAMCAPTURE_JAR])
                PTCAMERAS_DIR=cameras
                PTWEBCAMCAPTURE_JARS="$PTWEBCAMCAPTURE_JAR\${CLASSPATHSEPARATOR}$PTBRIDG_JAR"
                PTWEBCAMCAPTURE_PACKAGES=ptolemy.actor.lib.jjs.modules.cameras
                updateClasspath "$PTWEBCAMCAPTURE_JAR"
                updateClasspath "$PTBRIDG_JAR"
            else
                AC_MSG_WARN([Failed to find $PTBRIDG_JAR
   perhaps webcam-capture was not installed from
   https://github.com/sarxos/webcam-capture?
   The webcam accessor will not be compiled.])
           fi
        else
            AC_MSG_WARN([Failed to find $PTWEBCAMCAPTURE_JAR
   perhaps webcam-capture was not installed from
   https://github.com/sarxos/webcam-capture?
   The webcam accessor will not be compiled.])
	PTWEBCAMCAPTURE_JARS=
        fi
    fi
fi

if test -z "$PTCAMERAS_DIR"; then
   updateExcludes "ptolemy/actor/lib/jjs/modules/cameras/"
fi

#--------------------------------------------------------------------
#       XBee are wireless devices that are connected to via serial
#       We are using nrjavaserial from https://github.com/NeuronRobotics/nrjavaserial/, so we have our own custom version of xbjlib.
#       See https://chess.eecs.berkeley.edu/ptexternal/wiki/Main/XBee
#--------------------------------------------------------------------
# We only need to look for xbjlib if $PTII/ptolemy/actor/lib/jjs/modules/xbee is present
# See the webcam-capture section for the setting of XBJLIB_JAR
XBJLIB_JAR_DEFAULT='${PTII}/lib/xbjlib-1.1.0.nrjavaserial.jar'

# Jar files used in ptolemy/actor/lib/jjs/modules/xbee/makefile
PTXBJLIB_JARS=

# PTXBEE_DIR is set to xbee and used in 
# $PTII/ptolemy/actor/lib/jjs/modules/makefile if the XBee Java Interface was found
PTXBEE_DIR=
if test ! -d "$XBJLIB_USER_DIR"; then
    PT_MSG_STATUS([$XBJLIB_USER_DIR is not present,
    so we need not find the XBee xbjlib.])
    # Use curly brackets around PTII so that if xbjlib is not present
    # then ${PTII} will appear in ptinvoke.
else
    if test ! -z "$PTSLF4J_API_JAR" -a ! -z "$PTSLF4J_SIMPLE_JAR"; then
        AC_MSG_CHECKING([for xbjlib directory])
        AC_ARG_WITH(rxtx, [  --with-xbjlib=DIR       use Java Serial Port Interface rxtx from DIR,
                          defaults to $XBJLIB_JAR_DEFAULT],
	    XBJLIB_JAR=$withval,
	    XBJLIB_JAR=$PTII/lib/xbjlib-1.1.0.nrjavaserial.jar)

        if test -f "$XBJLIB_JAR"; then
            PT_MSG_RESULT($XBJLIB_JAR)
            PTXBEE_DIR=xbee
            # PTXBJLIB_PACKAGES is used in ptII/doc/makefile
            PTXBJLIB_PACKAGES="ptolemy.actor.lib.jjs.modules.xbee"
            PTXBJLIB_JARS="$XBJLIB_JAR"
            updateClasspath "$XBJLIB_JAR"
        else 
	    AC_MSG_RESULT([Did not find 
    '$XBJLIB_JAR'])
        fi
    fi
fi

if test -d "$XBJLIB_USER_DIR"; then
    if test -z "$PTXBEE_DIR"; then
        AC_MSG_WARN([$XBJLIB_USER_DIR exists, but the XBee Java Library xbjlib is not installed?
        You need not use xbjlib unless you plan on using the XBee Accessor
        in ptolemy/actor/lib/jjs/modules/xbee])
        XBJLIB_JAR="$XBJLIB_JAR_DEFAULT"
        updateExcludes "ptolemy/actor/lib/jjs/modules/xbee"
    fi
fi 

#--------------------------------------------------------------------
#       libexpat is used by the lbnl simulation interface in ptII/lbnl
#--------------------------------------------------------------------

# The include and lib dirs for libexpat
LIBEXPAT_INCLUDE_DIR=
LIBEXPAT_LIB_DIR=

# PTLIBEXPAT_DIR is set util if LIBEXPAT_INCLUDE_DIR and LIBEXPAT_LIB_DIR are set
PTLIBEXPAT_DIR=

# PTLBNL_DIR is set to lbnl if LIBEXPAT_INCLUDE_DIR and LIBEXPAT_LIB_DIR are set
PTLBNL_DIR=

LIBEXPAT_USER_DIR=$PTII/lbnl/lib/util
if test ! -d "$LIBEXPAT_USER_DIR"; then
    PT_MSG_STATUS([$LIBEXPAT_USER_DIR is not present,
    so we need not find libexpat.])
else
    # Cygwin gcc can be used to compile files that do not link
    # with Java, so we don't need mingw here
    AC_PATH_PROG(PTCC, gcc)
    if test "${PTCC:-none}" = "none"; then
        AC_MSG_WARN([Failed to find gcc])
        AC_PATH_PROG(PTCC, cc)
        if test "${PTCC:-none}" != "none"; then
            PT_MSG_RESULT([$PTCC])
        else    
            AC_MSG_WARN([Failed to find gcc or cc, so we will
    not be able use LIBEXPAT in $LIBEXPAT_USER_DIR]);
        fi
    fi

    if test "${PTCC:-none}" != "none"; then
       AC_MSG_CHECKING([for libexpat])
       # FIXME: This will not work if $PTII has spaces
       dirs="$PTII/vendors/libexpat /usr/local/lib /usr/lib64 /usr/lib /lib"
       for dir in $dirs
       do
	   # Mac OS X could have jnilib or dylib,
	   # Cygwin has /usr/lib/libexpat.dll.a
	   # Ubuntu could have .so.2 or /usr/lib/x86_64-linux-gnu/libexpat.so
	   if test -d $dir; then
	       libexpat=`$FIND $dir -name "libexpat.${PTJNI_SHAREDLIBRARY_SUFFIX}" -o -name "libexpat.${PTJNI_SHAREDLIBRARY_SUFFIX2}" | head -1`

               if test -f "$libexpat"; then
                   PT_MSG_RESULT([$libexpat}])
	           LIBEXPAT_LIB_DIR=`dirname $libexpat`
	           break;
               fi
           fi
       done
       if test ! -d "$LIBEXPAT_LIB_DIR"; then
           AC_MSG_WARN([Failed to find libexpat.${PTJNI_SHAREDLIBRARY_SUFFIX}
    The LBNL Simulation facility in \$PTII/lbnl/lib/util requires libexpat.
    However, Ptolemy will run without this facility.])
       fi
    fi
    AC_MSG_CHECKING([for expat.h])
    AC_ARG_WITH(expat-include, [  --with-expat-include=DIR       use expat.h from DIR
                          defaults to /usr/include],
	LIBEXPAT_INCLUDE_DIR=$withval,
	LIBEXPAT_INCLUDE_DIR=/usr/include)

    if test -f "$LIBEXPAT_INCLUDE_DIR/expat.h"; then
       PT_MSG_RESULT([$LIBEXPAT_INCLUDE_DIR/expat.h])
    else 
       # FIXME: This will not work if $PTII has spaces
       dirs="$PTII/vendors/libexpat /usr/local/include /usr/include"
       for dir in $dirs
       do
           if test -f "$dir/expat.h"; then
               LIBEXPAT_INCLUDE_DIR=$dir
	       PT_MSG_RESULT([$LIBEXPAT_INCLUDE_DIR/expat.h])
           fi
       done
       if test ! -f "$LIBEXPAT_INCLUDE_DIR/expat.h"; then
           AC_MSG_WARN([Failed to find expat.h
    Checked the following directories:
    $dirs
    The LBNL Simulation facility in \$PTII/lbnl/lib/util requires libexpat.
    However, Ptolemy will run without this facility.])
       fi
   fi
fi

if test -f "$LIBEXPAT_INCLUDE_DIR/expat.h" -a -d "$LIBEXPAT_LIB_DIR"; then
    # Used in $PTII/lbnl/lib/makefile
    PTLIBEXPAT_DIR=util
    # Used in $PTII/makefile
    PTLBNL_DIR=lbnl
    # Used in lbnl/demo/makefile because make can call make on lib/util
    PTLBNL_CROOM_DIR=CRoom
    PTLBNL_CROOM_JAR=CRoom/CRoom.jar
    # Set to the lbnl jars that need to be signed if libexpat was found
    # and used in jnlp.mk.
    PTLBNL_JARS="lbnl/lbnl.jar lbnl/demo/demo.jar"
    # Used in $PTII/doc/makefile
    PTLBNL_PACKAGES="lbnl.actor.lib lbnl.actor.lib.net lbnl.lib.labview lbnl.lib.xml.src lbnl.util"

    if test -d "$FMIPP_USER_DIR"; then
        if test -f "$PTBOOST_INCLUDE_DIR/boost/numeric/odeint.hpp"; then
            PTBOOST=yes
	    PTFMIPP_DIR=fmipp
	    PTFMIPP_PACKAGES="ptolemy.actor.lib.fmi.fmipp ptolemy.actor.lib.fmi.fmipp.swig"
        else
            AC_MSG_WARN([Failed to find boost/numeric/odeint.hpp, so FMI ++
    will not be compiled. FMI++ is an extension of the
    Functional Mockup Interface, see
    http://sourceforge.net/p/fmipp/wiki/Home/])
            updateExcludes "ptolemy/actor/lib/fmi/fmipp/"
        fi
    fi
fi

# Packages to exclude from Ant targets that call javadoc
ANT_JAVADOC_EXCLUDEPACKAGENAMES=`echo "$ANT_ALWAYS_EXCLUDE $ANT_EXCLUDE"| sed 's@<exclude name="@@g' | sed 's@" */>@@g' | sed 's@/@.@g' | awk '{for (i=1;i <= NF; i++) { if ($i !~ /\*\*/) {printf("%s*,", $i)}}}'`


# Warnings about $PTII being set incorrectly
if test ! -f confdefs.h; then
   AC_MSG_WARN([confdefs.h was not found.  Typically, this
    could happen if \$PTII ($PTII) is not the same as the
    current directory (`pwd`)])
fi

if test ! -z "$FINAL_WARNING"; then
   echo "CRITICAL WARNING: $FINAL_WARNING"
   echo "Please fix the above before attempting to build."
fi   


# Keep these substitutions alphabetical, with a description

# Ant directive for JavaC 9 to add --add-modules.
AC_SUBST(ANT_JAVAC_COMPILERARG) 

# Path to the ant binary, stored in lib/ptII.properteries, used while importing accessors in org/terraswarm/accessor/JSAccessor.java
AC_SUBST(ANT_PATH)

# Paths to always exclude in Ant's build.xml
AC_SUBST(ANT_ALWAYS_EXCLUDE)

# Jar files to include in Ant's build.xml
AC_SUBST(ANT_CLASSPATH)

# Paths to exclude in Ant's build.xml
AC_SUBST(ANT_EXCLUDE)

# Paths of tests to exclude in Ant's build.xml
AC_SUBST(ANT_EXCLUDE_TESTS)

# Packages to exclude from Ant targets that call javadoc
AC_SUBST(ANT_JAVADOC_EXCLUDEPACKAGENAMES)

# Variables used in build.xml by Ant to run Mav
AC_SUBST(ANT_MAVEN_ARTIFACT)
AC_SUBST(ANT_MAVEN_SUBPROJECTS)
AC_SUBST(ANT_MAVEN_BUILD_WEBSENSOR)
AC_SUBST(ANT_WEBSENSOR_FILESET)
AC_SUBST(ANT_WEBSENSOR_SOURCEPATH)
AC_SUBST(ANT_WEBSENSOR_SRC)

# Path of directories that contain source, used by the Ant's build rule.
AC_SUBST(ANT_SRC)

# Directory that contains the Caltrop jar file ptCal.jar
# used by bin/ptinvoke.in
AC_SUBST(CALTROP_DIR)

# The directory that contains the Checkstyle jar file.  Used in build.xml.in.
AC_SUBST(CHECKSTYLE_DIR)

# The Checkstyle jar file, used for code coverage.  Used in build.xml.in.
AC_SUBST(CHECKSTYLE_JAR)

# Directory that contains chic.jar.
# Chic is a modular verifier for behavioral compatibility checking of
# software and hardware components.
# Used in bin/ptinvoke.in
AC_SUBST(CHIC_DIR)

# Separator in CLASSPATH,  For Unix, this should be :, for Cygwin use ;
AC_SUBST(CLASSPATHSEPARATOR)

# Directory that contains colt.jar
# Colt is a "Open Source Libraries for High Performance Scientific
# and Technical Computing in Java" used in bin/ptinvoke.in
AC_SUBST(COLT_DIR)

# The directory that contains the Cobertura jar file.  Used in build.xml.in.
AC_SUBST(COBERTURA_DIR)

# The Cobertura jar file, used for code coverage.  Used in build.xml.in.
AC_SUBST(COBERTURA_JAR)

# Directory that contains the CaffeineMark Java Benchmark kit
# used by C code generation in copernicus/c
AC_SUBST(CMKIT_DIR)

# Text for .classpath.  Under all platforms other than Mac OS X, this will be:
# <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
# Under Mac OS X, the plug-ins will not work in the project, see
# http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Mac#EclipseProblems
AC_SUBST(ECLIPSE_CLASSPATHENTRY_PDE_REQUIREDPLUGINS)

# Location of Eclipse, which is used by ptolemy/backtracking
AC_SUBST(ECLIPSE_DIR)

# Location of GNU Awk, used by maven
AC_SUBST(GAWK)

# Directory that contains gc.h, used in copernicus/c
AC_SUBST(GC_INCLUDE_DIR)

# GC_LD_DIRECTIVE is set to the values to pass to cc or ld if
# GC_malloc() can be found either in the default compiler location
# or in $PTII/lib.
# GC_LD_DIRECTIVE is used in ptolemy/copernicus/c/
AC_SUBST(GC_LD_DIRECTIVE)

# Eclipse .classpath excluding src values
# of the form "vendors/|ptolemy/matlab/"
AC_SUBST(ECLIPSE_EXCLUDING_SRC)

# Eclipse .classpath lib elements of the format
#    <classpathentry kind="lib" path="lib/diva.jar"/>
AC_SUBST(ECLIPSE_CLASSPATHENTRY_LIBS)

# ImageJ jar file
AC_SUBST(IMAGEJ_JAR)

# Jar files for Java Advanced Imaging (JAI) used by ptolemy/actor/lib/jai/makefile
AC_SUBST(JAI_JARS)

# The jar command
AC_SUBST(JAR)

# Command to run that indexes a jar file named tmp.jar
# Usually it looks like '"$(JAR)" -i $@'
AC_SUBST(JAR_INDEX)

# The jarsigner command is used to create signed jar files for Webstart JNLP files
AC_SUBST(JARSIGNER)

# Location of rt.jar, usually $(PTJAVA_HOME)/lib/rt.jar
# However, we have to be careful of backslashes and /cygwin
# Soot uses this variable to find java.lang.Object
AC_SUBST(JAVA_SYSTEM_JAR)

# JAVA3D_JARS is the jar files to use with Java 3D.  Usually, this is
# empty, because most installations have Java 3D in the jdk
# jre/lib/ext directory, but some do not. If --with-java3D was used
# with configure, then JAVA3D_JARS will be set to include the jars.
AC_SUBST(JAVA3D_JARS)

# javac binary
AC_SUBST(JAVAC)

# javacc binary
AC_SUBST(JAVACC)

# Java 9 --add-modules directive for javax.xml.bind.DatatypeConverter.
AC_SUBST(JAVAC_MODULES)

# javacc command line arguments, -STATIC=false if javacc is 5.0 or later.
AC_SUBST(JAVACC_OPTIONS)

# Directory that contains JavaCC, which is used in ptolemy/data/expr
AC_SUBST(JAVACC_DIR)

# The JavaCV jar file, used in actor/lib/opencv/javacv for computer vision
AC_SUBST(JAVACV_JAR)

# The javadoc binary, used to create html documentation of java classes.
AC_SUBST(JAVADOC)

# The javah binary, used by jni for matlab.
AC_SUBST(JAVAH)

# The javaws command is used to test Webstart JNLP files.
AC_SUBST(JAVAWS)

# Location of jce.jar, usually $(PTJAVA_HOME)/lib/jce.jar
# Java 1.5 has javax.crypto.Cipher in jce.jar
# However, we have to be careful of backslashes and /cygwin
# Soot uses this variable to find java.lang.Object
AC_SUBST(JAVAX_CRYPTO_JAR)

# If we are running under JDK1.4, then set JDOCBREAKITERATOR = -breakiterator
AC_SUBST(JDOCBREAKITERATOR)

# Ptalon uses generics, if we are running JDK1.5,
# then JDOCSOURCEFLAGS = -source 1.5
AC_SUBST(JDOCSOURCEFLAGS)

# If we can compile in doc/doclets, we set JDOCTAG appropriately
# and use JDOCTAG in doc/makefile
AC_SUBST(JDOCTAG)

# If we can compile in doc/doclets, we set JDOCTAGLET appropriately
# and use JDOCTAGLET in doc/makefile
AC_SUBST(JDOCTAGLET)

# Jini home directory, see https://jini.dev.java.net/
AC_SUBST(JINI_DIR)

# If Jini is present, the set to yes, otherwise, set to no
AC_SUBST(JINI_PRESENT)

# Jar file that contains Joystick interface,
# see http://sourceforge.net/projects/javajoystick/
AC_SUBST(JOYSTICK_JAR)

# jtclsh script, used for test suites
AC_SUBST(JTCLSH)

# jjtree binary
AC_SUBST(JJTREE)

# jjtree command line arguments, -STATIC=false if javacc is 5.0 or later.
AC_SUBST(JJTREE_OPTIONS)

# JDK Version determined by running confTest.class and getting java.version
AC_SUBST(JVERSION)

# The Major and Minor version of the JDK.  1.6, 1.8 etc.  Used by ant in build.xml.in.
AC_SUBST(JVERSION_TARGET)

# Jar files for Java Media Framework (JMF) used by ptolemy/actor/lib/makefile
AC_SUBST(JMF_JARS)

# Directory that contains JModelica.
AC_SUBST(JMODELICA_HOME)

# Java Native Access jar file (jna.jar).  See
# https://jna.dev.java.net/.  Used in ptolemy/actor/lib/opencv
AC_SUBST(JNA_JAR)

# jode.jar used in bin/ptinvoke to start up Jode, the .class disassembler
AC_SUBST(JODE_CLASSES)


# Used in many test/makefiles
AC_SUBST(JUNIT_JARS)

# Jython home directory that contains jython.jar, see http://www.jython.org
AC_SUBST(JYTHON_DIR)

# keytool command used to generate a certificate for testing actor.lib.security actors
AC_SUBST(KEYTOOL)

# The Kieler jar file, used to layout models
AC_SUBST(KIELER_JAR)

# kvm/tools/classes.jar file used by the PalmOS KVM
AC_SUBST(KVM_CLASSES)

# Directory that contains the kvm used by PalmOS
AC_SUBST(KVM_DIR)

# Set to the location of the lejos installation, usually in
# $PTII/vendors/lejos
AC_SUBST(LEJOS_DIR)

# Set to the directory that contains expat.h and used in $PTII/lbnl/lib/util
AC_SUBST(LIBEXPAT_INCLUDE_DIR)

# Set to the directory that contains libexpat.{so,jnilib,dll} and used in $PTII/lbnl/lib/util
AC_SUBST(LIBEXPAT_LIB_DIR)

# The major type of OS we are running under.
# Under all forms Windows, this should be Windows; ynder Linux: Linux, etc.
# Used in ptolemy/matlab/makefile
AC_SUBST(MAJOR_OS_NAME)

# Set to the location of the matlab installation, e.g. /matlabr11
# This directory usually contains bin,...
AC_SUBST(MATLAB_DIR)

# Set the location of Matlab's engine libraries
AC_SUBST(MATLAB_LIBDIR)

# Set the location of Matlab's engine libraries (64bit)
AC_SUBST(MATLAB_64LIBDIR)

# Mysql Java Database jar (mysql-connector-java-5.1.6-bin.jar),
# used by domains/space and actor/lib/database
AC_SUBST(MYSQL_JAR)

# Jar file for Open Computer Vision (OpenCV)
AC_SUBST(OPENCV_JAR)

# Oracle Java Database jar (ojdbc6.jar), used by domains/space
# and actor/lib/database
AC_SUBST(ORACLE_OJDBC_JAR)

# Set to $PTII/lib if $PTII/lib/mapss.jar was found and used
# in $PTII/bin/ptinvoke.in
AC_SUBST(PSDF_DIR)

# Set to accessor and used in org/terraswarm/accessors/makefile if Nashorn is found.
AC_SUBST(PTACCESSOR_DIR)

# Set to ptango if jetty and javax.servlet jar files are found.
# Used in org/ptolemy/makefile.
AC_SUBST(PTANGO_DIR)

# Jar files for Ptango.
AC_SUBST(PTANGO_JARS)

# PTANGO_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTANGO_PACKAGES)

# Set to backtrack if Java 1.5 or later is present
AC_SUBST(PTBACKTRACK_DIR)

# Set to eclipse if Eclipse was found
AC_SUBST(PTBACKTRACK_ECLIPSE_DIR)

# Plugin Eclipse jar files, used by $PTII/doc
AC_SUBST(PTBACKTRACK_ECLIPSE_DOC_JARS)

# Eclipse jar files used by ptolemy/backtrack 
AC_SUBST(PTBACKTRACK_ECLIPSE_JARS)

# Ptolemy II packages that use Eclipse
# PTBACKTRACK_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTBACKTRACK_ECLIPSE_PACKAGES)

# Set to the directory that contains boost/numeric/odeint.hpp
# and used in actor/lib/fmi/fmipp
AC_SUBST(PTBOOST_INCLUDE_DIR)

# Set to the BSH jar file and used to compile org/mlc
AC_SUBST(PTBSH_JAR)

# Set to mlc and used in $PTII/org/makefile if Java Bean Shell is found.
AC_SUBST(PTBSH_MLC_DIR)

# PTBSH_RUN_DIR is set to run and used in
# $PTII/ptolemy/actor/gui/makefile if bsh.jar was found.
AC_SUBST(PTBSH_RUN_DIR)

# Set to the packages that require bsh and used in $PTII/doc/makefile
AC_SUBST(PTBSH_PACKAGES)

# Set to caltrop and used in $PTII/ptolemy/makefile if Cal was found.
AC_SUBST(PTCALTROP_DIR)

# Set to cameras and used in ptolemy/actor/lib/jjs/modules/makefile
# if webcam-capture*.jar and other jar files are found.
AC_SUBST(PTCAMERAS_DIR)

# Set to gcc if gcc was found and used in $PTII/ptolemy/matlab/makefile.
AC_SUBST(PTCC)

# Set to mingw32-gcc or gcc and used in $PTII/ptolemy/matlab/makefile and jni
AC_SUBST(PTCCJNI)

# Set to chic and used in $PTII/ptolemy/makefile if chic was found.
AC_SUBST(PTCHIC_DIR)

# PTCM_DIR is set to cm and used in $PTII/ptolemy/copernicus/c/test/makefile
# if the CaffeineMark Java Benchmark kit is found
AC_SUBST(PTCM_DIR)


# Set to colt and used in $PTII/ptolemy/actor/lib/makefile if colt was found.
AC_SUBST(PTCOLT_DIR)

# Colt jar files.  We ship $PTII/lib/ptcolt.jar, which is a subset
# of $PTII/vendors/misc/colt.jar
AC_SUBST(PTCOLT_JARS)

# Ptolemy II packages that use COLT
# PTCOLT_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTCOLT_PACKAGES)

# PTCOMM_DIR is set to comm and used in 
# $PTII/ptolemy/actor/lib/makefile if the Java Communications API was found
#
AC_SUBST(PTCOMM_DIR)

# Ptolemy II packages that use the Java Serial Communication facility
# PTCOMM_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTCOMM_PACKAGES)

# Set to copernicus and used in $PTII/ptolemy/makefile if Soot was found
AC_SUBST(PTCOPERNICUS_DIR)

# PTCORBA_DIR is used in ptolemy/actor/makefile
AC_SUBST(PTCORBA_DIR)

# PTCORBA_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTCORBA_PACKAGES)

# PTCUNIT_DIR is set to test and used in 
# ptolemy/cg/kernle/generic/program/procedural/c/type
# if CUnit is found
AC_SUBST(PTCUNIT_DIR)

# PTDATABASE_DIR is set to database and used in
# $PTII/ptolemy/actor/lib/makefile if ojdbc6.jar was found.
AC_SUBST(PTDATABASE_DIR)

# PTDATABASE_JNLP_JARS is set to the database jars that need to be signed
# and used in mk/jnlp.mk
AC_SUBST(PTDATABASE_JNLP_JARS)

# PTDATABASE_PACKAGES is set if ojdbc6.jar was found and 
# used in ptII/doc/makefile
AC_SUBST(PTDATABASE_PACKAGES)

# PTDB_DIR is set to ptdb and used in
# $PTII/makefile if dbxml is found
AC_SUBST(PTDB_DIR)

# PTDB_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTDB_PACKAGES)

# PTDBXML_JARS includes dbxml.jar and db.xml and is used by $PTII/ptdb
AC_SUBST(PTDBXML_JARS)

# Directory that contains libdbxml-X.Y.{so,dll,dylib}.  Used in $PTII/ptdb
AC_SUBST(PTDBXML_LIB)

# Set to distributed and used in
# $PTII/ptolemy/makefile if jini was found
AC_SUBST(PTDISTRIBUTED_DIR)

# Set to jini jar file and used
# $PTII/ptolemy/distributed/*/makefile if jini was found
AC_SUBST(PTDISTRIBUTED_JARS)

# Ptolemy II packages that use the distributed
# PTDISTRIBUTED_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTDISTRIBUTED_PACKAGES)

# PTDOCLETS_DIR is set to doclets and used in 
# $PTII/doc if tools.jar can be found.
AC_SUBST(PTDOCLETS_DIR)

# Set to eventbus if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTEVENTBUS_DIR)

# PTEXCEL_DIR is set to excel and used in
# $PTII/ptolemy/actor/lib/makefile if jxl was found
AC_SUBST(PTEXCEL_DIR)

# PTEXCEL_PACKAGES is used in doc/makefile
AC_SUBST(PTEXCEL_PACKAGES)

# PTFMI_DIR is set to fmi if jna.jar was found
# $PTII/ptolemy/actor/lib/makefile uses PTFMI_DIR
AC_SUBST(PTFMI_DIR)

# PTFMI_PACKAGES is used in doc/makefile
AC_SUBST(PTFMI_PACKAGES)

# Set to fmipp and used in ptolemy/actor/lib/fmi/makefile if odeint.hpp is found.
AC_SUBST(PTFMIPP_DIR)

# PTFMIPP_PACKAGES is used in doc/makefile
AC_SUBST(PTFMIPP_PACKAGES)

# The G4LTL jar file, used for Import an FSMActor using LTL synthesis (G4LTL)
AC_SUBST(PTG4LTL_JAR)

# If the g4ltl.jar file is set, then PTG4LTL_DIR is set to g4ltl and used in vergil/actor/makefile.
AC_SUBST(PTG4LTL_DIR)

# Packages in Ptolemy that depend on g4ltl.jar
AC_SUBST(PTG4LTL_PACKAGES)

# Set to -I$PTII/mescal/include or -I/usr/local/include if gmp.h is found
# and used in $PTII/mescal/relsat
AC_SUBST(PTGMP_INCLUDE)

# Set to -Wl,-R$PTII/mescal/lib or -Wl,-R/usr/local/lib if the gmp
# libraries are found and used in $PTII/mescal/relsat
AC_SUBST(PTGMP_LD_FLAGS)

# Set to -L$PTII/mescal/lib or -L/usr/local/lib if the gmp libraries are found
# and used in $PTII/mescal/relsat
AC_SUBST(PTGMP_LIB)

# Name of the jar file that includes the GR domain if Java 3D was found.
# Used in domains/makefile.
AC_SUBST(PTGRDOMAIN_JAR)

# Ptolemy II packages that use the Java 3D facility
# PTGR_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTGR_PACKAGES)

# Set to hlacerti and used in $PTII/ptolemy/apps/makefile is lib/jcerti.jar is found
AC_SUBST(PTHLACERTI_DIR)

# Ptolemy II packages that use jcerti.
AC_SUBST(PTHLACERTI_PACKAGES)

# Set to homer and used in $PTII/ptolemy/makefile if the netbeans visual gui code is found.
AC_SUBST(PTHOMER_DIR)

# Netbeans Jar files necessary for compilation of homer
AC_SUBST(PTHOMER_JARS)

# Ptolemy II packages that use Netbeans gui code
AC_SUBST(PTHOMER_PACKAGES)

# Set to httpClient if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTHTTPCLIENT_DIR)

# Set to httpServer if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTHTTPSERVER_DIR)

# Location of the the PTII directory
# $PTII/ptolemy/plot/ptplot.jnlp.in reads this
AC_SUBST(PTII)

# Set to itextpdf and used in
# $PTII/ptolemy/vergil/basic/export/makefile if iText.jar was found
AC_SUBST(PTITEXTPDF_DIR)

# iText PDF jar file.  iText is from
# http://itextpdf.com
AC_SUBST(PTITEXTPDF_JAR)

# PTITEXTPDF_PACKAGES is used in ptII/doc/makefile if iTextjar is found
AC_SUBST(PTITEXTPDF_PACKAGES)

# PTIMUSENSOR_DIR is set to IMUSensor and used in ptolemy/actor/lib/jjs/modules/makefile if the Java Communications API was found
AC_SUBST(PTIMUSENSOR_DIR)

# Set to ptjacl and used in
# $PTII/ptolemy/actor/gui/makefile if ptjacl.jar was found
AC_SUBST(PTJACL_DIR)

# ptjacl.jar file, used to run the test suites
AC_SUBST(PTJACL_JAR)

# Set to jai and used in 
# $PTII/ptolemy/actor/lib/makefile if Java Advanced Imaging was found
AC_SUBST(PTJAI_DIR)

# Ptolemy II packages that use Java Advanced Imaging
# PTJAI_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJAI_PACKAGES)

# Set to javacv and used in
# $PTII/ptolemy/actor/lib/opencv/makefile if JavaCV was found
AC_SUBST(PTJAVACV_DIR)

# Ptolemy II packages that use JavaCV.
# PTJAVACV_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJAVACV_PACKAGES)

# Location of the JDK
AC_SUBST(PTJAVA_DIR)

# Location of the JDK
AC_SUBST(PTJAVA_DIR_NO_CYGDRIVE)

# Value of java.home property, location of the JDK with /cygdrive/c/ converted to c:/
AC_SUBST(PTJAVA_HOME)

# Set to include packages that require Java 1.8, but do not require Vertx or other optional packages and used in doc/makefile.
AC_SUBST(PTJAVA18_PACKAGES)

# Location of the JDK
AC_SUBST(PTJAVA32_DIR)

# Set to gr and used in
# $PTII/ptolemy/domains/makefile if Java 3D was found
AC_SUBST(PTJAVA3D_DIR)

# PTJAVAFX_DIR is used in ptolemy/actor/lib/jjs/modules
AC_SUBST(PTJAVAFX_DIR)

# PTJAVAFX_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJAVAFX_PACKAGES)

# Set to mail and used in
# $PTII/ptolemy/actor/lib/makefile if JavaMail's javax.mail.jar was found.
AC_SUBST(PTJAVAMAIL_DIR)

# Java OpenGL (JavaMail) jar files.   Used to compile the mail actors.
AC_SUBST(PTJAVAMAIL_JARS)

# Ptolemy II packages that use JavaMail framework.
# PTJMF_PACKAGES is used in ptII/doc/makefile.
AC_SUBST(PTJAVAMAIL_PACKAGES)

# lib/jcerti.jar, used by ptolemy/apps/hlacerti
AC_SUBST(PTJCERTI_JAR)

# Jetty jar files used by Ptango and ptserver.
AC_SUBST(PTJETTY_JAR)

# Set to jjs and used in org/terraswarm/accessors/makefile if Nashorn (present in Java 1.8) is found.
AC_SUBST(PTJJS_DIR)

# Set to jmf if jmf.jar was found
AC_SUBST(PTJMF_DIR)

# Ptolemy II packages that use Java Media Framwork
# PTJMF_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJMF_PACKAGES)

# PTJMODELICA_DIR is set to jmodelica if JModelica was found
# $PTII/ptolemy/actor/lib/fmi/fmus/makefile uses PTJMODELICA_DIR
AC_SUBST(PTJMODELICA_DIR)

# PTJMODELICA_PACKAGES is used in doc/makefile
AC_SUBST(PTJMODELICA_PACKAGES)

# Set to jni if we can compile Java Native Interface code and used in ptolemy/actor/lib/fmi/makefile
AC_SUBST(PTJNI_DIR)

# JNI architecture, used to compile C files
AC_SUBST(PTJNI_ARCHITECTURE)

# set to jni include directory
AC_SUBST(PTJNI_INCLUDE)

# Set to -ldl for use by jni/launcher/makefile under Linux
AC_SUBST(PTJNI_DL_LIBRARY)

# JNI lib architecture, used to run jni/launcher
AC_SUBST(PTJNI_LIB_ARCHITECTURE)

# Flag to use with TinyOS under Cygwin (-mno-cygwin)
AC_SUBST(PTJNI_NO_CYGWIN)

# GCC shared flag.  Usually -shared, except on the mac, where it is -dynamiclib
AC_SUBST(PTJNI_GCC_SHARED_FLAG)

# JNI shared library C compiler flag, under Solaris this would be -fPIC.
AC_SUBST(PTJNI_SHAREDLIBRARY_CFLAG)

# JNI shared library linker flag, under Solaris this would be -fPIC.
AC_SUBST(PTJNI_SHAREDLIBRARY_LDFLAG)

# JNI shared library prefix, under Solaris this would be lib.
AC_SUBST(PTJNI_SHAREDLIBRARY_PREFIX)

# JNI shared library suffix, under Windows this would be dll.
AC_SUBST(PTJNI_SHAREDLIBRARY_SUFFIX)

# JNI shared library suffix, under Mac OS X, this would by dylib
AC_SUBST(PTJNI_SHAREDLIBRARY_SUFFIX2)

# JNI libraries needed to link, such as -lcygwin (Used by Viptos) 
AC_SUBST(PTJNI_LIBRARIES)

# Set to $PTII/vendors/jogl/* and used in ptinvoke.in under Mac OS X.
AC_SUBST(PTJOGL_DIR)

# Set to joystick if Joystick.jar was found 
AC_SUBST(PTJOYSTICK_DIR)

# Ptolemy II packages that use the Java Joystick facilty
# PTJOYSTICK_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJOYSTICK_PACKAGES)

# Set to json and used in $PTII/org/makefile if the JavaScript Object Notation was found.
AC_SUBST(PTJSON_DIR)

# Set to actor/lib/conversions/json/json.jar and used in $PTII/ptolemy/makefile if org/json was found.
AC_SUBST(PTJSON_JAR)

# Set to json.org and used in $PTII/doc/makefile if JSON was found.
AC_SUBST(PTJSON_PACKAGES)

# JSoup jar files used by export html facility
AC_SUBST(PTJSOUP_JAR)

# Set to jsoup if jsoup is found and used in $PTII/ptolemy/vergil/basic/export/makefile
AC_SUBST(PTJSOUP_DIR)

# Set to ptolemy.vergil.basic.export.html.jsoup and used int $PTII/doc/makefile if jsoup is found.
AC_SUBST(PTJSOUP_PACKAGES)

# Set to junit and used in $PTII/util/testsuite/makefile if junit was found.
AC_SUBST(PTJUNIT_DIR)

# PTJUNIT_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJUNIT_PACKAGES)

# Used in ptolemy/actor/lib/excel/makefile
AC_SUBST(PTJXL_JAR)

# Set to python if jython.jar was found
AC_SUBST(PTJYTHON_DIR)

# Ptolemy II packages that use Jython
# PTJYTHON_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTJYTHON_PACKAGES)

# Set to kieler and used in
# $PTII/ptolemy/vergil/basic/layout/makefile if kieler was found
AC_SUBST(PTKIELER_DIR)

# Set to kvm and used in
# $PTII/ptolemy/apps/makefile if kvm was found
AC_SUBST(PTKVM_DIR)

# Set to lbnl and used in $PTII/makefile if libexpat was found.
AC_SUBST(PTLBNL_DIR)

# Set to CRoom if libexpat is found and used in lbnl/demo/makefile
AC_SUBST(PTLBNL_CROOM_DIR)

# Set to CRoom/CRoom.jar if libexpat is found and used in lbnl/demo/makefile
AC_SUBST(PTLBNL_CROOM_JAR)

# Set to the lbnl jars that need to be signed if libexpat was found
# and used in jnlp.mk and $PTII/doc/makefile.
AC_SUBST(PTLBNL_JARS)

# PTLBNL_PACKAGES is set to the packages in lbnl if libexpat was found and
# used in ptII/doc/makefile.
AC_SUBST(PTLBNL_PACKAGES)

# Set to lego and used in
# $PTII/ptolemy/apps/makefile if the Java Communications API was found
AC_SUBST(PTLEGO_DIR)

# Set to lejos and used in
# $PTII/ptolemy/apps/makefile if the Java Communications API was found
# and Legos was found
AC_SUBST(PTLEJOS_DIR)

# Set to util and used in $PTII/lbnl/lib/makefile if libexpat was found
AC_SUBST(PTLIBEXPAT_DIR)

# Set to gcc or cl and used in
# $PTII/ptolemy/matlab/makefile if the Matlab was found.
AC_SUBST(PTMATLAB_CC)

# Set to -m64 under Solaris if libs are in bin/sol64
# and used $PTII/ptolemy/matlab/makefile if the Matlab was found.
AC_SUBST(PTMATLAB_CC_FLAGS)

# Set to matlab and used in
# $PTII/ptolemy/makefile if the Matlab was found.
AC_SUBST(PTMATLAB_DIR)

# Set to the matlab jars that need to be signed if matlab was found.
# Used in jnlp.mk
AC_SUBST(PTMATLAB_JARS)

# Linker args for Matlab
# $PTII/ptolemy/matlab/makefile
AC_SUBST(PTMATLAB_LD_ARGS)

# Linker args for Matlab
# $PTII/ptolemy/matlab/makefile
AC_SUBST(PTMATLAB_64LD_ARGS)

# Extension for matlab .mex files, for example "mexmaci64"
AC_SUBST(PTMATLAB_MEXEXT)

# Used in $PTII/doc/makefile
AC_SUBST(PTMATLAB_PACKAGES)

# Set to mbed and used in
# $PTII/ptolemy/cg/adapter/generic/program/procedural/c/makefile
# if vendors/mbed/gcc-arm/bin/arm-none-eabi-gcc was found
AC_SUBST(PTMBED_DIR)

# Set to mescal and used in $PTII/makefile 
# if $PTII/mescal was found
AC_SUBST(PTMESCAL_DIR)

# PTMETROII_DIR is set to metroII if the ProtoBuf jar file was found
# $PTII/ptolemy/domains/makefile uses PTMETROII_DIR
AC_SUBST(PTMETROII_DIR)

# PTMETROII_PACKAGES is used in doc/makefile
AC_SUBST(PTMETROII_PACKAGES)

# Set to opencv and used in 
# $PTII/ptolemy/actor/lib/makefile if OpenCV Open Computer Vision was found
AC_SUBST(PTOPENCV_DIR)

# Directory that contains cv.h
AC_SUBST(PTOPENCV_INCLUDE_DIR)

# Ptolemy II packages that use OpenCV
# PTOPENCV_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTOPENCV_PACKAGES)

# PTOMC_DIR is set to omc if OpenModelica is found and used in ptII/ptolemy/actor/lib/fmi/fmus/makefile
AC_SUBST(PTOMC_DIR)

# PTOPENMODELICA_DIRS is set to omc if OpenModelica is found and used in ptII/ptolemy/actor/lib/fmi/fmus/makefile
AC_SUBST(PTOPENMODELICA_DIR)

# PTOPENMODELICADOMAIN_JAR is set to openmodelica/openmodelica.jar if OpenModelica is found and used in ptII/ptolemy/domains/makefile.
AC_SUBST(PTOPENMODELICADOMAIN_JAR)

#There are no OMC FMU .java files, so there is no PTOMC_PACKAGES.

# PTOPENMODELICA_PACKAGES is used in doc/makefile.  
AC_SUBST(PTOPENMODELICA_PACKAGES)

# Open Sound Control/Processing.org jar file used by org.ptolemy.js
AC_SUBST(PTOSCP5_JAR)

# Set to osc if oscp5.jar is found
AC_SUBST(PTOSCP5_DIR)

# Set to org.ptolemy.osc and used int $PTII/doc/makefile if oscp5 is found
AC_SUBST(PTOSCP5_PACKAGES)

# PTPAHO_MQTT_DIR is set to localStorage and mqtt if Paho MQTT is found and used in ptII/ptolemy/actor/lib/jjs/modules/
AC_SUBST(PTPAHO_MQTT_DIRS)

# The Paho MQTT Client Library, defaults to $PTII/lib/org.eclipse.paho.client.mqttv3.jar.
AC_SUBST(PTPAHO_MQTT_JAR)

# PTPAHO_MQTT_PACKAGES is used in doc/makefile
AC_SUBST(PTPAHO_MQTT_PACKAGES)

# Set to pdf and used in ptolemy/vergil/makefile if
# PDFRenderer.jar is found.
AC_SUBST(PTPDFRENDERER_DIR)

# Jar file used in ptolemy/vergil/pdf
AC_SUBST(PTPDFRENDERER_JAR)

# Set to psdf and used in $PTII/ptolemy/domains/makefile if
# $PTII/lib/mapss.jar was found
AC_SUBST(PTPSDF_DIR)

# PTRSYNTAXTEXTAREA_DIR is set to syntax and used in
# $PTII/ptolemy/actor/gui/makefile if ptolemy/actor/gui/syntax is present.
AC_SUBST(PTRSYNTAXTEXTAREA_DIR)

# RSyntaxTextArea jar file, typically downloaded from Maven.
AC_SUBST(PTRSYNTAXTEXTAREA_JAR)

# Java packages that use RSyntaxTextArea, typically ptolemy.actor.gui.syntax.
AC_SUBST(PTRSYNTAXTEXTAREA_PACKAGES)

# Jar file for Sphinx speech recognition
AC_SUBST(SPHINX4_JAR)

# PTSVG_DIR is set to svg and used in
# $PTII/diva/util/java2d/makefile if Batik SVG jar files were found
AC_SUBST(PTSVG_DIR)

# Jar file used by diva/util/java2d/svg/makefile
AC_SUBST(PTSVG_JAR)

# PTSVGSALAMANDER_DIR is set to svg and used in com/jhlabs/image/svg/makefile
AC_SUBST(PTSVGSALAMANDER_DIR)

# svgSalamander Jar file.
AC_SUBST(PTSVGSALAMANDER_JAR)

# PTSVGSALAMANDER_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTSVGSALAMANDER_PACKAGES)

# PTPOWERMOCK_DIR is set to test and used in
# $PTII/ptdb/makefile
AC_SUBST(PTPOWERMOCK_DIR)

# PowerMock, used for testing, see http://code.google.com/p/powermock/
# Used in ptolemy/ptdb/test/makefile
AC_SUBST(PTPOWERMOCK_JARS)

# Jar files used by the Image Processing library from http://processing.org
AC_SUBST(PTPROCESSING_JARS)

# The location of the protobuf jar file, typically $PTII/lib/protobuf-java-2.4.1.jar 
AC_SUBST(PTPROTOBUF_JAR)

# PTPTALON_DIR is set to ptalon and used in
# $PTII/ptolemy/actor/makefile if antlr.jar was found.
AC_SUBST(PTPTALON_DIR)

# PTALON_PACKAGES is used in $PTII/doc/makefile
AC_SUBST(PTPTALON_PACKAGES)

# Directory that contains the antlr.jar file, used by ptalon
AC_SUBST(ANTLR_DIR)

# PTRTOOL_DIR is set to r and used in
# $PTII/ptolemy/actor/lib/makefile if the jars necessary for the R interface were found.
AC_SUBST(PTRTOOL_DIR)

# Jar files used by the interface to the R statistical tool.
AC_SUBST(PTRTOOL_JARS)

# Used in mk/jnlp.jar
AC_SUBST(PTRTOOL_JNLP_JARS)

# PTRTOOL_PACKAGES is used in $PTII/doc/makefile
AC_SUBST(PTRTOOL_PACKAGES)

# Ptolemy II packages that use the RXTX Java Serial Communication facility
# PTRXTX_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTRXTX_PACKAGES)

# PTSCALA_DIR is set to scala and used in
# $PTII/org/ptolemy/makefile if the scala binary was found
AC_SUBST(PTSCALA_DIR)

# PTSCALA_PACKAGES is used in $PTII/doc/makefile
AC_SUBST(PTSCALA_PACKAGES)

# PTSERIAL_DIR is set to serial and used in
# $PTII ptolemy/actor/lib/jjs/modules/makefile if the Java Communications API was found
AC_SUBST(PTSERIAL_DIR)

# PTSERVER_DIR is set to ptserver and used in
# $PTII/makefile if dbxml is found
AC_SUBST(PTSERVER_DIR)

# PTSERVER_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTSERVER_PACKAGES)

# PTSERVER_JARS includes hessian, jetty, servlet and mqtt jars and is used by $PTII/ptserver
AC_SUBST(PTSERVER_JARS)

# javax.servlet-api*.jar used by Ptango and ptserver.
AC_SUBST(PTSERVLET_JAR)

# slf4j-api*.jar, used by webcam-capture and xbjlib (XBee).
AC_SUBST(PTSLF4J_API_JAR)

# slf4j-simple*.jar, used by webcam-capture and xbjlib (XBee).
AC_SUBST(PTSLF4J_SIMPLE_JAR)

# PTSPACE_DIR is set to space and used in
# $PTII/ptolemy/domains/makefile if ojdbc6.jar was found.
AC_SUBST(PTSPACE_DIR)

# PTSPACEDOMAIN_JAR is the name of the jar file that includes the space
# domain if ojdbc6.jar was found.  PTSPACEDOMAIN_JAR used in domains/makefile
AC_SUBST(PTSPACEDOMAIN_JAR)

# PTSPACEDOMAIN_PACKAGES is set if ojdbc6.jar was found and 
# used in ptII/doc/makefile
AC_SUBST(PTSPACEDOMAIN_PACKAGES)

# PTSPHINX4_CORE_JAR is set to the Sphinx4 speech recognition core jar.
AC_SUBST(PTSPHINX4_CORE_JAR)

# PTSPHINX4_DATA_JAR is set to the Sphinx4 speech recognition data jar.
AC_SUBST(PTSPHINX4_DATA_JAR)

# PTSPHINX4_DIR is set to speechRecognition and used in
# ptolemy/actor/lib/jjs/modules/makefile if the Sphinx 4 jars are found.
AC_SUBST(PTSPHINX4_DIR)

# PTSPHINX4_PACKAGES is used in doc/makefile
AC_SUBST(PTSPHINX4_PACKAGES)

# PTSTRUCTURALCODER_JAR is set if $PTII/lib/StructuralCoder.jar was found
# and used in ptolemy/vergil/actor/g4ltl/makefile
AC_SUBST(PTSTRUCTURALCODER_JAR)

# Set to tini and used in
# $PTII/ptolemy/apps/makefile if TINI was found
AC_SUBST(PTTINI_DIR)

# PTTINYOS_DIR is set to ptinyos and used in
# $PTII/ptolemy/domains/makefile if TinyOS is found
AC_SUBST(PTTINYOS_DIR)

# Set to giotto and used in
# $PTII/ptolemy/apps/makefile if Giotto was found
AC_SUBST(PTGIOTTO_DIR)

# Set to waba and used in
# $PTII/ptolemy/apps/makefile if Waba was found
AC_SUBST(PTWABA_DIR)

# Jar files used in ptolemy/actor/lib/jjs/modules/webcam/makefile
AC_SUBST(PTWEBCAMCAPTURE_JARS)

# PTWEBCAMCAPTURE_PACKAGES is used in doc/makefile
AC_SUBST(PTWEBCAMCAPTURE_PACKAGES)

# PTXBEE_DIR is set to xbee and used in 
# $PTII/ptolemy/actor/lib/io/makefile if the Java Communications API was found
AC_SUBST(PTXBEE_DIR)

# Jar files used in ptolemy/actor/lib/jjs/modules/xbee/makefile
AC_SUBST(PTXBJLIB_JARS)

# PTXBJLIB_PACKAGES is used in ptII/doc/makefile
AC_SUBST(PTXBJLIB_PACKAGES)

# PTXMPP_DIR is set to xmpp if smack.jar and smackx.jar are found.  See org/ptolemy/ptango/makefile
AC_SUBST(PTXMPP_DIR)

# Location of the local $PTII directory as a file:/// URL
# This variable is used with the Java Network Launching Protocol files
AC_SUBST(PTII_LOCALURL)

# Jar file that contains RXTX Serial Port Interface
AC_SUBST(RXTX_JAR)

# If Rxtx is present, then set to yes, otherwise set to no
AC_SUBST(RXTX_PRESENT)

# The scala binary.
AC_SUBST(SCALA)

# The scalac binary.
AC_SUBST(SCALAC)

# tini/bin/tinclasses.jar file used Soot - a Java Optimization Framework
AC_SUBST(SOOT_CLASSES)

# Directory that contains the Soot installation
AC_SUBST(SOOT_DIR)

# tini/bin/tiniclasses.jar file used by the Dallas Semi Tini
AC_SUBST(TINI_CLASSES)

# Directory that contains the Tini installation
AC_SUBST(TINI_DIR)

# Location of tools.jar, usually $(PTJAVA_HOME)/../lib/tools.jar
AC_SUBST(TOOLS_JAR)

# Location of TinyOS, used by ptinyos domain
AC_SUBST(TOSROOT_NO_CYGDRIVE)
AC_SUBST(TOSDIR_NO_CYGDRIVE)

# giotto/gdk.jar file used by GiottoSDK
AC_SUBST(GIOTTO_CLASSES)

# Directory that contains the GiottoSDK installation
AC_SUBST(GIOTTO_DIR)

# Set to textDisplay if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTTEXTDISPLAY_DIR)

# Set to udpSocket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTUDPSOCKET_DIR)

# Set to userInterface if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTUSERINTERFACE_DIR)

# Set to socket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTVERTX_SOCKET_DIR)

# Vertx jars used by Vert.x modules
AC_SUBST(PTVERTX_JARS)

# Set to vertx if the Vertx jars are found
AC_SUBST(PTVERTX_DIR)

# Set to packages that use Vert.x and used in $PTII/doc/makefile if the Vert.x jars are found
AC_SUBST(PTVERTX_PACKAGES)

# PTVIEWER_DIR is set to viewer and used in ptolemy/media/makefile for JVM < 9
AC_SUBST(PTVIEWER_DIR)

# PTVIEWER_PACKAGES is used in doc/makefile
AC_SUBST(PTVIEWER_PACKAGES)

# waba/tools/classes.jar file used by the PalmOS WABA
AC_SUBST(WABA_CLASSES)

# Directory that contains the waba used by PalmOS
AC_SUBST(WABA_DIR)

# Set to webSocket if the Vertx jars are found and used in ptolemy/actor/lib/jjs/modules/makefile
AC_SUBST(PTWEBSOCKET_DIR)

# Files we substitute in
AC_OUTPUT(mk/ptII.mk bin/ptinvoke build.xml .classpath bin/comm.policy lib/ptII.properties ptolemy/util/test/junit/javachdir32, chmod a+x bin/ptinvoke ptolemy/util/test/junit/javachdir32)