hi chris,
thanks for your reply,and soory for bothering
further:
you were right. i have problem with jni itself.
the demos donot run correctly and making jni/test
returns an error:
jar" "-Dptolemy.ptII.dir=/usr/PTII" 
tcl/lang/Shell alljtests.tcl
Error: dlopen("libjvm.so") failed with libjvm.so:
cannot open shared object file: No such file or
directory.
this is while i have that file in the following
locations:
find / |grep libjvm.so
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/lib/i386/client/libjvm.so
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/lib/i386/server/libjvm.so
/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/i386/client/libjvm.so
/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/i386/server/libjvm.so

and for your information :
1-$LD_LIBRARY_PATH=
/usr/lib/jvm/java-1.5.0-sun/jre/lib/i386
2-java -version=java version "1.6.0"
3-find / |grep jni.h :
/usr/lib/jvm/java-6-sun-1.6.0.00/include/jni.h
/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/include/jni.h
4- PTII/configure  had some warnings:
a)was giving me a warning about not being able to
find 'unknown' jni architecture. in order to
remove the problem, i created a link known as
unknown to: 
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/lib/i386
b)configure: WARNING: Could not find directory
    '/usr/PTII/vendors/sun/javacc-4.0'. I first
installed javacc-4.0 and then created
/usr/PTII/vendors/sun/javacc-4.0/bin directory
myself and in there, i created two links to
jjtree and javacc the final output of ./configure
looks like this:

checking if $PTII ('/usr/PTII') has
backslashes... ok
    '/usr/PTII' does not contain backslashes
checking if $PTII ('/usr/PTII') contains
"cygdrive"... ok
    '/usr/PTII' does not contain cygdrive or
cygwin, which is right.
checking for find... /usr/bin/find
PTJAVA_DIR environment variable was not set,
    so we search for the java compiler.
checking for javac... /usr/bin/javac
checking for the java runtime in /usr/bin...
/usr/bin/java
checking that you have the right java in your
path.... checking for java... /usr/bin/java
    You have the right java in your path,
    "/usr/bin/java"
      = "/usr/bin/java"
checking for the java compiler in /usr/bin...
/usr/bin/javac
checking that you have the right javac in your
path.... checking for javac... (cached)
/usr/bin/javac
    You have the right javac in your path,
    "/usr/bin/javac"
      = "/usr/bin/javac"
checking the Java compiler with a simple
compile... ok
checking the value of the java.version Property
... 1.6.0
checking the JDK version... ok, you are running
1.6.0
checking for java.home property by compiling a
test program ... ok
checking for java.home property by running a test
program ... /usr/lib/jvm/java-6-sun-1.6.0.00/jre
checking for the jar command in /usr/bin...
/usr/bin/jar
checking that /usr/bin/jar can handle -i...
/usr/bin/jar -i worked
checking for the proper CLASSPATH separator...
':'
/usr/PTII/mescal/views/simulation/model/UINT.H is
not present,
    so we need not find Boost.
/usr/PTII/ptolemy/copernicus/c is not present,
    so we need not find the CaffeineMark Kit.
/usr/PTII/ptolemy/caltrop is not present,
    so we need not find the Cal, the actor
language.
/usr/PTII/ptolemy/chic is not present,
    so we need not find Chic, the modular
verifier for
    behavioral compatibility checking of software
and hardware components.
checking for Ptolemy subset of Colt, the
scientific computing lib...
/usr/PTII/lib/colt.jar
checking for Full version of Colt, the scientific
computing lib...
/usr/PTII/vendors/misc/colt/colt.jar not found,
using /usr/PTII/lib/ptcolt.jar
/usr/PTII/ptolemy/actor/lib/io/comm is not
present,
    so we need not find commapi.
checking for tools.jar for use with doclets...
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/../lib/tools.jar
checking for javadoc... /usr/bin/javadoc
/usr/PTII/ptolemy/backtrack/eclipse is not
present,
    so we need not find Eclipse.
/usr/PTII/ptolemy/copernicus/c is not present,
    so we need not find the Boehm GC.
/usr/PTII/mescal/relsat is not present,
    so we need not find GMP.
/usr/PTII/ptolemy/actor/lib/jai is not present,
    so we need not find JAI - The Java Advanced
Imaging API.
/usr/PTII/ptolemy/copernicus/jhdl is not present,
    so we need not find the JHDL - a Java
Optimization Framework.
/usr/PTII/ptolemy/actor/lib/jmf is not present,
    so we need not find the JMF - The Java Media
Framework.
/usr/PTII/ptolemy/actor/lib/joystick is not
present,
    so we need not find the Joystick interface.
checking for Jython, the Java implementation of
Jython... /usr/PTII/lib
/usr/PTII/ptolemy/actor/lib/jxta is not present,
    so we need not find JXTA.
/usr/PTII/ptolemy/apps/lejos is not present,
    so we need not find lejos.
checking for JavaCC...
/usr/PTII/vendors/sun/javacc-4.0
checking for jjtree... $(JAVACC_DIR)/bin/jjtree
checking for javacc... $(JAVACC_DIR)/bin/javacc
checking for ptjacl.jar...
/usr/PTII/lib/ptjacl.jar
checking for how to run jacl with
"/usr/bin/java"... % ok
/usr/PTII/ptolemy/domains/gr is not present,
    so we need not find Java 3D.
checking for jini directory...
/usr/PTII/ptolemy/distributed/jini
checking for jars used by jini... jini-core.jar
jini-ext.jar sun-util.jar ok
checking for gcc... /usr/bin/gcc
checking for the proper JNI architecture...
'linux'
checking for the proper JNI architecture include
directory...
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/../include/linux
checking for the proper JNI architecture...
'unknown'
checking for the proper JNI architecture lib
directory...
/usr/lib/jvm/java-6-sun-1.6.0.00/jre/lib/linux
checking for if the -mno-cygwin flag is
available... ''
checking for the proper shared library cc flag...
''
checking for the proper shared library link
flag... ''
checking for the proper shared library prefix...
'lib'
checking for the proper shared library suffix...
'so'
checking for JNI libraries needed to link JNI...
''
/usr/PTII/vendors/jode is not present,
    so we need not find Jode, which is a java
disassembler.
/usr/PTII/ptolemy/apps/kvm is not present,
    so we need not find the PalmOS kvm.
checking for matlab... no
configure: WARNING: 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.
/usr/PTII/ptolemy/domains/psdf is not present,
    so we need not find the mapss.jar.
/usr/PTII/ptolemy/actor/ptalon is not present,
    so we need not find anltr.jar.
/usr/PTII/ptolemy/domains/gr/lib/quicktime is not
present,
    so we need not find Quicktime for Java.
/usr/PTII/ptolemy/copernicus is not present,
    so we need not find the Soot - a Java
Optimization Framework.
checking for Batik SVG... configure: WARNING:
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/
/usr/PTII/ptolemy/apps/tini is not present,
    so we need not find the Dallas Semiconductor
tini.
checking the for TinyOS...
/usr/PTII/vendors/ptinyos/tinyos-1.x
checking for TOSDIR directory...
/usr/PTII/vendors/ptinyos/tinyos-1.x/tos
checking for PTINYOS_MOMLROOT... ok
checking for PTINYOS_MOMLROOT directory...
/usr/PTII/vendors/ptinyos/moml
/usr/PTII/ptolemy/domains/giotto is not present,
    so we need not find the Giotto SDK.
/usr/PTII/ptolemy/apps/kvm is not present,
    so we need not find the PalmOS waba.
/usr/PTII/ptolemy/actor/lib/x10 is not present,
    so we need not find the X10 SDK. X10 is the
power line comm interface.
configure: creating ./config.status
config.status: creating mk/ptII.mk
config.status: creating bin/ptinvoke
config.status: creating .classpath
config.status: creating bin/comm.policy
config.status: creating lib/ptII.properties
config.status: executing default commands

sorry for such a long mail,appreciate your help
wahid




      
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