Re: Compiling Ptolemy with Eclipse
Thanks for your help, I also tried the method described but I can not get the project compiled, here is what I tried : tar xfz ptII3.0.2.src.tar.gz mv ptII3.0.2 ptII export PTII=/home/franck/bin/my_PTII/ptII cd $PTII ./configure cd ~/bin/my_PTII eclipse File-New Project Project Name : ptII Directory: /home/franck/bin/my_PTII Finish -- An error occured while creating the java project Reason : invalid project description /home/franck/bin/my_PTII and /home/franck/bin/my_PTII/workspace overlap If I change the directory with : /home/franck/bin/my_PTII/ptII -- An error occurred while creating the java project See error log for more details. (java.lang.NullPointerException in the .log of Eclipse !) I tried other thinks but I can only compile and run (make fast install) without Eclipse ! Franck On Mon, 2004-05-03 at 17:14, Christopher Hylands Brooks wrote: With Eclipse, usually it is necessary to run configure so that the .classpath file is properly set up. An alternative is to set up the project class path by hand. Locally, our Eclipse users run configure, so the by hand section of the doc could probably use some testing and updating. One issue is that Ptolemy II includes many packages that use other external packages that might not be present, so setting the classpath and excluding packages by hand can be time consuming. -Christopher Good morning, I'm a software designer in the Pasteur Institute (Paris) and I'm involved with a workflow definition and conception for sequence analysis (mainly). Ptolemy II seems to correspond to the core functionalities I need and seems to be easy to customize (thanks to have made docs and UML diagrams !) Unfortunatly I'm trying to make an eclipse project following the instructions described but without success. I'm now trying to install Ptolemy by hand following the chapter Setting up for Ptolemy II By Hand described in doc/coding/eclipse.htm and I have these errors : 1 - The project was not built since its classpath is incomplete. Cannot find the class file for ptolemy.math.Complex. Fix the classpath then try rebuilding this project. 2 - For the file /ptolemy/matlab/test/TestEngine.java : This compilation unit indirectly references the missing type ptolemy.math.Complex (typically some required class file is referencing a type outside the classpath) (Weird because I can see ptolemy.math in Eclipse) Can you say me if there is a mistake in the procedure described or I made something wrong. Thanks a lot ! Regards Franck Valentin --- - Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED] Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED] Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED]
Re: Compiling Ptolemy with Eclipse
Hmm, this sounds like an Eclipse bug tickled by Ptolemy adjusting
setting up the ptII/.classpath file.
I've seen stack traces inside eclipse 2.1.2. Rather than
reinstalling, what I usually what I ended up doing was removing my
eclipse/workspace directory and trying various things.
You could try removing ptII/.classpath and seeing if the setup
completes. That worked for me.
I was able to build after hacking adding the following to .classpath.in:
classpathentry excluding=cm/ kind=src path=ptolemy/copernicus/c/test/
and I had to add
ptolemy/copernicus/c/test/cm/|
to the list of excluded files.
At one point, the Java build path window came up and I had
to remove jmf.jar and sound.jar
I later removed the jxta jar files because they had this
bogus ${PTII} inside of them. I'll fix configure momentarily.
This bug occurred because our devel tree contains the jxta jar files,
but we don't ship these jar files.
To remove the jxta jar files, right click on the ptII project, select
Properties - Java Build Path - Libraries
You may later want to exclude ptolemy/moml/jxta from the build.
Below is a copy of the .classpath.in that worked for me:
--start--
?xml version=1.0 encoding=UTF-8?
classpath
classpathentry excluding=cm/ kind=src path=ptolemy/copernicus/c/test/
classpathentry
excluding=**/CVS/|**/codeDoc/|config/|doc/coding/templates/|ptolemy/apps/agilent/|ptolemy/apps/anytimecontrol/|ptolemy/apps/charon/|ptolemy/apps/crazyboard/|ptolemy/apps/etherealSting/|ptolemy/apps/fullscreen/|ptolemy/apps/giotto/|ptolemy/apps/ia/|ptolemy/apps/kurt/|ptolemy/apps/jmf/|ptolemy/apps/kvm/|ptolemy/apps/lego/|ptolemy/apps/lejos/|ptolemy/apps/midp/|ptolemy/apps/mobileCoding/|ptolemy/apps/pendulum/|ptolemy/apps/rijndael/|ptolemy/apps/robot/|ptolemy/apps/security/|ptolemy/apps/sobel/|ptolemy/apps/softwalls/|ptolemy/apps/soot/|ptolemy/apps/throttle/|ptolemy/apps/tini/|ptolemy/apps/transmission/|ptolemy/apps/vergil/|ptolemy/apps/waba/|ptolemy/apps/webstart/|ptolemy/apps/xsl/|ptolemy/copernicus/c/test/|ptolemy/copernicus/c/test/cm/|ptolemy/domains/ct/demo/Saber/|ptolemy/domains/gr/lib/experimental/|ptolemy/domains/pdf/|ptolemy/plot/servlet/|vendors/@ECLIPSE_EXCLUDING_SRC@
kind=src path=/
classpathentry kind=con path=org.eclipse.jdt.launching.JRE_CONTAINER/
@ECLIPSE_CLASSPATHENTRY_LIBS@
classpathentry kind=output path=/
/classpath
--end--
I'll add a note to the website about this
-Christopher
Thanks for your help, I also tried the method described but I can not
get the project compiled, here is what I tried :
tar xfz ptII3.0.2.src.tar.gz
mv ptII3.0.2 ptII
export PTII=/home/franck/bin/my_PTII/ptII
cd $PTII
./configure
cd ~/bin/my_PTII
eclipse
File-New Project
Project Name : ptII
Directory: /home/franck/bin/my_PTII
Finish
-- An error occured while creating the java project
Reason : invalid project description
/home/franck/bin/my_PTII and /home/franck/bin/my_PTII/workspace overlap
If I change the directory with : /home/franck/bin/my_PTII/ptII
-- An error occurred while creating the java project
See error log for more details.
(java.lang.NullPointerException in the .log of Eclipse !)
I tried other thinks but I can only compile and run (make fast install)
without Eclipse !
Franck
On Mon, 2004-05-03 at 17:14, Christopher Hylands Brooks wrote:
With Eclipse, usually it is necessary to run configure so that the
.classpath file is properly set up. An alternative is to set up the
project class path by hand. Locally, our Eclipse users run configure,
so the by hand section of the doc could probably use some testing
and updating.
One issue is that Ptolemy II includes many packages that
use other external packages that might not be present, so setting the
classpath and excluding packages by hand can be time consuming.
-Christopher
Good morning,
I'm a software designer in the Pasteur Institute (Paris) and I'm
involved with a workflow definition and conception for sequence analy
sis
(mainly). Ptolemy II seems to correspond to the core functionalities
I
need and seems to be easy to customize (thanks to have made docs and
UML
diagrams !)
Unfortunatly I'm trying to make an eclipse project following the
instructions described but without success.
I'm now trying to install Ptolemy by hand following the chapter
Setting up for Ptolemy II By Hand described in doc/coding/eclipse.h
tm
and I have these errors :
1 - The project was not built since its classpath is incomplete. Cann
ot
find the class file for ptolemy.math.Complex.
Re: Compiling Ptolemy with Eclipse
Hi Franck: fyi: you may also be interested in the following Ptolemy II spin-off called Kepler that has been used for bioinformatics and other scientific workflows: http://kepler.ecoinformatics.org The first official Kepler release is planned for later this month, but the code is available already (and earlier pre-releases). There is also a page contributed by one of the Kepler folks to using Eclipse: http://kepler.ecoinformatics.org/eclipse.html Bertram FV == Franck Valentin [EMAIL PROTECTED] writes: FV FV Good morning, FV I'm a software designer in the Pasteur Institute (Paris) and I'm FV involved with a workflow definition and conception for sequence analysis FV (mainly). Ptolemy II seems to correspond to the core functionalities I FV need and seems to be easy to customize (thanks to have made docs and UML FV diagrams !) FV FV Unfortunatly I'm trying to make an eclipse project following the FV instructions described but without success. FV FV I'm now trying to install Ptolemy by hand following the chapter FV Setting up for Ptolemy II By Hand described in doc/coding/eclipse.htm FV and I have these errors : FV FV 1 - The project was not built since its classpath is incomplete. Cannot FV find the class file for ptolemy.math.Complex. Fix the classpath then try FV rebuilding this project. FV FV 2 - For the file /ptolemy/matlab/test/TestEngine.java : FV This compilation unit indirectly references the missing type FV ptolemy.math.Complex (typically some required class file is referencing FV a type outside the classpath) FV FV (Weird because I can see ptolemy.math in Eclipse) FV Can you say me if there is a mistake in the procedure described or I FV made something wrong. FV FV Thanks a lot ! FV FV FV FV Regards FV FV Franck Valentin FV FV FV FV Posted to the ptolemy-hackers mailing list. Please send administrative FV mail for this list to: [EMAIL PROTECTED] Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED]
Re: Compiling Ptolemy with Eclipse
With Eclipse, usually it is necessary to run configure so that the .classpath file is properly set up. An alternative is to set up the project class path by hand. Locally, our Eclipse users run configure, so the by hand section of the doc could probably use some testing and updating. One issue is that Ptolemy II includes many packages that use other external packages that might not be present, so setting the classpath and excluding packages by hand can be time consuming. -Christopher Good morning, I'm a software designer in the Pasteur Institute (Paris) and I'm involved with a workflow definition and conception for sequence analysis (mainly). Ptolemy II seems to correspond to the core functionalities I need and seems to be easy to customize (thanks to have made docs and UML diagrams !) Unfortunatly I'm trying to make an eclipse project following the instructions described but without success. I'm now trying to install Ptolemy by hand following the chapter Setting up for Ptolemy II By Hand described in doc/coding/eclipse.htm and I have these errors : 1 - The project was not built since its classpath is incomplete. Cannot find the class file for ptolemy.math.Complex. Fix the classpath then try rebuilding this project. 2 - For the file /ptolemy/matlab/test/TestEngine.java : This compilation unit indirectly references the missing type ptolemy.math.Complex (typically some required class file is referencing a type outside the classpath) (Weird because I can see ptolemy.math in Eclipse) Can you say me if there is a mistake in the procedure described or I made something wrong. Thanks a lot ! Regards Franck Valentin --- - Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED] Posted to the ptolemy-hackers mailing list. Please send administrative mail for this list to: [EMAIL PROTECTED]
