Cytoscape 3 eclipse problem

[Omen]

Hi all
I would like to say You have done amazing job during Cytoscape
developement.
I want to contribute to this project by creating plugins. I am making
my phD project to help students in discovering world of mathematic
graphs. During my plugin development on Windows XP with NetBeans I
found bug in Cytoscape 2.6.2 release in edge directionality. Luckly it
has been solved by Daniel Abel which you can see in
http://cytoscape.org/cgi-bin/moin.cgi/DanielAbel/EdgeDirectionality .
However its not available in Cytoscape 2.6.2. So I've decided to make
runable Cytoscape 3. And later on do my project.

I tried to find downloadable version of Cytoscape 3 and found out that
its only on cvs. NetBeans tips to compile which you can check on
http://cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Netbeans didn't
gave me any clue how to make runable version.

So I wanted to compile it under Eclipse. I've install newest Java
1.6.0.13, Maven 2.1.0 and Eclipse PDE as
http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Eclipse/CoreDevelopment
suggest.

Now I'm in step 1.4.5 trying to install Cytoscape IDE for Eclipse with
error
"Cannot complete the request. See the details.
Cannot find a solution satisfying the following requirements
org.eclipse.swt [3.4.0.v3448f]."

1.Do You have any suggestions what should I do?

Daniel Abel have told me to try apply changes by hand to Cytoscape
2.6.2 from his Cytoscape 3 branch. But I will need to give this
release to everybody who will want to use my plugins correctly. And if
its already applied in Cytoscape 3 its seems to be kind of useless to
make this.

2. Can I make runnable version of Cytoscape 3 from cvs trunk at
current stage of development.

Thanks in advance for each constructive reply.

[Keiichiro Ono]

Hi.

> "Cannot complete the request.  See the details.
> Cannot find a solution satisfying the following requirements
> org.eclipse.swt [3.4.0.v3448f]."
>
> 1.Do You have any suggestions what should I do?

Looks like this is a common Eclipse 3.4.x series problems:

http://www.google.com/search?q=Cannot+find+a+solution+satisfying+the+following+requirements+org.eclipse.swt+[3.4.0.v3448f]&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:ja:official&client=firefox

I had the same problem before, but once I start from a clean
installation of Eclipse, and installed plugins one by one, I could
install everything. I think mylyn related plugins caused this issue,
so I've tried to install everything but mylyn, and then installed it.

By the way, I think you can use both embedded version of Maven and
stand-alone version of Maven if you use latest version of Eclipse and
m2eclipse plugin.

> 2. Can I make runnable version of Cytoscape 3 from cvs trunk at
> current stage of development.

Yes. You can checkout this:

http://chianti.ucsd.edu/svn/cytoscape3/trunk/

and in the directory, you need to type

"mvn clean install pax:run"

to execute Cytoscape 3. Current runnable version has only limited
functions (load network and create view), but core data structures
(model/viewmodel) are nearly complete.


Kei

>
> Thanks in advance for each constructive reply.
>
>
>
>
>
> >
>

--
Keiichiro Ono ko...@ucsd.edu

Cytoscape Core Developer Team: http://www.cytoscape.org/
UCSD Bioengineering Ideker Lab: http://chianti.ucsd.edu/idekerlab/

[Omen]

Thanks for reply
I've got "Can't read file '/cellar/common/svn/db/revs/16773': Input/
output error"

[Keiichiro Ono]

Currently, we have a file server problem and SVN server is also down.
I'll let you know when it's back.

Thanks.
Kei

2009/5/12 Omen <adamsz...@gmail.com>: