Error Message when starting Cytoscape:

[gladexp]

Hi all,

These days I just install some plugins, but after that there always
displays Error Message when starting Cytoscape as follows,

=======================================================
cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error:
java.lang.NumberFormatException: Cytoscape version numbers must be in
the format: \d+.\d+ optional to add: .\d+-[a-z] Caused by: Cytoscape
version numbers must be in the format: \d+.\d+ optional to add: .\d+-
[a-z] at
cytoscape.plugin.DownloadableInfo.addCytoscapeVersion(DownloadableInfo.java:
188) at
cytoscape.plugin.PluginTracker.createBasicObject(PluginTracker.java:
508) at
cytoscape.plugin.PluginTracker.createPluginObject(PluginTracker.java:
600) at
cytoscape.plugin.PluginTracker.getPluginContent(PluginTracker.java:
569) at
cytoscape.plugin.PluginTracker.getDownloadableContent(PluginTracker.java:
588) at
cytoscape.plugin.PluginTracker.getDownloadableListByStatus(PluginTracker.java:
196) at
cytoscape.plugin.PluginManager.getDownloadables(PluginManager.java:
314) at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:636) at
cytoscape.CytoscapeInit.init(CytoscapeInit.java:209) at
cytoscape.CyMain. (CyMain.java:144) at
cytoscape.CyMain.main(CyMain.java:108) at
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at
java.lang.reflect.Method.invoke(Unknown Source) at
com.exe4j.runtime.LauncherEngine.launch(Unknown Source) at
com.exe4j.runtime.WinLauncher.main(Unknown Source)
=======================================================

Please help and give any response if someone knows about it. Thanks a
lot.

[Alexander Pico]

Try turning off your virus checker during install.
- Alex

[amysu...@yahoo.com]

Hi,
I got the same problem here. I installed a plugin which is not tested
with the Cytoscape 2.8version, then this error message came out
everytime when I initiate Cytoscape. I also lost the Import "Network
from Web Service" function, and I could not manage plugin in the
toolbar. Anyway, the whole programe is messed up. Has anyone found a
solution to it? I have uninstalled the program and reinstalled it. It
did not help at all!

HELP!

On Jun 9, 1:05 pm, gladexp <bme.t...@gmail.com> wrote:
> Hi all,
>
> These days I just install some plugins, but after that there always
> displays Error Message when starting Cytoscape as follows,
>
> =======================================================
> cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error:
> java.lang.NumberFormatException: Cytoscape version numbers must be in
> the format: \d+.\d+ optional to add: .\d+-[a-z]  Caused by: Cytoscape
> version numbers must be in the format: \d+.\d+ optional to add: .\d+-
> [a-z] at
> cytoscape.plugin.DownloadableInfo.addCytoscapeVersion(DownloadableInfo.java­:
> 188) at
> cytoscape.plugin.PluginTracker.createBasicObject(PluginTracker.java:
> 508) at
> cytoscape.plugin.PluginTracker.createPluginObject(PluginTracker.java:
> 600) at
> cytoscape.plugin.PluginTracker.getPluginContent(PluginTracker.java:
> 569) at
> cytoscape.plugin.PluginTracker.getDownloadableContent(PluginTracker.java:
> 588) at

> cytoscape.plugin.PluginTracker.getDownloadableListByStatus(PluginTracker.ja­va:

[Scooter Morris]

What you need to do is to remove the plugin.  Generally, plugins will be installed in your .cytoscape/version/plugins directory where version is the version number of cytoscape (e.g. .cytoscape/2.8/plugins).   You should be able to delete the subdirectory containing the plugin you just installed and restart Cytoscape.

-- scooter

[Scooter Morris]

This problem comes from a plugin error.  Plugins that you download are generally stored in your ".cytoscape" directory, so even when you reinstall cytoscape the "bad" plugin will remain.  You can move your .cytoscape directory aside and try again, then you'll need to look at each plugin you've installed to find the "bad" one.

-- scooter

On 08/02/2012 04:24 AM, Ali Altıntaş wrote:

Sorry about bothering with the same issue again.

I have been using Cytoscape 2.8.2, and the same error happened to me as well. The erros message is:

0

cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error: java.lang.NumberFormatException: Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".) Caused by: Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".) at cytoscape.plugin.DownloadableInfo.addCytoscapeVersion(DownloadableInfo.java:176)

at cytoscape.plugin.PluginTracker.createBasicObject(PluginTracker.java:508) at cytoscape.plugin.PluginTracker.createPluginObject(PluginTracker.java:600) at cytoscape.plugin.PluginTracker.getPluginContent(PluginTracker.java:569) at cytoscape.plugin.PluginTracker.getDownloadableContent(PluginTracker.java:588)

at cytoscape.plugin.PluginTracker.getDownloadableListByStatus(PluginTracker.java:196) at cytoscape.plugin.PluginManager.getDownloadables(PluginManager.java:313)

at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:636) at cytoscape.CytoscapeInit.init(CytoscapeInit.java:209)

at cytoscape.CyMain.(CyMain.java:144)

at cytoscape.CyMain.main(CyMain.java:108) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at com.exe4j.runtime.LauncherEngine.launch(Unknown Source) at com.install4j.runtime.MacLauncher.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at apple.launcher.LaunchRunner.run(LaunchRunner.java:116) at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51) at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

I uninstalled Cytoscape and installed the newer version (2.8.3), but it gives the same error. I also cannot find "Import Network from Table" function anymore in both versions.

May I ask for your help with this issue?

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[Saurabh Sharma]

I got this error today with Cytoscape 2.8.3 on Linux Mint 16, 64Bit. I found a simple solution to thi:
Go to the ".Cytoscape" directory and delete the file named "track_plugins.xml". Then copy all your plugins from this directory to a visible folder and install them one by one by choosing "install from file". Problem solved.

Saurabh

On Thursday, 2 August 2012 16:54:00 UTC+5:30, Ali Altıntaş wrote:

Sorry about bothering with the same issue again.

I have been using Cytoscape 2.8.2, and the same error happened to me as well. The erros message is:

0

cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error: java.lang.NumberFormatException: Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".)

Caused by:

Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".) at cytoscape.plugin.DownloadableInfo.addCytoscapeVersion(DownloadableInfo.java:176)

at cytoscape.plugin.PluginTracker.createBasicObject(PluginTracker.java:508) at cytoscape.plugin.PluginTracker.createPluginObject(PluginTracker.java:600) at cytoscape.plugin.PluginTracker.getPluginContent(PluginTracker.java:569) at cytoscape.plugin.PluginTracker.getDownloadableContent(PluginTracker.java:588)

at cytoscape.plugin.PluginTracker.getDownloadableListByStatus(PluginTracker.java:196) at cytoscape.plugin.PluginManager.getDownloadables(PluginManager.java:313)

at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:636) at cytoscape.CytoscapeInit.init(CytoscapeInit.java:209)

at cytoscape.CyMain.(CyMain.java:144)

at cytoscape.CyMain.main(CyMain.java:108) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at com.exe4j.runtime.LauncherEngine.launch(Unknown Source) at com.install4j.runtime.MacLauncher.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at apple.launcher.LaunchRunner.run(LaunchRunner.java:116) at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51) at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

I uninstalled Cytoscape and installed the newer version (2.8.3), but it gives the same error. I also cannot find "Import Network from Table" function anymore in both versions.

May I ask for your help with this issue?

On Thursday, June 23, 2011 7:29:22 PM UTC+2, Scooter Morris wrote:

[Tim Hull]

Could it just be hidden from view? Files/directories with names starting with a dot (.) are hidden from most directory view by default in many cases. To see these directories, you can use the "ls -a" command, or the equivalent in the GUI. Changing to it from your home directory (i.e. "cd .cytoscape") will always work regardless of whether it appears in the directory list.

Tim

On Fri, Jan 8, 2016 at 10:47 AM, Alvaro Sechinel <sech...@gmail.com> wrote:

Hi,

I'm using the Cytoscape v2.8.3 and Ubuntu 14.04.3 LTS . The Cytoscape is with the same error, but I can not find the .cytoscape directory. It is not in my home directory.

Could you help me?

Thank you,

Alvaro

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