search

nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
Other
47 stars 23 forks source link

Problems producing PDFs #67

Closed nbjorkstrom closed 8 years ago

nbjorkstrom commented 11 years ago

Hi,

Sorry to bother but I'm having some problems producing PDFs after rearranging my tree in Cytoscape using SPADE. After clicking on Produce PDFs I see the Generate PDFs window with the option to change node size scale factor. After that, nothing happens independently if I click on 'Generate PDFs' or on 'Next'. The original PDFs are still in the output/pdf/ folder and are not being replaced. Any thought on what I'm doing wrong?

Thanks, Niklas

zbjornson commented 11 years ago

Hey Niklas,

Have you already got R and the SPADE R package installed and working? If so, which version of R are you using?

Please also have a look at the error console, Help > Error Console, and let us know if there are any messages there after an unsuccessful attempt to produce PDFs.

Best, Zach

nbjorkstrom commented 11 years ago

Hi Zach,

Yes, I've got R and the SPADE R package installed and I can use SPADE through Cytoscape to create trees. My R-version is "R 2.15.3 GUI 1.53 Leopard build 32-bit (6451)".

I'm pasting the warnings I see in the Cytoscape Error Console below. However, no new ones are showing up after I try to produce PDFs after rearranging the generated trees. So the ones in the console might be related to other things?

Thanks, Niklas

0 cytoscape.plugin.PluginManager[WARN]: ERROR registering plugin: Unable to load cytospade/plugin.props. File is not in the expected location: cytospade

Caused by: Unable to load cytospade/plugin.props. File is not in the expected location: cytospade at cytoscape.plugin.PluginProperties.readPluginProperties(PluginProperties.java:99) at cytoscape.plugin.PluginProperties.(PluginProperties.java:86) at cytoscape.plugin.PluginManager.registerPlugin(PluginManager.java:357) at cytoscape.plugin.PluginManager.register(PluginManager.java:346) at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:987) at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:944) at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:837) at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:656) 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)

1 cytoscape.plugin.PluginManager[WARN]: cytospade.CytoSpade loaded but not registered, this will not affect the operation of the plugin

On Jul 9, 2013, at 4:58 PM, Zach Bjornson notifications@github.com<mailto:notifications@github.com> wrote:

Hey Niklas,

Have you already got R and the SPADE R package installed and working? If so, which version of R are you using?

Please also have a look at the error console, Help > Error Console, and let us know if there are any messages there after an unsuccessful attempt to produce PDFs.

Best, Zach

— Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/spade/issues/67#issuecomment-20679779.

fongming commented 11 years ago

Hi Niklas,

I have the same problem as you. Did you manage to solve it?

Thanks, Fong

nbjorkstrom commented 11 years ago

Dear Fong,

I still have the same problem.

Best, Niklas

On Aug 7, 2013, at 11:50 PM, fongming notifications@github.com<mailto:notifications@github.com> wrote:

Hi Niklas,

I have the same problem as you. Did you manage to solve it?

Thanks, Fong

— Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/spade/issues/67#issuecomment-22287077.

Niklas Björkström, Assistant Professor, MD PhD niklas.bjorkstrom@ki.semailto:niklas.bjorkstrom@ki.se

Liver Immunology Laboratory and Center for Infectious Medicine Karolinska University Hospital Karolinska Institutet

Phone: +46-706977195 Web: http://www.ki.se/research/niklasbjorkstrom / http://www.ki.se/cim

zbjornson commented 8 years ago

Closing this because we no longer support the Cytoscape plugin...