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zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
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Collision of plugins dependencies in Fiji (relates to issue #9) #27

Open zitmen opened 8 years ago

zitmen commented 8 years ago

Issue originally reported by Christophe in the forums (https://groups.google.com/forum/#!topic/thunderstorm-users/YxbUUAE-iIc).

Hi,

Using latest TS build (02082015) I get the following exception in the Fiji Console when launching ThunderSTORM>About ThunderSTORM... (OSX 10.10, Fiji latest version and Java 1.6.0_65). I also happens when clicking on any "?" help in TS dialogs (for exemple the one in the camera setup dialog). When launching these help windows I also have the Console window starting to flickering very rapidly until I click somewhere and it just displays the exception.

Christophe

stream : jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/plugins/Thunder_STORM.jar!/resources/help/about.html SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/jars/logback-classic-1.1.1.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/plugins/Thunder_STORM.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. Failed to auto configure default logger context Reported exception: ch.qos.logback.core.joran.spi.JoranException: Parser configuration error occurred at ch.qos.logback.core.joran.event.SaxEventRecorder.buildSaxParser(SaxEventRecorder.java:88) at ch.qos.logback.core.joran.event.SaxEventRecorder.recordEvents(SaxEventRecorder.java:59) at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:134) at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:99) at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:49) at ch.qos.logback.classic.util.ContextInitializer.configureByResource(ContextInitializer.java:75) at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:148) at org.slf4j.impl.StaticLoggerBinder.init(StaticLoggerBinder.java:85) at org.slf4j.impl.StaticLoggerBinder.(StaticLoggerBinder.java:55) at org.slf4j.LoggerFactory.bind(LoggerFactory.java:128) at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:107) at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:295) at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:269) at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:281) at org.fit.cssbox.css.DOMAnalyzer.(DOMAnalyzer.java:49) at org.fit.cssbox.swingbox.util.DefaultAnalyzer.analyze(DefaultAnalyzer.java:52) at org.fit.cssbox.swingbox.util.ContentReader.read(ContentReader.java:112) at org.fit.cssbox.swingbox.SwingBoxEditorKit.readImpl(SwingBoxEditorKit.java:402) at org.fit.cssbox.swingbox.SwingBoxEditorKit.read(SwingBoxEditorKit.java:234) at org.fit.cssbox.swingbox.BrowserPane.read(BrowserPane.java:795) at org.fit.cssbox.swingbox.BrowserPane.loadPage(BrowserPane.java:556) at org.fit.cssbox.swingbox.BrowserPane.setPage(BrowserPane.java:499) at cz.cuni.lf1.lge.ThunderSTORM.AboutPlugIn.run(AboutPlugIn.java:62) at ij.IJ.runUserPlugIn(IJ.java:212) at ij.IJ.runPlugIn(IJ.java:176) at ij.Executer.runCommand(Executer.java:132) at ij.Executer.run(Executer.java:65) at java.lang.Thread.run(Thread.java:695) Caused by: java.lang.ClassCastException: org.apache.xerces.jaxp.SAXParserFactoryImpl cannot be cast to javax.xml.parsers.SAXParserFactory at javax.xml.parsers.SAXParserFactory.newInstance(Unknown Source) at ch.qos.logback.core.joran.event.SaxEventRecorder.buildSaxParser(SaxEventRecorder.java:81) ... 27 more 21:42:15,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy] 21:42:15,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 21:42:15,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] 21:42:15,787 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath. 21:42:15,787 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] 21:42:15,787 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/plugins/Thunder_STORM.jar!/logback.xml] 21:42:15,798 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@16334cb9 - URL [jar:file:/Users/christo/Travail/Labo/Processing/Fiji_current/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] is not of type file 21:42:15,803 |-ERROR in ch.qos.logback.core.joran.event.SaxEventRecorder@1f21112 - Parser configuration error occurred java.lang.ClassCastException: org.apache.xerces.jaxp.SAXParserFactoryImpl cannot be cast to javax.xml.parsers.SAXParserFactory at java.lang.ClassCastException: org.apache.xerces.jaxp.SAXParserFactoryImpl cannot be cast to javax.xml.parsers.SAXParserFactory at at javax.xml.parsers.SAXParserFactory.newInstance(Unknown Source) at at ch.qos.logback.core.joran.event.SaxEventRecorder.buildSaxParser(SaxEventRecorder.java:81) at at ch.qos.logback.core.joran.event.SaxEventRecorder.recordEvents(SaxEventRecorder.java:59) at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:134) at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:99) at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:49) at at ch.qos.logback.classic.util.ContextInitializer.configureByResource(ContextInitializer.java:75) at at ch.qos.logback.classic.util.ContextInitializer.autoConfig(ContextInitializer.java:148) at at org.slf4j.impl.StaticLoggerBinder.init(StaticLoggerBinder.java:85) at at org.slf4j.impl.StaticLoggerBinder.(StaticLoggerBinder.java:55) at at org.slf4j.LoggerFactory.bind(LoggerFactory.java:128) at at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:107) at at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:295) at at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:269) at at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:281) at at org.fit.cssbox.css.DOMAnalyzer.(DOMAnalyzer.java:49) at at org.fit.cssbox.swingbox.util.DefaultAnalyzer.analyze(DefaultAnalyzer.java:52) at at org.fit.cssbox.swingbox.util.ContentReader.read(ContentReader.java:112) at at org.fit.cssbox.swingbox.SwingBoxEditorKit.readImpl(SwingBoxEditorKit.java:402) at at org.fit.cssbox.swingbox.SwingBoxEditorKit.read(SwingBoxEditorKit.java:234) at at org.fit.cssbox.swingbox.BrowserPane.read(BrowserPane.java:795) at at org.fit.cssbox.swingbox.BrowserPane.loadPage(BrowserPane.java:556) at at org.fit.cssbox.swingbox.BrowserPane.setPage(BrowserPane.java:499) at at cz.cuni.lf1.lge.ThunderSTORM.AboutPlugIn.run(AboutPlugIn.java:62) at at ij.IJ.runUserPlugIn(IJ.java:212) at at ij.IJ.runPlugIn(IJ.java:176) at at ij.Executer.runCommand(Executer.java:132) at at ij.Executer.run(Executer.java:65) at at java.lang.Thread.run(Thread.java:695)

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]