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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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jar error #26

Closed easch closed 8 years ago

easch commented 8 years ago

Mac OSX 10.10.4; ImageJ 2.0.0-rc-32/1.49v; Thunderstorm 1.3 (2014-11-8)

Click on "About ThunderSTORM" produces output below. Subsequent attempt to "Merge" produces java.lang.NullPointerException error

pageProperties

stream : jar:file:/Users/ea/Desktop/Fiji.app/plugins/Thunder_STORM.jar!/resources/help/about.html SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/ea/Desktop/Fiji.app/jars/logback-classic-1.1.1.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/ea/Desktop/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:199) at ij.IJ.runPlugIn(IJ.java:163) 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 12:25:01,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy] 12:25:01,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 12:25:01,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/Users/ea/Desktop/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] 12:25:01,895 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath. 12:25:01,895 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/Users/ea/Desktop/Fiji.app/plugins/Thunder_STORM.jar!/logback.xml] 12:25:01,895 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/Users/ea/Desktop/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] 12:25:01,909 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@70d18a80 - URL [jar:file:/Users/ea/Desktop/Fiji.app/jars/scijava-config-2.0.0.jar!/logback.xml] is not of type file 12:25:01,916 |-ERROR in ch.qos.logback.core.joran.event.SaxEventRecorder@4cdc135d - 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:199) at at ij.IJ.runPlugIn(IJ.java:163) 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]

zitmen commented 8 years ago

Hi,

I was not able to replicate youe problem with the About dialog. This might be caused by some incompatibility with another plugin. As for the merging, I replicated this. This is probably an old issue, which has been already resolved, because it didn't happen after I updated to the latest daily build. Please be sure to update to the latest daily version before reporting bugs. The dev branch is usually stable and contains fixes of reported bugs.

Best, Martin