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problem generating graphs

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problem generating graphs mark.shifman  2014-05-12 07:41
Status: Closed
 
(I think I just sent an empty message arggg)
I am having problems generating graphs from a page that starts like this

Flow Experiment Runs > 96 WellBatch0 - PanSurf1-4 >
FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'

Run Name:    96 WellBatch0 - PanSurf1-4
Analysis Folder:    Flow Experiment Runs
Well Name:    Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs

and ends like this.
FCS Files derived from this file and associated FCS Analyses:
Name     Run Name     Analysis Folder
FCS File 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'     Panel L1.wsp     Flow Experiment Runs
FCSAnalysis 'Panel L1_C1-L1_110191_PBMC_10182011_C01.fcs'     Panel L1.wsp     Flow Experiment Runs

More Graphs
Keywords from the FCS file
Download FCS file
Experiment Run Graph Details

the complete error message is shown below.
but the jar is indeed there
root@labkey:/usr/local/labkey/labkeywebapp/WEB-INF/lib# ls jfree* jcom*
jcommon-1.0.17.jar jfreechart-1.0.14.jar

any help would be appreciated.

 ERROR WellController 2014-05-12 10:32:51,576 http-8080-6 : Error generating graph
java.lang.NoClassDefFoundError: Could not initialize class org.jfree.chart.JFreeChart
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:138)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:166)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraph(FCSAnalyzer.java:177)
    at org.labkey.flow.analysis.web.FCSAnalyzer.generateGraphs(FCSAnalyzer.java:199)
    at org.labkey.flow.script.FlowAnalyzer.generateGraph(FlowAnalyzer.java:80)
    at org.labkey.flow.controllers.well.WellController$GenerateGraphAction.getView(WellController.java:358)
    at org.labkey.flow.controllers.well.WellController$GenerateGraphAction.getView(WellController.java:349)
    at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:58)
    at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:177)
    at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
    at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:354)
    at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:989)
    at org.labkey.api.view.ViewServlet.service(ViewServlet.java:165)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:800)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:171)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:861)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:606)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:724)
 
 
Greg Taylor responded:  2014-05-12 09:17
Which version of LabKey are you running and could you describe your install a little bit? We most frequently see error messages of this type when running LabKey compiled locally from source. The solution in this case (if you have a version compiled from source) is to rebuild the application. Sometimes a sync to the source tree requires a rebuild.
Greg
 
mark.shifman responded:  2014-05-12 09:56
I am using
Core Database Configuration
Server URL    jdbc:postgresql://localhost/labkey
Product Name    PostgreSQL
Product Version    9.2.6
JDBC Driver Name    PostgreSQL Native Driver
JDBC Driver Version    PostgreSQL 9.2 JDBC4 (build 1002)
JDBC Driver Location    file:/usr/local/tomcat/lib/postgresql.jar

but hope to upgrade soon, which as you imply, should fix this problem.
LabeKey was installed before I was working on the project but I don't think they did any local
recompiling.


Thanks
mas

ps I also got a nasty message see below. Have you seen this? do I have to run tomcat as headless

-Djava.awt.headless=true

ERROR WebPartView 2014-05-12 10:11:38,362 http-8080-8 : renderView() exception in org.labkey.experiment.controllers.exp.ExperimentRunGraphView while responding to /labkey/experiment/FLU_PBMC_2010/showRunGraph.view?rowId=59
java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:190)
    at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:102)
    at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:81)
    at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1182)
    at org.labkey.api.util.ImageUtil.resizeImage(ImageUtil.java:126)
    at org.labkey.experiment.ExperimentRunGraph.generateRunGraph(ExperimentRunGraph.java:237)
    at org.labkey.experiment.controllers.exp.ExperimentRunGraphView.renderView(ExperimentRunGraphView.java:65)
 
Matthew Bellew responded:  2014-05-12 15:40
NoClassDefFoundError usually indicates a bad build. But since both of these are related to graphics, I have another idea. I'm guessing that this server is running on Linux box with no monitor (not running X11). In this case you may need to run Xvfb on the server. I don't know the gory details, but Linux can't seem to draw things without some version of X running.

https://www.labkey.org/wiki/home/Documentation/page.view?name=configVirtualFrame

Matt