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PathVisio / pathvisio4-ant

Apache License 2.0
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NPE during booting #8

Open egonw opened 2 years ago

egonw commented 2 years ago

It starts up fine, but I notice this NPE (with two lines of context):

Bundle com.sun.xml.bind.jaxb-osgi started
Core Bundle 4 with location jar:file:/home/egonw/Downloads/pathvisio.jar!/org.bridgedb.webservice.bridgerest-3.0.13.jar failed to start.
java.lang.NullPointerException
        at org.pathvisio.launcher.PathVisioMain.startBundle(PathVisioMain.java:241)
        at org.pathvisio.launcher.PathVisioMain.startBundles(PathVisioMain.java:210)
        at org.pathvisio.launcher.PathVisioMain$1.doInBackground(PathVisioMain.java:167)
        at org.pathvisio.launcher.PathVisioMain$1.doInBackground(PathVisioMain.java:131)
        at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at java.base/java.lang.Thread.run(Thread.java:829)
Bundle org.apache.xml.serializer started
Bundle org.glassfish.hk2.osgi-resource-locator started
mkutmon commented 2 years ago

same here - we are looking into it since we are not using that library in the basic PV application we are not sure where it comes from.

egonw commented 2 years ago

I think the problem is that the BridgeDb pom.xml does not have the instructions to create the bundle manifest. I will fix this in BridgeDb 3.0.15.