imagej / imagej/imagej2

Java runtime errors on launch: namespace reporting not enabled

Open
#249 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Java
Stars
1.4k
Forks
350
PR merge metrics
No merged PRs in 30d

Description

I'm getting a couple errors on launch of Fiji that seem to be keeping me from being able to update the updatesites list, too.

I'm using a Macbook Pro (mid 2014) running Mojave 10.14.6
ImageJ version is 2.0.0-rc-69/1.52u (same errors appeared on 1.52p)
Build 269a0ad53f

Java is Version 8 Update 221 (build 1.8.0_221-b11) and my Java control panel claims that my system has the recommended version of Java.

The error message I get is below in the code tags, and when I google it, it appears that the error isn't something I can fix by changing settings at my end.

[ERROR] Error processing available update sites from ImageJ wiki
java.lang.RuntimeException: XPathFactory#newInstance() failed to create an XPathFactory for the default object model: http://java.sun.com/jaxp/xpath/dom with the XPathFactoryConfigurationException: javax.xml.xpath.XPathFactoryConfigurationException: java.util.ServiceConfigurationError: javax.xml.xpath.XPathFactory: jar:file:/Library/Java/Extensions/saxon9he.jar!/META-INF/services/javax.xml.xpath.XPathFactory:2: Illegal configuration-file syntax
	at javax.xml.xpath.XPathFactory.newInstance(XPathFactory.java:102)
	at org.scijava.util.XML.<init>(XML.java:142)
	at org.scijava.util.XML.<init>(XML.java:103)
	at net.imagej.util.MediaWikiClient.request(MediaWikiClient.java:234)
	at net.imagej.util.MediaWikiClient.query(MediaWikiClient.java:243)
	at net.imagej.util.MediaWikiClient.getPageSource(MediaWikiClient.java:109)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:79)
	at net.imagej.updater.util.AvailableSites.tryGetAvailableSites(AvailableSites.java:177)
	at net.imagej.updater.util.AvailableSites.initializeAndAddSites(AvailableSites.java:140)
	at net.imagej.ui.swing.updater.ImageJUpdater.refreshUpdateSites(ImageJUpdater.java:257)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:145)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
org.xml.sax.SAXException: Parser configuration problem: namespace reporting is not enabled
	at net.sf.saxon.event.ReceivingContentHandler.getNodeName(ReceivingContentHandler.java:383)
	at net.sf.saxon.event.ReceivingContentHandler.startElement(ReceivingContentHandler.java:291)
	at net.imagej.updater.XMLFileWriter.write(XMLFileWriter.java:156)
	at net.imagej.updater.FilesCollection.write(FilesCollection.java:439)
	at net.imagej.updater.util.AvailableSites.applySitesURLUpdates(AvailableSites.java:299)
	at net.imagej.ui.swing.updater.ImageJUpdater.refreshUpdateSites(ImageJUpdater.java:262)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:145)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the stack-trace entry points in org.scijava.util.XML, net.imagej.util.MediaWikiClient, AvailableSites, and XMLFileWriter, then reproduce launch and update-site refresh on the reported Java and macOS setup. Trace the XPathFactory and namespace-reporting failures; done means Fiji launches and refreshes the update-sites list without either error.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.