These are chat archives for fiji/fiji

25th
Jul 2018
Varun Kapoor
@kapoorlab
Jul 25 2018 15:34

Hi all, I was trying to update Fiji on a Client's computer which has windows installed on it and it gave me an error and just froze the update, I do not understand this error, can anyone help? : ```
(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52e; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 1034MB of 48985MB (2%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Error: The element type "previous-version" must be terminated by the matching end-tag "</previous-version>".

Public ID: None, System ID: None,
Line number: 148, Column number: 7
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.Error: The element type "previous-version" must be terminated by the matching end-tag "</previous-version>".

Public ID: None, System ID: None,
Line number: 148, Column number: 7
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:299)
... 5 more
Caused by: java.lang.Error: The element type "previous-version" must be terminated by the matching end-tag "</previous-version>".

Public ID: None, System ID: None,
Line number: 148, Column number: 7
at net.imagej.updater.XMLFileErrorHandler.throwError(XMLFileErrorHandler.java:65)
at net.imagej.updater.XMLFileErrorHandler.fatalError(XMLFileErrorHandler.java:52)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:135)
at net.imagej.updater.XMLFileDownloader.start(XMLFileDownloader.java:94)
at net.imagej.updater.FilesCollection.downloadIndexAndChecksum(FilesCollection.java:1147)
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$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
```

Ellen T Arena
@etarena
Jul 25 2018 15:51
Just a quick question - looking for the correct 'home' for this issue: imagej/imagej1#64 ... I am wondering if it should live in the Fiji repository instead? Was a result of this recent Forum thread.
Curtis Rueden
@ctrueden
Jul 25 2018 18:23
@kapoorlab It was a problem I introduced in the db.xml.gz file on the server side. Fixed now; try updating again.
@etarena I do think that is likely to be an ImageJ1 issue. So the issue is in an OK place.
Do you know if paste() create an image overlay? Or does it bake in the pixels?
If it creates an overlay, then it makes sense that saving the file will not include the pasted pixels. A draw operation may be needed first.
"I’ve also wondered whether one should apply flatten() after the paste(), but I get a null pointer exception…" <-- I was wondering the same thing. An NPE sounds like a bug.
Ellen T Arena
@etarena
Jul 25 2018 18:26
I tried the flatten() call myself... but also got the same exception...
yes - seems to be an overlay. thanks for confirming, etc. @ctrueden