I've just upgraded to IGB 8.5.1 and I can't see any of my QuickLoad servers or all - bar three (strange?!) - of my bookmarks. Annoying!
What's odd is that I can see the bookmarks in ~/.igb/bookmarks.html
How can I get these things back? Especially the bookmarks as I've crafted them over many years....
Hello Chris,
I will notify the team and figure out what has happened. I'm very sorry for the inconvenience. Losing bookmarks is not good.
Yours,
Ann
Hi Chris,
Its not clear from your post if you were able to get all of your servers restored on IGB 8.5.1? Your description of only being able to add new servers every second attempt is something I personally am not able to reproduce, but I will make sure to follow up with my testing team further to ensure we don't miss anything.
Are your bookmarks still not showing up in IGB 8.5.1? If not, could you please send me the content of your logs after starting IGB? To see the logs, navigate to Help -> Show Console, or press Ctrl-Shift-C (or CMD+Shift+C on Mac). Your log output could be very helpful for me to understand what may be happening to prevent bookmarks from loading.
I apologize for the instability you seem to be experiencing in the latest release. I can assure you we will patch any bugs we can reproduce on our end very quickly, so your help understanding the cause of the problems you have described would be very much appreciated.
Best Regards,
David Norris
Hi David,
I can restore my servers, but they only appear after every second attempt. To clarify, I click 'Configure' on the 'Data Access' tab, click 'Add...', fill in the details of Server A and click submit. There are no errors and the console suggests it's recognised, but the new server does not show up on the list. Then if I add another server (e.g. Server B) in the same way upon submit 'Server A' appears on the list, but not server B.
I note that the servers are not saved. If I restart IGB the servers are gone again. Might be related to the loss of bookmarks?
Btw here's the output from the console, there appears to a be few errors. This is on OSX 10.10.5 BTW
| 10:15:08.084 INFO c.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor | |
| 10:15:09.219 INFO c.l.quickload.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/ | |
| 10:15:10.098 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading old data providers from preferences | |
| 10:15:10.110 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem | |
| ERROR: igb (31): [PrefsLoader(39)] The activate method has thrown an exception | |
| java.lang.IllegalArgumentException: encrypted string was null or empty | |
| at com.affymetrix.genometry.util.StringEncrypter.decrypt(StringEncrypter.java:98) | |
| at com.affymetrix.genometry.data.BaseDataProvider.lambda$loadPersistedConfiguration$18(BaseDataProvider.java:69) | |
| at java.util.Optional.ifPresent(Optional.java:159) | |
| at com.affymetrix.genometry.data.BaseDataProvider.loadPersistedConfiguration(BaseDataProvider.java:69) | |
| at com.affymetrix.genometry.data.BaseDataProvider.<init>(BaseDataProvider.java:49) | |
| at com.lorainelab.quickload.QuickloadDataProvider.<init>(QuickloadDataProvider.java:61) | |
| at com.lorainelab.quickload.QuickloadFactory.createDataProvider(QuickloadFactory.java:39) | |
| at com.affymetrix.igb.general.DataProviderManager.lambda$initializeDataProvider$12(DataProviderManager.java:192) | |
| at java.util.Optional.ifPresent(Optional.java:159) | |
| at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:189) | |
| at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) | |
| at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) | |
| at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948) | |
| at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) | |
| at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) | |
| at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) | |
| at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) | |
| at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) | |
| at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) | |
| at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.loadFromPersistenceStorage(IgbPreferencesLoadingOrchestrator.java:102) | |
| at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.loadIGBPrefs(IgbPreferencesLoadingOrchestrator.java:72) | |
| at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.activate(IgbPreferencesLoadingOrchestrator.java:50) | |
| at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) | |
| at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) | |
| at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) | |
| at java.lang.reflect.Method.invoke(Method.java:497) | |
| at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231) | |
| at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39) | |
| at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624) | |
| at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508) | |
| at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149) | |
| at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315) | |
| at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127) | |
| at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871) | |
| at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850) | |
| at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931) | |
| at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432) | |
| at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987) | |
| at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838) | |
| at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545) | |
| at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560) | |
| at org.apache.felix.framework.Felix.registerService(Felix.java:3542) | |
| at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992) | |
| at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841) | |
| at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931) | |
| at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148) | |
| at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432) | |
| at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987) | |
| at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838) | |
| at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545) | |
| at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560) | |
| at org.apache.felix.framework.Felix.registerService(Felix.java:3542) | |
| at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992) | |
| at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841) | |
| at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419) | |
| at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376) | |
| at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172) | |
| at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120) | |
| at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258) | |
| at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45) | |
| at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185) | |
| at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259) | |
| at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232) | |
| at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479) | |
| at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414) | |
| at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232) | |
| at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443) | |
| at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:913) | |
| at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:834) | |
| at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:516) | |
| at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4544) | |
| at org.apache.felix.framework.Felix.startBundle(Felix.java:2166) | |
| at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1365) | |
| at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308) | |
| at java.lang.Thread.run(Thread.java:745) | |
| ERROR: igb (31): [PrefsLoader(39)] Failed creating the component instance; see log for reason | |
| 10:15:10.241 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. | |
| 10:15:10.241 INFO c.a.igb.IgbServiceDependencyManager - Console Service now available. | |
| 10:15:10.242 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. | |
| 10:15:10.242 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. | |
| 10:15:10.242 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. | |
| 10:15:10.243 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. | |
| 10:15:10.243 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. | |
| 10:15:10.243 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. | |
| 10:15:10.244 INFO com.affymetrix.igb.Activator - Starting IGB | |
| 10:15:10.976 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 8.5.1 | |
| 10:15:10.977 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_66 from Oracle Corporation | |
| 10:15:10.986 INFO com.affymetrix.igb.IGB - System memory: 1.9 GB | |
| 10:15:12.473 INFO c.l.quickload.QuickloadDataProvider - Initializing Quickload Server http://www.igbquickload.org/pollen/ | |
| 10:15:13.672 WARN c.l.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://www.igbquickload.org/pollen/synonyms.txt | |
| 10:15:13.904 WARN c.l.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://www.igbquickload.org/pollen/species.txt | |
| 10:15:13.912 INFO c.l.quickload.QuickloadDataProvider - Initializing Quickload Server http://www.igbquickload.org/cyto/ | |
| 10:15:15.099 WARN c.l.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://www.igbquickload.org/cyto/synonyms.txt | |
| 10:15:15.350 WARN c.l.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://www.igbquickload.org/cyto/species.txt | |
| 10:15:15.356 INFO c.l.quickload.QuickloadDataProvider - Initializing Quickload Server http://www.igbquickload.org/blueberry/ | |
| 10:15:16.575 WARN c.l.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://www.igbquickload.org/blueberry/synonyms.txt | |
| 10:15:16.809 WARN c.l.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://www.igbquickload.org/blueberry/species.txt | |
| 10:15:21.142 ERROR com.affymetrix.igb.IGB - Trying to add set keystroke for action com.lorainelab.logging.console.ShowConsoleAction. But action class com.lorainelab.logging.console.ShowConsoleAction exists with same keystroke "shift ctrl pressed C". | |
| Using keystroke with latest action. | |
| 10:15:21.143 ERROR com.affymetrix.igb.IGB - Trying to add set keystroke for action com.affymetrix.igb.action.HomeAction. But action class com.affymetrix.igb.action.HomeAction exists with same keystroke "meta pressed H". | |
| Using keystroke with latest action. | |
| 10:15:23.226 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file /Users/ccole/.igb/bookmarks.html | |
| 10:15:23.238 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file /Users/ccole/.igb/bookmarks.html~ | |
| 10:15:23.845 INFO com.affymetrix.igb.Activator - IGB Started | |
| 10:15:24.114 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework | |
| 10:15:24.114 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common | |
| 10:15:24.115 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab | |
| 10:15:24.115 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library | |
| 10:15:24.115 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.bam | |
| 10:15:24.115 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.bed | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: BigWig | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.cache | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.cache-api | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec | |
| 10:15:24.116 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-gui | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das | |
| 10:15:24.117 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das2 | |
| 10:15:24.118 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.external-sort | |
| 10:15:24.118 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView | |
| 10:15:24.118 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.feedback | |
| 10:15:24.118 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager | |
| 10:15:24.119 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry | |
| 10:15:24.119 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz | |
| 10:15:24.119 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab | |
| 10:15:24.119 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson | |
| 10:15:24.119 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava | |
| 10:15:24.120 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor | |
| 10:15:24.120 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb | |
| 10:15:24.120 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions | |
| 10:15:24.120 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util | |
| 10:15:24.120 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch | |
| 10:15:24.121 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry | |
| 10:15:24.122 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic | |
| 10:15:24.122 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core | |
| 10:15:24.122 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.logging-config | |
| 10:15:24.122 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.narrowpeak | |
| 10:15:24.123 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast | |
| 10:15:24.123 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository | |
| 10:15:24.123 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr | |
| 10:15:24.123 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.plugins-manager | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps | |
| 10:15:24.124 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView | |
| 10:15:24.125 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer | |
| 10:15:24.125 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager | |
| 10:15:24.125 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper | |
| 10:15:24.125 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api | |
| 10:15:24.125 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: tutorial | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update | |
| 10:15:24.126 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks | |
| 10:15:24.127 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service | |
| 10:15:24.127 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.lorainelab.protannot | |
| 10:15:24.127 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0 |
Hi Chris,
Thank you for passing along this stacktrace. Thanks to this, we were able to reproduce the problem.
Sorry for not getting back to you sooner - my biostars account seems to be broken at the moment and I am just now seeing your email.
In a nutshell, what has happened is that IGB has saved an empty string as a password for one of your Quickload servers. Probably this happened by accident - not your fault at all. When IGB tries to initialize those servers, the password decryption routine throws an exception.
I'll email you off-line (please send me your email) with ideas for a potential fix that will save you the trouble of re-setting your preferences. But if you are able to do that, I'm confident that will fix the problem.
In the meantime, if anyone else encounters this problem, an easy, fast fix is to reset your Preferences.
Chris, please feel free to use my personal email to accelerate our exchange. (dcnorris@uncc.edu)
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Trying to re-add my QL servers and it's very inconsistent. IGB only seems to be able to add new servers for every second entry.
8.5 doesn't seem like a great upgrade to me, unfortunately.