[IGBF-1457] Startup Error in Console (ERROR com.affymetrix.main.OSGiHandler) - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.0.2 Minor Release
Labels:
- Advanced

Story Points:
0.25
Sprint:
Fall 2018 Sprint 4, Fall 2018 Sprint 5

Description

The following error is seen in the console when starting 9.0.2:

09:51:16.336 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve htsjdk-igb [34](R 34.0): missing requirement [htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)]
org.osgi.framework.BundleException: Unable to resolve htsjdk-igb [34](R 34.0): missing requirement [htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4114) ~[igb_exe.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2111) ~[igb_exe.jar:na]
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:977) ~[igb_exe.jar:na]
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:964) ~[igb_exe.jar:na]
at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) [igb_exe.jar:na]
at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) [igb_exe.jar:na]
at com.affymetrix.main.Main.main(Main.java:30) [igb_exe.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_152]
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_152]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_152]
at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_152]
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:81) [i4jruntime.jar:na]
at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94) [i4jruntime.jar:na]
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25) [i4jruntime.jar:na]

Attachments

Issue Links

relates to

IGBF-1418 Import htsjdk as OSGi bundle

Closed

Activity

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Mason Meyer (Inactive) created issue - 08/Nov/18 9:53 AM

Ann Loraine made changes - 08/Nov/18 9:54 AM

Field	Original Value	New Value
Rank		Ranked higher

Ann Loraine made changes - 08/Nov/18 9:54 AM

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Mason Meyer (Inactive) added a comment - 08/Nov/18 9:54 AM

Rest of Console Content:

09:51:10.069 INFO org.amdatu.remote.AbstractComponent - Adding Remote Service Admin: [org.osgi.service.remoteserviceadmin.RemoteServiceAdmin]
09:51:10.082 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor
09:51:10.123 INFO org.amdatu.remote.AbstractComponent - Configured export filter updated: (service.exported.interfaces=*)
09:51:10.135 INFO org.amdatu.remote.AbstractComponent - Configured import filter updated: (!(endpoint.framework.uuid=fac6ff4c-c115-40da-a6dd-eb375688f4c1))
09:51:10.564 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem
09:51:10.572 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem
09:51:10.633 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available.
09:51:10.637 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available.
09:51:10.637 INFO c.a.igb.IgbServiceDependencyManager - Console Service now available.
09:51:10.638 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available.
09:51:10.639 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available.
09:51:10.642 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available.
09:51:10.645 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available.
09:51:10.645 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available.
09:51:10.648 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available.
09:51:10.648 INFO com.affymetrix.igb.Activator - Starting IGB
09:51:11.169 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/rnaseq/
09:51:11.629 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 9.0.2
09:51:11.629 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_152 from Oracle Corporation
09:51:11.632 INFO com.affymetrix.igb.IGB - System memory: 3.8 GB
09:51:11.830 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/rnaseq/synonyms.txt
09:51:12.061 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/rnaseq/species.txt
09:51:12.133 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/
09:51:13.259 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/quickload/synonyms.txt
09:51:13.852 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/blueberry/
09:51:16.029 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file C:\Users\Mason\AppData\Roaming\IGB\bookmarks.html
09:51:16.033 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file C:\Users\Mason\AppData\Roaming\IGB\bookmarks.html~
09:51:16.270 INFO com.affymetrix.igb.Activator - IGB Started
09:51:16.324 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework
09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common
09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab
09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig
09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv
09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io
09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl
09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3
09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging
09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-gui
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das2
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView
09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson
09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava
09:51:16.331 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor
09:51:16.331 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb
09:51:16.336 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve htsjdk-igb [34](R 34.0): missing requirement [htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)]
org.osgi.framework.BundleException: Unable to resolve htsjdk-igb [34](R 34.0): missing requirement [htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34](R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)]
at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4114) ~[igb_exe.jar:na]
at org.apache.felix.framework.Felix.startBundle(Felix.java:2111) ~[igb_exe.jar:na]
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:977) ~[igb_exe.jar:na]
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:964) ~[igb_exe.jar:na]
at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) [igb_exe.jar:na]
at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) [igb_exe.jar:na]
at com.affymetrix.main.Main.main(Main.java:30) [igb_exe.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_152]
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_152]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:1.8.0_152]
at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.8.0_152]
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:81) [i4jruntime.jar:na]
at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94) [i4jruntime.jar:na]
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25) [i4jruntime.jar:na]
09:51:16.338 [main] ERROR com.affymetrix.main.OSGiHandler - Error starting bundle htsjdk-igb:2.16.1
09:51:16.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb
09:51:16.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions
09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util
09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences
09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services
09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript
09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-annotations
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-core
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-databind
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch
09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast
09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.dependencymanager
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api
09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.api
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.commons
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.discovery.provider.configured
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.distribution.provider.http
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.topology.manager
09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn
09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.remoteserviceadmin
09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor
09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager
09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView
09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api
09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz
09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0
09:51:17.508 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/blueberry/synonyms.txt
09:51:17.631 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/blueberry/species.txt
09:51:17.638 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/soyseq/
09:51:18.300 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/soyseq/synonyms.txt
09:51:18.419 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/soyseq/species.txt
09:51:18.420 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/
09:51:18.707 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt
09:51:18.820 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt
09:51:18.821 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/dnaseq/
09:51:19.141 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/dnaseq/synonyms.txt
09:51:19.261 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/dnaseq/species.txt
09:51:19.262 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/
09:51:19.542 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt
09:51:19.663 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt

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Mason Meyer (Inactive) added a comment - 08/Nov/18 9:54 AM Rest of Console Content: 09:51:10.069 INFO org.amdatu.remote.AbstractComponent - Adding Remote Service Admin: [org.osgi.service.remoteserviceadmin.RemoteServiceAdmin] 09:51:10.082 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor 09:51:10.123 INFO org.amdatu.remote.AbstractComponent - Configured export filter updated: (service.exported.interfaces=*) 09:51:10.135 INFO org.amdatu.remote.AbstractComponent - Configured import filter updated: (!(endpoint.framework.uuid=fac6ff4c-c115-40da-a6dd-eb375688f4c1)) 09:51:10.564 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem 09:51:10.572 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem 09:51:10.633 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available. 09:51:10.637 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. 09:51:10.637 INFO c.a.igb.IgbServiceDependencyManager - Console Service now available. 09:51:10.638 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. 09:51:10.639 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. 09:51:10.642 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. 09:51:10.645 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. 09:51:10.645 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. 09:51:10.648 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. 09:51:10.648 INFO com.affymetrix.igb.Activator - Starting IGB 09:51:11.169 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/rnaseq/ 09:51:11.629 INFO com.affymetrix.igb.IGB - Starting: Integrated Genome Browser 9.0.2 09:51:11.629 INFO com.affymetrix.igb.IGB - Java version: 1.8.0_152 from Oracle Corporation 09:51:11.632 INFO com.affymetrix.igb.IGB - System memory: 3.8 GB 09:51:11.830 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/rnaseq/synonyms.txt 09:51:12.061 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/rnaseq/species.txt 09:51:12.133 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/quickload/ 09:51:13.259 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/quickload/synonyms.txt 09:51:13.852 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/blueberry/ 09:51:16.029 INFO c.a.i.b.action.BookmarkActionManager - Loading bookmarks from file C:\Users\Mason\AppData\Roaming\IGB\bookmarks.html 09:51:16.033 INFO c.a.i.b.action.BookmarkActionManager - Saving bookmarks to file C:\Users\Mason\AppData\Roaming\IGB\bookmarks.html~ 09:51:16.270 INFO com.affymetrix.igb.Activator - IGB Started 09:51:16.324 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.framework 09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: affymetrix-common 09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: annotation-tab 09:51:16.325 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: apollo-library 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bam 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.bed 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigBedHandler 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bigWigHandler 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.broad.igv.bigwig 09:51:16.326 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: bookmark 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.cache-api 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.codec 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.compress 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.csv 09:51:16.327 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.io 09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.jexl 09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.lang3 09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.logging 09:51:16.328 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.commons.pool 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: console-gui 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: context-menu-service 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: das2 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.external-sort 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: externalView 09:51:16.329 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.feedback 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: frameManager 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: genometry 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.affymetrix.genoviz 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: graphTab 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.gson 09:51:16.330 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.google.guava 09:51:16.331 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: heatmap-editor 09:51:16.331 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: htsjdk-igb 09:51:16.336 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve htsjdk-igb [34] (R 34.0): missing requirement [htsjdk-igb [34] (R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34] (R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)] org.osgi.framework.BundleException: Unable to resolve htsjdk-igb [34] (R 34.0): missing requirement [htsjdk-igb [34] (R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect) Unresolved requirements: [[htsjdk-igb [34] (R 34.0)] osgi.wiring.package; (osgi.wiring.package=scala.reflect)] at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4114) ~ [igb_exe.jar:na] at org.apache.felix.framework.Felix.startBundle(Felix.java:2111) ~ [igb_exe.jar:na] at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:977) ~ [igb_exe.jar:na] at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:964) ~ [igb_exe.jar:na] at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) [igb_exe.jar:na] at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) [igb_exe.jar:na] at com.affymetrix.main.Main.main(Main.java:30) [igb_exe.jar:na] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~ [na:1.8.0_152] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~ [na:1.8.0_152] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~ [na:1.8.0_152] at java.lang.reflect.Method.invoke(Unknown Source) ~ [na:1.8.0_152] at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:81) [i4jruntime.jar:na] at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94) [i4jruntime.jar:na] at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25) [i4jruntime.jar:na] 09:51:16.338 [main] ERROR com.affymetrix.main.OSGiHandler - Error starting bundle htsjdk-igb:2.16.1 09:51:16.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb 09:51:16.339 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-genoviz-extensions 09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-javafx-util 09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-preferences 09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igb-services 09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbScript 09:51:16.340 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: igbSwingExt 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: image-exporter 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-annotations 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-core 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.fasterxml.jackson.core.jackson-databind 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: com.jidesoft.ultimate 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keyWordSearch 09:51:16.341 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: keybinding-registry 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.classic 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ch.qos.logback.core 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.logging-config 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.narrowpeak 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: ncbiBlast 09:51:16.342 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.bundlerepository 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.configadmin 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.dependencymanager 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.bundle 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.jetty 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.http.servlet-api 09:51:16.343 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.apache.felix.scr 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.api 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.error.reporter.manager 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.menu.api 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.commons 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.discovery.provider.configured 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.distribution.provider.http 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.remote.services.topology.manager 09:51:16.344 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: osgi.cmpn 09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.osgi.service.remoteserviceadmin 09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: paired-data-preprocessor 09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.lorainelab.igb.plugins-manager 09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: propertyView 09:51:16.345 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: quickload 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: restrictionSites 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchModelIdOrProps 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: searchView 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: sequenceViewer 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: session-manager 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: shared-lib-wrapper 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: slf4j.api 09:51:16.346 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: survey 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: synonym-lookup 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: thresholding 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: track-operations-panel 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: update 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: weblinks 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: window-service 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - Starting Bundle: org.tukaani.xz 09:51:16.347 [main] INFO com.affymetrix.main.OSGiHandler - OSGi is started with org.apache.felix.framework version 5.2.0 09:51:17.508 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/blueberry/synonyms.txt 09:51:17.631 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/blueberry/species.txt 09:51:17.638 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/soyseq/ 09:51:18.300 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://igbquickload.org/soyseq/synonyms.txt 09:51:18.419 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://igbquickload.org/soyseq/species.txt 09:51:18.420 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/bar/ 09:51:18.707 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/bar/synonyms.txt 09:51:18.820 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/bar/species.txt 09:51:18.821 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/dnaseq/ 09:51:19.141 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/dnaseq/synonyms.txt 09:51:19.261 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/dnaseq/species.txt 09:51:19.262 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/chipseq/ 09:51:19.542 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://lorainelab-quickload.scidas.org/chipseq/synonyms.txt 09:51:19.663 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://lorainelab-quickload.scidas.org/chipseq/species.txt

Ann Loraine made changes - 08/Nov/18 9:55 AM

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Ann Loraine [ aloraine ]

Kiran Korey [ kkorey ]

Ann Loraine made changes - 08/Nov/18 9:56 AM

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Kiran Korey (Inactive) made changes - 08/Nov/18 12:41 PM

Status

Open [ 1 ]

In Progress [ 3 ]

Kiran Korey (Inactive) made changes - 08/Nov/18 2:32 PM

Status

In Progress [ 3 ]

Pull Request Submitted [ 10101 ]

Kiran Korey (Inactive) made changes - 08/Nov/18 2:32 PM

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Kiran Korey [ kkorey ]

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Ann Loraine added a comment - 08/Nov/18 2:48 PM

Merged, built, deployed to https://nexus.bioviz.org as htsjdk-2.16.2
Note we are departing from previous intended convention of mirroring htsjdk release tags in our artifact id.

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Ann Loraine added a comment - 08/Nov/18 2:48 PM Merged, built, deployed to https://nexus.bioviz.org as htsjdk-2.16.2 Note we are departing from previous intended convention of mirroring htsjdk release tags in our artifact id.

Ann Loraine made changes - 08/Nov/18 4:26 PM

Link

This issue relates to ~~IGBF-1418~~ [ ~~IGBF-1418~~ ]

Ann Loraine made changes - 08/Nov/18 4:26 PM

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0.25

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Ann Loraine added a comment - 08/Nov/18 4:30 PM

Pull request to update pom.xml in IGB project is merged into release branch from https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1457-startup

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Ann Loraine added a comment - 08/Nov/18 4:30 PM Pull request to update pom.xml in IGB project is merged into release branch from https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1457-startup

Ann Loraine made changes - 08/Nov/18 5:01 PM

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Pull Request Submitted [ 10101 ]

Needs Testing [ 10002 ]

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Ann Loraine added a comment - 08/Nov/18 5:02 PM

Please test.

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Ann Loraine added a comment - 08/Nov/18 5:02 PM Please test.

Ann Loraine made changes - 08/Nov/18 5:02 PM

Assignee

Mason Meyer [ mason ]

Mason Meyer (Inactive) made changes - 12/Nov/18 8:23 AM

Status

Needs Testing [ 10002 ]

Testing In Progress [ 10003 ]

Ann Loraine made changes - 12/Nov/18 3:17 PM

Rank

Ranked higher

Ann Loraine made changes - 12/Nov/18 3:19 PM

Sprint

Fall 2018 Sprint 4 [ 54 ]

Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 54, 55 ]

Ann Loraine made changes - 12/Nov/18 3:19 PM

Rank

Ranked lower

Ann Loraine made changes - 28/Nov/18 1:03 PM

Resolution		Done [ 10000 ]
Status	Testing In Progress [ 10003 ]	Closed [ 6 ]

Ann Loraine made changes - 28/Nov/18 1:04 PM

Assignee

Mason Meyer [ mason ]

Kiran Korey [ kkorey ]

Ann Loraine made changes - 27/Aug/19 4:59 PM

Workflow

Loraine Lab Workflow [ 18165 ]

Fall 2019 Workflow Update [ 19977 ]

Ann Loraine made changes - 16/Oct/19 5:49 PM

Workflow

Fall 2019 Workflow Update [ 19977 ]

Revised Fall 2019 Workflow Update [ 22099 ]

People

Assignee:

Kiran Korey (Inactive)

Reporter:

Mason Meyer (Inactive)

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Dates

Created:

08/Nov/18 9:53 AM

Updated:

28/Nov/18 1:04 PM

Resolved:

28/Nov/18 1:03 PM