{"action":"closed","issue":{"url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/issues/52","labels_url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/issues/52/labels{/name}","comments_url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/issues/52/comments","events_url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/issues/52/events","html_url":"https://github.com/BaderLab/EnrichmentMapApp/issues/52","id":50380098,"number":52,"title":"AutoAnnotate error log","user":{"login":"veroniquevoisin","id":7570379,"avatar_url":"https://avatars.githubusercontent.com/u/7570379?v=3","gravatar_id":"","url":"https://api.github.com/users/veroniquevoisin","html_url":"https://github.com/veroniquevoisin","followers_url":"https://api.github.com/users/veroniquevoisin/followers","following_url":"https://api.github.com/users/veroniquevoisin/following{/other_user}","gists_url":"https://api.github.com/users/veroniquevoisin/gists{/gist_id}","starred_url":"https://api.github.com/users/veroniquevoisin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/veroniquevoisin/subscriptions","organizations_url":"https://api.github.com/users/veroniquevoisin/orgs","repos_url":"https://api.github.com/users/veroniquevoisin/repos","events_url":"https://api.github.com/users/veroniquevoisin/events{/privacy}","received_events_url":"https://api.github.com/users/veroniquevoisin/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/labels/AutoAnnotate","name":"AutoAnnotate","color":"bfdadc"},{"url":"https://api.github.com/repos/BaderLab/EnrichmentMapApp/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2014-11-28T14:38:39Z","updated_at":"2015-02-12T15:39:39Z","closed_at":"2015-02-12T15:39:39Z","body":"Hi Ruth,\r\nhere is the log from yesterday's trial:\r\n\r\n###########################\r\ntried to remove the annotations: Annotation Sets: \"REMOVE\"\r\n###########################\r\n\r\njava.util.ConcurrentModificationException\r\n\tat java.util.HashMap$HashIterator.nextEntry(HashMap.java:894)\r\n\tat java.util.HashMap$KeyIterator.next(HashMap.java:928)\r\n\tat org.cytoscape.ding.impl.cyannotator.CyAnnotator.updateNetworkAttributes(CyAnnotator.java:357)\r\n\tat org.cytoscape.ding.impl.cyannotator.CyAnnotator.removeAnnotation(CyAnnotator.java:280)\r\n\tat org.cytoscape.ding.impl.cyannotator.annotations.AbstractAnnotation.removeAnnotation(AbstractAnnotation.java:320)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.model.Cluster.eraseText(Cluster.java:260)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.model.Cluster.erase(Cluster.java:254)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.task.cluster.DeleteClusterTask.destroyCluster(DeleteClusterTask.java:97)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.task.cluster.DeleteClusterTask.run(DeleteClusterTask.java:55)\r\n\tat org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:337)\r\n\tat org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)\r\n\tat java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)\r\n\tat java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)\r\n\tat java.util.concurrent.FutureTask.run(FutureTask.java:166)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:724)\r\n\r\n==> the new annotations were removed but the old annotations from the stored session \"re-appeared\".\r\n\r\n##################################################\r\nmoving some nodes and/or selecting multiple nodes\r\n##################################################\r\n\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 40\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 37\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 120\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 22\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 37\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 22\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 62\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 96\" updateNodeSelection=false\r\nwordcloud select cloudName=\"MCL Cluster Annotation Set Cloud 23\" updateNodeSelection=false\r\nThu Nov 27 11:16:47 MacPro9.local java[9445] <Error>: kCGErrorInvalidOperation: Cannot merge groups (yet) for wid 4b65, otherwid 4933\r\nThu Nov 27 11:16:47 MacPro9.local java[9445] <Error>: kCGErrorInvalidOperation: Cannot merge groups (yet) for wid 4b67, otherwid 4933\r\nThu Nov 27 11:16:48 MacPro9.local java[9445] <Error>: kCGErrorInvalidOperation: Cannot merge groups (yet) for wid 4b69, otherwid 4933\r\nThu Nov 27 11:16:48 MacPro9.local java[9445] <Error>: kCGErrorInvalidOperation: Cannot merge groups (yet) for wid 4b6b, otherwid 4933\r\n \r\n ==> \"Cytoscape task\" window is running and running: I don't know what Cytoscape is trying to do ==> force quit Cytoscape at that point\r\n\r\n####################################################\r\nselecting nodes from 2 different clusters: --> \"Drawing Ellipse/Box around cluster\" error window \r\n####################################################\r\n java.util.ConcurrentModificationException\r\n\tat java.util.HashMap$HashIterator.nextEntry(HashMap.java:894)\r\n\tat java.util.HashMap$KeyIterator.next(HashMap.java:928)\r\n\tat org.cytoscape.ding.impl.cyannotator.CyAnnotator.updateNetworkAttributes(CyAnnotator.java:357)\r\n\tat org.cytoscape.ding.impl.cyannotator.CyAnnotator.addAnnotation(CyAnnotator.java:275)\r\n\tat org.cytoscape.ding.impl.cyannotator.annotations.AbstractAnnotation.updateAnnotationAttributes(AbstractAnnotation.java:432)\r\n\tat org.cytoscape.ding.impl.cyannotator.annotations.AbstractAnnotation.update(AbstractAnnotation.java:385)\r\n\tat org.cytoscape.ding.impl.cyannotator.create.ShapeAnnotationFactory.createAnnotation(ShapeAnnotationFactory.java:54)\r\n\tat org.cytoscape.ding.impl.cyannotator.create.ShapeAnnotationFactory.createAnnotation(ShapeAnnotationFactory.java:41)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.task.cluster.DrawClusterEllipseTask.drawEllipse(DrawClusterEllipseTask.java:86)\r\n\tat org.baderlab.csplugins.enrichmentmap.autoannotate.task.cluster.DrawClusterEllipseTask.run(DrawClusterEllipseTask.java:122)\r\n\tat org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)\r\n\tat org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)\r\n\tat java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)\r\n\tat java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)\r\n\tat java.util.concurrent.FutureTask.run(FutureTask.java:166)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:724)\r\n\r\n==> just close the error window: the ellipse around the node cluster that has been selected is not drawn but cytoscape is not crashing\r\n\r\nThanks,\r\nVeronique"}}