Java version: 1.8.0_45 amd64 Linux 3.18.11 Jalview Version: 2.8.2 (installAnywhere) # INFO: Setting default net timeout to 30 seconds. Non-fatal exceptions when checking version at www.jalview.org : java.net.UnknownHostException: www.jalview.org May 06, 2015 8:05:24 PM jalview.util.MessageManager INFO: Getting messages for lang: en_US Error connecting to server: http://www.compbio.dundee.ac.uk/jabaws: java.net.UnknownHostException: www.compbio.dundee.ac.uk WARN : jalview.bin.Jalview - Ignoring invalid Jws2 service url http://www.compbio.dundee.ac.uk/jabaws WARN - Ignoring invalid Jws2 service url http://www.compbio.dundee.ac.uk/jabaws ERROR: jalview.bin.Jalview - Errors reported by JABA discovery service. Check web services preferences. URLs that could not be contacted: http://www.compbio.dundee.ac.uk/jabaws ERROR - Errors reported by JABA discovery service. Check web services preferences. URLs that could not be contacted: http://www.compbio.dundee.ac.uk/jabaws java.net.UnknownHostException: www.jalview.org at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:178) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1168) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1104) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:998) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:932) at org.robsite.jswingreader.model.SimpleRSSParser.parse(SimpleRSSParser.java:251) at org.robsite.jswingreader.model.SimpleRSSParser.parse(SimpleRSSParser.java:214) at jalview.gui.BlogReader.initItems(BlogReader.java:594) at jalview.gui.BlogReader.(BlogReader.java:271) at jalview.gui.Desktop$7.run(Desktop.java:455) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:301) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Building ws menu again Thread[Thread-13,6,main] Warning - overwriting a sequenceSetId for a viewport! Failed to contact DAS1 registry at http://www.dasregistry.org/das/ org.biodas.jdas.exceptions.DASClientException: I/O error: www.dasregistry.org; nested exception is java.net.UnknownHostException: www.dasregistry.org at org.biodas.jdas.client.SourcesClient.fetchData(SourcesClient.java:77) at org.biodas.jdas.client.SourcesClient.fetchDataRegistry(SourcesClient.java:126) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:120) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:103) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getSources(DasSourceRegistry.java:169) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.run(DasSourceRegistry.java:161) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.refreshSources(DasSourceRegistry.java:343) at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(SequenceFetcher.java:122) at jalview.gui.AlignFrame$19.run(AlignFrame.java:5444) at java.lang.Thread.run(Thread.java:745) Caused by: java.net.UnknownHostException: www.dasregistry.org at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:178) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1168) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1104) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:998) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:932) at org.springframework.http.client.SimpleClientHttpRequest.executeInternal(SimpleClientHttpRequest.java:69) at org.springframework.http.client.AbstractClientHttpRequest.execute(AbstractClientHttpRequest.java:52) at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:438) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:401) at org.springframework.web.client.RestTemplate.exchange(RestTemplate.java:377) at org.biodas.jdas.client.SourcesClient.fetchData(SourcesClient.java:74) ... 9 more WARN : jalview.bin.Jalview - Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869 java.lang.ClassCastException at javax.swing.LayoutComparator.compare(LayoutComparator.java:75) at javax.swing.LayoutComparator.compare(LayoutComparator.java:42) at java.util.TimSort.countRunAndMakeAscending(TimSort.java:356) at java.util.TimSort.sort(TimSort.java:230) at java.util.Arrays.sort(Arrays.java:1512) at java.util.ArrayList.sort(ArrayList.java:1454) at java.util.Collections.sort(Collections.java:175) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(SortingFocusTraversalPolicy.java:172) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(SortingFocusTraversalPolicy.java:143) at javax.swing.SortingFocusTraversalPolicy.getFirstComponent(SortingFocusTraversalPolicy.java:500) at javax.swing.LayoutFocusTraversalPolicy.getFirstComponent(LayoutFocusTraversalPolicy.java:166) at javax.swing.SortingFocusTraversalPolicy.getDefaultComponent(SortingFocusTraversalPolicy.java:590) at javax.swing.InternalFrameFocusTraversalPolicy.getInitialComponent(InternalFrameFocusTraversalPolicy.java:66) at javax.swing.JInternalFrame.getMostRecentFocusOwner(JInternalFrame.java:1436) at javax.swing.JInternalFrame.restoreSubcomponentFocus(JInternalFrame.java:1466) at javax.swing.JInternalFrame.setSelected(JInternalFrame.java:1116) at jalview.gui.Desktop.addInternalFrame(Desktop.java:841) at jalview.gui.Desktop.addInternalFrame(Desktop.java:645) at jalview.gui.Jalview2XML.loadViewport(Jalview2XML.java:3703) at jalview.gui.Jalview2XML.LoadFromObject(Jalview2XML.java:2877) at jalview.gui.Jalview2XML.LoadJalviewAlign(Jalview2XML.java:2004) at jalview.gui.Jalview2XML.LoadJalviewAlign(Jalview2XML.java:1884) at jalview.gui.Desktop$16.run(Desktop.java:1531) at java.lang.Thread.run(Thread.java:745) WARN - Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869 java.lang.ClassCastException at javax.swing.LayoutComparator.compare(LayoutComparator.java:75) at javax.swing.LayoutComparator.compare(LayoutComparator.java:42) at java.util.TimSort.countRunAndMakeAscending(TimSort.java:356) at java.util.TimSort.sort(TimSort.java:230) at java.util.Arrays.sort(Arrays.java:1512) at java.util.ArrayList.sort(ArrayList.java:1454) at java.util.Collections.sort(Collections.java:175) at javax.swing.SortingFocusTraversalPolicy.enumerateAndSortCycle(SortingFocusTraversalPolicy.java:172) at javax.swing.SortingFocusTraversalPolicy.getFocusTraversalCycle(SortingFocusTraversalPolicy.java:143) at javax.swing.SortingFocusTraversalPolicy.getFirstComponent(SortingFocusTraversalPolicy.java:500) at javax.swing.LayoutFocusTraversalPolicy.getFirstComponent(LayoutFocusTraversalPolicy.java:166) at javax.swing.SortingFocusTraversalPolicy.getDefaultComponent(SortingFocusTraversalPolicy.java:590) at javax.swing.InternalFrameFocusTraversalPolicy.getInitialComponent(InternalFrameFocusTraversalPolicy.java:66) at javax.swing.JInternalFrame.getMostRecentFocusOwner(JInternalFrame.java:1436) at javax.swing.JInternalFrame.restoreSubcomponentFocus(JInternalFrame.java:1466) at javax.swing.JInternalFrame.setSelected(JInternalFrame.java:1116) at jalview.gui.Desktop.addInternalFrame(Desktop.java:841) at jalview.gui.Desktop.addInternalFrame(Desktop.java:645) at jalview.gui.Jalview2XML.loadViewport(Jalview2XML.java:3703) at jalview.gui.Jalview2XML.LoadFromObject(Jalview2XML.java:2877) at jalview.gui.Jalview2XML.LoadJalviewAlign(Jalview2XML.java:2004) at jalview.gui.Jalview2XML.LoadJalviewAlign(Jalview2XML.java:1884) at jalview.gui.Desktop$16.run(Desktop.java:1531) at java.lang.Thread.run(Thread.java:745) Building ws menu again Thread[Thread-16,6,main] Warning - overwriting a sequenceSetId for a viewport!