Hi there, I'm having a hard time getting Jalview installed/started under ubuntu 18.04. I have tried several things.
1) The Jalview Desktop Method: When I start jalview.jnlp with IcedTea I get this message: Web Servie Configuration Problem URLs that could not be contacted: http://www.compbio.dundee.ac.uk/jabaws It may be that you have invalid JABA URLs in your web service preferences, or as a command-line argument, or mis-configured HTTP proxy settings. Check the Connections and Web services tab of the Tool->Preferences dialog box to change them. Jalview starts with the three demo windows but web services are unavailable and I cannot open the Tool->Preferences dialog box either. (When I click Preferences just nothing happens.) When I start jalview.jnlp from the command line I get the following warnings/errors: user@user-ThinkPad-T440:~/applications/jalview$ javaws jalview.jnlp selected jre: /usr/lib/jvm/java-8-oracle/jre/ Gtk-Message: 14:49:29.707: Failed to load module "canberra-gtk-module" selected jre: /usr/lib/jvm/java-8-oracle/jre/ Gtk-Message: 14:49:41.090: Failed to load module "canberra-gtk-module" Codebase matches codebase manifest attribute, and application is signed. Continuing. See: http://docs.oracle.com/javase/7/docs/technotes/guides/jweb/security/no_redeploy.html for details. Starting application [jalview.bin.Jalview] ... Java version: 1.8.0_201 amd64 Linux 4.15.0-51-generic Jalview Version: 2.10.5 (webstart git-commit:5610d0f [releases/Release_2_10_5_Branch]) Jun 16, 2019 2:50:07 PM jalview.util.MessageManager <clinit> INFO: Getting messages for lang: en_US Jun 16, 2019 2:50:10 PM compbio.ws.client.Jws2Client connectToRegistry INFO: Connected to RegistryWS successfully! registry.getSupportedServices: [ClustalWS, GLprobsWS, RNAalifoldWS, JronnWS, TcoffeeWS, GlobPlotWS, MuscleWS, MSAprobsWS, MafftWS, ProbconsWS, ClustalOWS, IUPredWS, AAConWS, DisemblWS] Attempting to connect with MafftWS... Warning - overwriting a sequenceSetId for a viewport! Jun 16, 2019 2:50:11 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2f1ef60 Exception in thread "Thread-30" javax.xml.transform.TransformerFactoryConfigurationError: Provider for class javax.xml.transform.TransformerFactory cannot be created at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:297) at javax.xml.transform.FactoryFinder.find(FactoryFinder.java:251) at javax.xml.transform.TransformerFactory.newInstance(TransformerFactory.java:106) at org.springframework.http.converter.xml.AbstractXmlHttpMessageConverter.<init>(AbstractXmlHttpMessageConverter.java:47) at org.springframework.http.converter.xml.SourceHttpMessageConverter.<init>(SourceHttpMessageConverter.java:45) at org.springframework.web.client.RestTemplate.<init>(RestTemplate.java:141) at org.biodas.jdas.client.SourcesClient.<init>(SourcesClient.java:32) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:119) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:104) 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:187) at jalview.gui.AlignFrame$19.run(AlignFrame.java:4927) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.RuntimeException: Provider for class javax.xml.transform.TransformerFactory cannot be created at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:294) ... 14 more Caused by: java.util.ServiceConfigurationError: javax.xml.transform.TransformerFactory: Provider org.apache.xalan.processor.TransformerFactoryImpl not found at java.util.ServiceLoader.fail(ServiceLoader.java:239) at java.util.ServiceLoader.access$300(ServiceLoader.java:185) at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:372) at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404) at java.util.ServiceLoader$1.next(ServiceLoader.java:480) at javax.xml.transform.FactoryFinder$1.run(FactoryFinder.java:280) at java.security.AccessController.doPrivileged(Native Method) at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:275) ... 14 more Attempting to connect with MuscleWS... (C) 2015 Jmol Development Jmol Version: 14.6.4_2016.10.26 2016-10-26 12:26 java.vendor: Java: Oracle Corporation java.version: Java 1.8.0_201 os.name: Linux Access: ALL memory: 255.6/775.4 processors available: 4 useCommandThread: false FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb932697906139742350.txt) FileManager opening file /tmp/jalview_pdb932697906139742350.txt The Resolver thinks Pdb Jun 16, 2019 2:50:11 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! IRON-SULFUR PROTEIN 19-MAR-98 1A70 SPINACH FERREDOXIN Setting space group name to P 21 21 21 1A70 Time for openFile(/tmp/jalview_pdb932697906139742350.txt): 122 ms reading 817 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@49d8b37e Default Van der Waals type for model set to Jmol 817 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Operating headless display=null nographicsallowed=true (C) 2015 Jmol Development Jmol Version: 14.6.4_2016.10.26 2016-10-26 12:26 java.vendor: Java: Oracle Corporation java.version: Java 1.8.0_201 os.name: Linux Access: ALL memory: 127.8/833.1 processors available: 4 useCommandThread: false The Resolver thinks Pdb IRON-SULFUR PROTEIN 19-MAR-98 1A70 SPINACH FERREDOXIN Setting space group name to P 21 21 21 1A70 reading 817 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 817 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Time for creating model: 27 ms Time for creating model: 68 ms unrecognized SET parameter in Jmol state script (set anyway): usearcball measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665] Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665] Attempting to connect with ClustalWS... Warning - overwriting a sequenceSetId for a viewport! Jun 16, 2019 2:50:13 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@12603f01 Operating headless display=null nographicsallowed=true (C) 2015 Jmol Development Jmol Version: 14.6.4_2016.10.26 2016-10-26 12:26 java.vendor: Java: Oracle Corporation java.version: Java 1.8.0_201 os.name: Linux Access: ALL memory: 172.2/759.7 processors available: 4 useCommandThread: false Exception in thread "Thread-47" javax.xml.transform.TransformerFactoryConfigurationError: Provider for class javax.xml.transform.TransformerFactory cannot be created at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:297) at javax.xml.transform.FactoryFinder.find(FactoryFinder.java:251) at javax.xml.transform.TransformerFactory.newInstance(TransformerFactory.java:106) at org.springframework.http.converter.xml.AbstractXmlHttpMessageConverter.<init>(AbstractXmlHttpMessageConverter.java:47) at org.springframework.http.converter.xml.SourceHttpMessageConverter.<init>(SourceHttpMessageConverter.java:45) at org.springframework.web.client.RestTemplate.<init>(RestTemplate.java:141) at org.biodas.jdas.client.SourcesClient.<init>(SourcesClient.java:32) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:119) at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:104) 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:187) at jalview.gui.AlignFrame$19.run(AlignFrame.java:4927) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.RuntimeException: Provider for class javax.xml.transform.TransformerFactory cannot be created at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:294) ... 14 more Caused by: java.util.ServiceConfigurationError: javax.xml.transform.TransformerFactory: Provider org.apache.xalan.processor.TransformerFactoryImpl not found at java.util.ServiceLoader.fail(ServiceLoader.java:239) at java.util.ServiceLoader.access$300(ServiceLoader.java:185) at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:372) at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404) at java.util.ServiceLoader$1.next(ServiceLoader.java:480) at javax.xml.transform.FactoryFinder$1.run(FactoryFinder.java:280) at java.security.AccessController.doPrivileged(Native Method) at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:275) ... 14 more The Resolver thinks Pdb IRON-SULFUR PROTEIN 19-MAR-98 1A70 SPINACH FERREDOXIN Setting space group name to P 21 21 21 1A70 reading 817 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 817 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Time for creating model: 30 ms Attempting to connect with ClustalOWS... Jun 16, 2019 2:50:14 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@71cb836b Attempting to connect with TcoffeeWS... Warning - overwriting a sequenceSetId for a viewport! Jun 16, 2019 2:50:15 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@4dd3e986 Exception in thread "Thread-62" javax.xml.transform.TransformerFactoryConfigurationError: Provider for class javax.xml.transform.TransformerFactory cannot be created at javax.xml.transform.FactoryFinder.findServiceProvider(FactoryFinder.java:297) and so on ... The GUI opens as before, but still no access to the Preferences menu. 2) The InstallAnywhere Method: I downloaded the Linux installer including Java (137Mb). user@user-ThinkPad-T440:~/applications/jalview/install$ sh ./install-jalview.bin Preparing to install Extracting the JRE from the installer archive... Unpacking the JRE... Extracting the installation resources from the installer archive... Configuring the installer for this system's environment... Launching installer... Gtk-Message: 14:54:33.189: Failed to load module "canberra-gtk-module" The Jalview Installer opens and installation finishes with warnings (refering to an installation log which I cannot find). The Jalview installation directory is smaller than expected (42Mb as compared to 137Mb of the bin file). When I then try user@user-ThinkPad-T440:~/applications/jalview/install$ java -classpath "/home/user/Jalview/lib/*" -jar /home/user/Jalview/jalview.jar I get Java version: 1.8.0_201 amd64 Linux 4.15.0-51-generic Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/log4j/Layout at jalview.bin.Jalview.doMain(Jalview.java:220) at jalview.bin.Jalview.main(Jalview.java:190) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.Layout at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 2 more When I use the fix suggested under faq mcengeholm@laptop-VPCEB1Z1E:~/JalViewInstall$ cp install-jalview.bin install.bak mcengeholm@laptop-VPCEB1Z1E:~/JalViewInstall$ cat install.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > install.bin this does not make any difference. 3) Using conda: The installation works fine. When I try to start it I get mcengeholm@laptop-VPCEB1Z1E:~$ jalview Java version: 11.0.1 amd64 Linux 4.15.0-51-generic Jalview Version: 2.10.5 (bioconda (build 3) git-commit: []) # INFO: Setting default net timeout to 30 seconds. Jun 15, 2019 9:21:48 PM jalview.util.MessageManager <clinit> INFO: Getting messages for lang: en_US Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74) at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247) at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265) at java.desktop/sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:1231) at java.desktop/javax.swing.JComponent.getFontMetrics(JComponent.java:1646) at java.desktop/javax.swing.text.PlainView.calculateLongestLine(PlainView.java:783) at java.desktop/javax.swing.text.PlainView.updateMetrics(PlainView.java:332) at java.desktop/javax.swing.text.PlainView.updateDamage(PlainView.java:670) at java.desktop/javax.swing.text.PlainView.insertUpdate(PlainView.java:591) at java.desktop/javax.swing.plaf.basic.BasicTextUI$RootView.insertUpdate(BasicTextUI.java:1709) at java.desktop/javax.swing.plaf.basic.BasicTextUI$UpdateHandler.insertUpdate(BasicTextUI.java:1968) at java.desktop/javax.swing.text.AbstractDocument.fireInsertUpdate(AbstractDocument.java:203) at java.desktop/javax.swing.text.AbstractDocument.handleInsertString(AbstractDocument.java:757) at java.desktop/javax.swing.text.AbstractDocument.insertString(AbstractDocument.java:716) at java.desktop/javax.swing.text.PlainDocument.insertString(PlainDocument.java:131) at java.desktop/javax.swing.JTextArea.insert(JTextArea.java:450) at jalview.gui.Console.setHeader(Console.java:679) at jalview.gui.Desktop.<init>(Desktop.java:383) at jalview.bin.Jalview.doMain(Jalview.java:337) at jalview.bin.Jalview.main(Jalview.java:190) Caused by: java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84) ... 21 more Caused by: java.lang.NullPointerException at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262) at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225) at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107) at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719) at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312) at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35) at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56) Any suggestions how to proceed? Your help would be much appreciated. Regards, Maik _______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
