jalview with ubuntu 18.04

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

Thanks for the email, Maik!

I can only apologise for the issues you’ve encountered. Both Java Web Start and InstallAnywhere are now extremely problematic and we have moved away from them for the next Jalview release.

The official announcement is due for tomorrow, but you (and everyone else on the list) can get Jalview 2.11 now at http://www.jalview.org/getdown/release/

We are still putting the finishing touches to the release so please let us know how you get on.

Jim.

PS. There is as yet no conda distribution for Jalview 2.11, but we will work with bioconda over the next few weeks to update their Jalview recipe.

···
I'm having a hard time getting Jalview installed/started under ubuntu
18.04. I have tried several things.
Any suggestions how to proceed? Your help would be much appreciated.
-- 
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)

Hi Maik,

Just to add to what Jim said and the release-candidate installers currently on http://www.jalview.org/getdown/release/

The .deb and .rpm both have a dependency for openjdk8 (I assume you will be using the .deb on Ubuntu 18.04). Alternatively, if you use the shell installer, or the .tar.gz file then you will need to make sure you have a java 8 runtime (either a JRE or a JDK) available in your PATH. We’re recommending either openjdk in your package management system, or using an installation from adoptopenjdk.net

We’d really like to hear how you get on with the installation so we can make it as easy as possible in as many environments as possible!

Best wishes,

Ben

···


University of Dundee shield logo Ben Soares
Research Software Engineer
Jalview Team, Computational Biology, School of Life Sciences, University of Dundee
b.soares@dundee.ac.uk

One of the UK’s top 30 universities
The Times/Sunday Times Good University Guide 2019 and The Guardian University Guide 2019

On 19 Jun 2019, at 09:35, Maik Engeholm <engeholm@gmx.net> wrote:

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
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.(AbstractXmlHttpMessageConverter.java:47)
at
org.springframework.http.converter.xml.SourceHttpMessageConverter.(SourceHttpMessageConverter.java:45)
at
org.springframework.web.client.RestTemplate.(RestTemplate.java:141)
at org.biodas.jdas.client.SourcesClient.(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.(AbstractXmlHttpMessageConverter.java:47)
at
org.springframework.http.converter.xml.SourceHttpMessageConverter.(SourceHttpMessageConverter.java:45)
at
org.springframework.web.client.RestTemplate.(RestTemplate.java:141)
at org.biodas.jdas.client.SourcesClient.(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.

  1. 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.

  1. 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
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.(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.(SunFontManager.java:312)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)

Any suggestions how to proceed? Your help would be much appreciated.

Regards,

Maik


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