Hi Daniel.
This is cc'ed to the jalview-discuss list, just in case anyone out there
has had/dealt with this problem already.
Jim edited what Daniel Rigden wrote:
I've just got a new machine, running (64 bit) Ubuntu 8.04, and I'd
like to get Jalview working on it. Unfortunately, both
[InstallAnywhere and webstart] methods fail for me.I first tried install anywhere, including jre, but I get a series
of errors like 'Locking assertion failure'.I got this when installing for the first time, and when subsequently
trying to run it.On Web Start off the webpage, the Exception text goes like this
JNLPException[category: Download Error : Exception:
java.net.UnknownHostException: www.jalview.org : LaunchDesc: null ]
at
com.sun.javaws.cache.DownloadProtocol.doDownload(DownloadProtocol.java:611)
at
com.sun.javaws.cache.DownloadProtocol.getDownloadSize(DownloadProtocol.java:808)
at
com.sun.javaws.LaunchDownload.downloadJarFiles(LaunchDownload.java:674)
at
com.sun.javaws.LaunchDownload.downloadEagerorAll(LaunchDownload.java:638)
at com.sun.javaws.Launcher.downloadResources(Launcher.java:969)
at com.sun.javaws.Launcher.handleApplicationDesc(Launcher.java:335)
at com.sun.javaws.Launcher.handleLaunchFile(Launcher.java:217)
at com.sun.javaws.Launcher.run(Launcher.java:164)
at java.lang.Thread.run(Thread.java:595)
um. clear as mud. looks like www.jalview.org is not resolving for the
javaws program, which is pretty serious. I've seen this kind of thing
when the JNLP is broken - but both jalview.org and the ws-dev1 JNLP
files work fine on Sun java 4,5,and 6 javaws implementations.
I'm perfectly happy to use the command line. I installed openjdk and
pointed JAVA_HOME to /usr/lib/jvm/ [don't know if that's right]Then I get
daniel@adenine:~/progs/jalview_cl$ java -Djava.ext.dirs=.
jalview.bin.Jalview
Java version: 1.6.0
amd64 Linux 2.6.24-19-generic
Jalview Version: Automated Build
Exception in thread "Thread-0" java.lang.NullPointerException
at java.util.Hashtable.put(Hashtable.java:411)
at java.util.Properties.setProperty(Properties.java:160)
at java.lang.System.setProperty(System.java:748)
at jalview.bin.Cache$1VersionChecker.run(Cache.java:269)
Exception in thread "main" java.awt.AWTError: Assistive Technology not
found: org.GNOME.Accessibility.JavaBridge
at java.awt.Toolkit.loadAssistiveTechnologies(Toolkit.java:788)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:874)
at
javax.swing.UIManager.getSystemLookAndFeelClassName(UIManager.java:617)
at jalview.bin.Jalview.main(Jalview.java:122)
yuk. That looks like an issue with the installation of openJDK. I have
to admit, we have not had much luck at all with *any* non sun JVMs - did
you have a go with the sun 1.(4,5,6) JRE - particularly - try the 32bit
version ? (googling the java.awt.AWTError yielded a page which suggests
this isn't an openJDK issue though, so.. no idea - herer really).
I appear not to have BERYL installed (though it looks quite cool)
There are some more explicit guidlines which are Compiz/Beryl related...
but it might be something that helps this issue too (the issues are all
LookAndFeel related.. so...). You could give them a go and see what
happens - :
http://66.102.9.104/search?q=cache:ED_njtYjQQcJ:dmartin.org/weblog/how-to-get-java-swing-apps-working-under-beryl-or-compiz-including-java-web-start+how-to-get-java-swing-apps-working-under-beryl-or-compiz-including-java-web-start&hl=en&client=firefox-a&gl=uk&strip=1
(this is a google-cached version of a blog entry that isn't accessible
any more...)
I'll have an ask around to see if anyone else in the lab has a recent
ubuntu install. There may be some workarounds I can introduce into
jalview to get it going on your system... but until then, the floor is
open to you all at jalview-discuss !
Jim