[Jalview-discuss] Re: installation problems

[James Procter]

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 at 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