Jalview installation SOS!

111 · 28 January 2010 02:12

Under Linux, I meet a problem when installing jalview. The whole story is as follows, and I do not know what is "InvocationTargetException":

[zhu@localhost ~]$ sh ./install.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...

Graphical installers are not supported by the VM. The console mode will be used instead...

Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)

Stack Trace:
java.lang.UnsatisfiedLinkError: /tmp/install.dir.13040/Linux/resource/jre/lib/i386/xawt/libmawt.so: libXext.so.6: cannot open shared object file: No such file or directory
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(Unknown Source)
        at java.lang.ClassLoader.loadLibrary(Unknown Source)
        at java.lang.Runtime.load0(Unknown Source)
        at java.lang.System.load(Unknown Source)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(Unknown Source)
        at java.lang.ClassLoader.loadLibrary(Unknown Source)
        at java.lang.Runtime.loadLibrary0(Unknown Source)
        at java.lang.System.loadLibrary(Unknown Source)
        at sun.security.action.LoadLibraryAction.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.awt.NativeLibLoader.loadLibraries(Unknown Source)
        at sun.awt.DebugHelper.<clinit>(Unknown Source)
        at java.awt.Component.<clinit>(Unknown Source)
        at com.zerog.ia.installer.util.BidiUtilImpl.setDefaultLocale(DashoA10*..)
        at ZeroGbd.a(DashoA10*..)
        at com.zerog.ia.installer.LifeCycleManager.s(DashoA10*..)
        at com.zerog.ia.installer.LifeCycleManager.b(DashoA10*..)
        at com.zerog.ia.installer.LifeCycleManager.a(DashoA10*..)
        at com.zerog.ia.installer.Main.main(DashoA10*..)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at com.zerog.lax.LAX.launch(DashoA10*..)
        at com.zerog.lax.LAX.main(DashoA10*..)
This Application has Unexpectedly Quit: Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)

···

________________________________________
From: jalview-discuss-bounces@jalview.org [jalview-discuss-bounces@jalview.org] On Behalf Of jalview-discuss-request@jalview.org [jalview-discuss-request@jalview.org]
Sent: 28 January 2010 09:58
To: 朱浩
Subject: Welcome to the "Jalview-discuss" mailing list

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ajperry · 28 January 2010 03:28

2010/1/28 朱浩 <zhuhao@smu.edu.cn>

Under Linux, I meet a problem when installing jalview. The whole story is as follows, and I do not know what is “InvocationTargetException”:

[zhu@localhost ~]$ sh ./install.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…

Graphical installers are not supported by the VM. The console mode will be used instead…

Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)

Stack Trace:
java.lang.UnsatisfiedLinkError: /tmp/install.dir.13040/Linux/resource/jre/lib/i386/xawt/libmawt.so: libXext.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.load0(Unknown Source)
at java.lang.System.load(Unknown Source)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.NativeLibLoader.loadLibraries(Unknown Source)
at sun.awt.DebugHelper.(Unknown Source)
at java.awt.Component.(Unknown Source)
at com.zerog.ia.installer.util.BidiUtilImpl.setDefaultLocale(DashoA10*…)
at ZeroGbd.a(DashoA10*…)
at com.zerog.ia.installer.LifeCycleManager.s(DashoA10*…)
at com.zerog.ia.installer.LifeCycleManager.b(DashoA10*…)
at com.zerog.ia.installer.LifeCycleManager.a(DashoA10*…)
at com.zerog.ia.installer.Main.main(DashoA10*…)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.zerog.lax.LAX.launch(DashoA10*…)
at com.zerog.lax.LAX.main(DashoA10*…)
This Application has Unexpectedly Quit: Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)

Could you clarify which version of Linux you are using (Ubuntu 9.10 ? Fedora x.x ?). Are you running under the graphical X11 (Xorg) interface ?

You should try downloading the version “without Java VM” (eg 13.3 Mb, not 69.8 Mb) from http://www.jalview.org/Web_Installers/install.htm and installing that instead.

Also, make sure that you have Java installed.

(eg, on Debian/Ubuntu run:
$ sudo apt-get install sun-java6-jre
… and possibly:
$ sudo update-alternatives --config java
[to select the default version of Java your system will use] )

Andrew Perry

jalviewcrowdadmin · 28 January 2010 09:48

Hello Zhu.

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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
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