[Jalview-discuss] Jalview 2.4 fails to run from the command line

[James Procter]

Hello Yi-Shiou.

Sorry for not getting back to you sooner about this.

I get the same behaviour as you, and I think it is actually an issue
arising from the new version of InstallAnywhere that we use to package
the 2.4 version of the local install of the application. But, there is a
workaround!

Yi-Shiou Chen wrote:
> Jalview 2.4 fails to run from the following command line on win32:
> 
> C:\temp>java -Djava.ext.dirs="C:/Program Files/Jalview/lib" -cp
> "C:/Program File
> s/Jalview/jalview.jar" jalview.bin.Jalview -open y.msf  (The sequence
> file y.msf is attached.)
> 
> The error message:
> Java version: 1.6.0_05
> x86 Windows XP 5.1
> Jalview Version: 2.4
> # INFO: Setting default net timeout to 30 seconds.
> Opening file: y.msf
> Exception in thread "Thread-7" java.lang.VerifyError: (class:
> jalview/datamodel/
> Sequence, method: parseId signature: ()V) Incompatible object argument
> for funct
> ion call
>         at jalview.io.AlignFile.parseId(AlignFile.java:250)
This error suggests the problem is actually at the bytecode level, since
I can use this command line to launch a view of the alignment with the
jars build from source, and the ones downloaded via webstart.

The workaround I would suggest is simply to use the InstallAnywhere
Jalview.exe executable :
C:\temp>"C:/Program Files/Jalview/Jalview.exe" -open y.msf

This seems to work for me.

Jim

-- 
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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.