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

[Yi-Shiou Chen]

Hi Jim,

Thanks for your checking and suggestion.

My company (Accelrys) is distributing Jalview with the Sequence Analysis
Collection product. We are using 2.3 and plan to use 2.4 for the next
product release. We prefer not to distribute the Jalview.exe because it
works for win32 only. Any other way to workaround? Thanks,

Yi-Shiou

On Wed, Oct 15, 2008 at 9:30 AM, James Procter <jimp at compbio.dundee.ac.uk>wrote:

> 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
>
> --
> -------------------------------------------------------------------
> 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.
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss at jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20081015/550963a2/attachment.html