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)
at jalview.io.MSFfile.parse(MSFfile.java:155)
at jalview.io.AlignFile.(AlignFile.java:80)
at jalview.io.MSFfile.(MSFfile.java:56)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:179)
at jalview.io.FileLoader.run(FileLoader.java:279)
at java.lang.Thread.run(Unknown Source)
error
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.
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,
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.