Recent changes to bugs

#38 Export to SBGN throws error

Tobias Czauderna — Tue, 08 Dec 2015 05:42:02 -0000

Thanks, Venkat!

When you download a model from the Biomodels database it is visualized in Vanted in a generic style.
If you want to save it as .sbgn file, you have to translate it to SBGN first.
1) Load a model from Biomodels database
2) Go to SBGN-ED tab -> Tools, Click "Translate SBML to SBGN"
3) optional: do some layout and adapt the compartment shapes
4) Save as .sbgn file

Regards,
Tobias

Export to SBGN throws error

Venkatesh Muthukrishnan — Fri, 04 Dec 2015 16:08:06 -0000

Hi,

I have installed SBGN-ED plugin and while trying to save us sbgn, it creates a empty file with a name and throws an error.

I am using VANTED - 2.6.0 Any ideas ?

With thanks,
Venkat

#37 SVG export

Tobias Czauderna — Thu, 28 May 2015 03:53:57 -0000

status: open --> pending

#36 Exception in thread "main" java.lang.UnsupportedClassVersionError

Tobias Czauderna — Thu, 28 May 2015 03:51:23 -0000

status: open --> closed-fixed

SVG export

Ondrej Kuda — Thu, 21 May 2015 12:09:06 -0000

When exporting to SVG, axis labels (numbers) are exported as paths, while they should be accessible as "text" elements.

SVG export

Ondrej Kuda — Thu, 21 May 2015 12:09:06 -0000

Ticket 37 has been modified: SVG export
Edited By: Tobias Czauderna (tczauderna)
Status updated: u'open' => u'pending'

#36 Exception in thread "main" java.lang.UnsupportedClassVersionError

Joe Cursons — Tue, 27 Jan 2015 07:55:55 -0000

OK, that was an easy fix – thanks for the information.

If you’re at all interested, the startup script is causing a crash (by assigning too much memory – see below) but if I run it manually with 1024 MB then it runs fine.

C:\Program Files (x86)\VANTED>starter.cmd
hello world
physical memory 16335
vanted memory 8167
Invalid maximum heap size: -Xmx8167m
The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

C:\Program Files (x86)\VANTED>java -jar -Xmx1024m vanted.jar
Welcome! About to start the application...
Trying to load Add-ons...
Add-on sbgn-ed.jar processed
Add-ons loaded in 170ms
Task null finished after 5 sec.

Exception in thread "main" java.lang.UnsupportedClassVersionError

Joe Cursons — Tue, 27 Jan 2015 06:27:55 -0000

I just upgraded to VANTED v2.2 and it is not loading - the error output is:

C:\Program Files (x86)\VANTED>starter.cmd
hello world
physical memory 16335
vanted memory 8167
Exception in thread "main" java.lang.UnsupportedClassVersionError: de/ipk_gaters
leben/ag_nw/graffiti/plugins/gui/webstart/Main : Unsupported major.minor version
51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(Unknown Source)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$000(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Could not find the main class: de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.web
start.Main. Program will exit.

If I open the .jar file without the starter.cmd batch file, then it will open and I get a "Low memory configuration detected!" warning.

If I try and run the .jar file from command line, with or without a -Xmx command to increase memory, I get the same error as above.

Please feel free to contact me if any further information is required - joseph.cursons@unimelb.edu.au

Thanks,
Joe

Exception in thread "main" java.lang.UnsupportedClassVersionError

Joe Cursons — Tue, 27 Jan 2015 06:27:55 -0000

Ticket 36 has been modified: Exception in thread "main" java.lang.UnsupportedClassVersionError
Edited By: Tobias Czauderna (tczauderna)
Status updated: u'open' => u'closed-fixed'

#3 Expression mapping on KEGG pathways may fail

Matthias Klapperstück — Thu, 06 Mar 2014 13:36:59 -0000

status: open --> closed-wont-fix