CenTOS Standardizer installation errors

User d6d35b90ea

14-07-2009 16:02:24

Dear ChemAxon,

I've worked with the chemaxon software (JChem 5.2) on my personal macintosh and it has always run pretty well.  I attempted to install on my linux workstation (CenTOS 4.7) and came out with a number of errors when using the standardizer.  Both the commandline and the gui versions seem to fail.  Attached are the errors for the commandline, then the errors for the gui follow.  Any guidance is appreciated.


 


thanks,

Pahk


[pthepch@spider01 tautomer-lib]$ /opt/chemaxon/jchem/bin/standardize ko-tat.smi -o ko-stand.smi
Warning: -Xmx200M not understood. Ignoring.
Exception in thread "main" java.lang.NoClassDefFoundError: while resolving class: chemaxon.reaction.ConcurrentStandardizerProcessor
   at java.lang.VMClassLoader.resolveClass(java.lang.Class) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.initializeClass() (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String, boolean, java.lang.ClassLoader) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String) (/usr/lib/libgcj.so.5.0.0)
   at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0)
   at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) (/usr/lib/libgcj.so.5.0.0)
   at __gcj_personality_v0 (/home/pthepch/QNAP/exercises/tautomer-lib/java.version=1.4.2)
   at __libc_start_main (/lib/tls/libc-2.3.4.so)
   at _Jv_RegisterClasses (/home/pthepch/QNAP/exercises/tautomer-lib/java.version=1.4.2)
Caused by: java.lang.ClassNotFoundException: java.util.concurrent.ExecutionException not found in [file:/opt/chemaxon/jchem/bin/../lib/jchem.jar, file:/usr/share/java/libgcj-3.4.6.jar, file:./, core:/]
   at java.net.URLClassLoader.findClass(java.lang.String) (/usr/lib/libgcj.so.5.0.0)
   at gnu.gcj.runtime.VMClassLoader.findClass(java.lang.String) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.ClassLoader.loadClass(java.lang.String, boolean) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_FindClass(_Jv_Utf8Const, java.lang.ClassLoader) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.Class.forName(java.lang.String, boolean, java.lang.ClassLoader) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_BytecodeVerifier.pop_init_ref(_Jv_BytecodeVerifier.type) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_BytecodeVerifier.verify_instructions_0() (/usr/lib/libgcj.so.5.0.0)
   at _Jv_VerifyMethod(_Jv_InterpMethod) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_PrepareClass(java.lang.Class) (/usr/lib/libgcj.so.5.0.0)
   at _Jv_WaitForState(java.lang.Class, int) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.VMClassLoader.linkClass0(java.lang.Class) (/usr/lib/libgcj.so.5.0.0)
   at java.lang.VMClassLoader.resolveClass(java.lang.Class) (/usr/lib/libgcj.so.5.0.0)
   ...9 more


[pthepch@spider05 tautomer-lib]$ Standardizer
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at javax.swing.ImageIcon.<init>(Unknown Source)
        at chemaxon.alchemist.utils.AlchemistLabel.refreshIcon(Unknown Source)
        at chemaxon.alchemist.utils.AlchemistLabel.initialize(Unknown Source)
        at chemaxon.alchemist.utils.AlchemistLabel.<init>(Unknown Source)
        at chemaxon.alchemist.Alchemist.getLicenseLabel(Unknown Source)
        at chemaxon.alchemist.Alchemist.setProgressObjects(Unknown Source)
        at chemaxon.alchemist.AlchemistController.initAlchemist(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemistController.<init>(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemistController.<init>(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemistController.<init>(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemistController.<init>(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemist.createAndShowGUI(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemist.access$000(Unknown Source)
        at chemaxon.alchemist.standardizer.StandardizerAlchemist$1.run(Unknown Source)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)

ChemAxon e08c317633

14-07-2009 16:42:02

Hi,


It seems you are using GCJ java, which is not supported by ChemAxon's applications. Marvin and JChem support Java distributed by Sun only, so please install Sun's Java. For more see our System Requirements page.


If you use Standardize via command line, then you have to specify a standardizer configuration file or string.


Example:


standardize -c config.xml input.sdf -o output.sdf


or


standardize -c aromatize..neutralize input.sdf -o output.sdf


I hope this helps.


Zsolt