cartridge install issue

ChemAxon 60ee1f1328

06-10-2009 12:17:23

Hello,


Trying to install the cartridge in oracle 11g, o/s is windows xp.


When starting up the jchem server - see this error:


(you do not mention this requirement in the new docs prior to run install_interactive.bat)


C:\Program Files\ChemAxon\JChem\cartridge>"C:\Program Files\Java\jdk1.6.0_05\bin
\java.exe" -server -Xrs -XX:-OmitStackTraceInFastThrow -Dchemaxon.jchem.cartridg
e.config.file="C:\Program Files\ChemAxon\JChem\cartridge\\conf\jcart.properties"
 -Djava.util.logging.config.class=chemaxon.jchem.cartridge.util.LoggingConfigura
tor -Djava.awt.headless=true -classpath "C:\Program Files\ChemAxon\JChem\lib\jch
em.jar"  chemaxon.jchem.cartridge.server.Bootstrapper start
INFO: Server control process started
INFO: Using classpath: C:\Program Files\ChemAxon\JChem\lib\jchem.jar;
INFO: Server process start-ed.
java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
        at chemaxon.jchem.cartridge.rmi.impl.AdminImpl.main(AdminImpl.java:295)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.logging.LogFacto
ry
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
        ... 1 more
SEVERE: Server process exited with code: 1
INFO: Server shutdown thread started


i placed commons-logging-1.1.1.jar in JChem/lib and referenced in PATH...


alas problem remains.


thanks,


daniel.


 


 


 


 

ChemAxon 9c0afc9aaf

07-10-2009 04:00:33

Hi Daniel,


Could you let us know the JChem version you are trying to install ?


Please alsways specify the version, as we ask on the left side of the post editor window.


 





i placed commons-logging-1.1.1.jar in JChem/lib and referenced in PATH...


THe file commons-logging-1.1.jar should be already present in <jchem_root>/lib, adding this adiitional jar to the CLASSPATH is neither necessary nor advised.


In the PATH it should not have any effect at all (though harmlessly ineffective).


 


(you do not mention this requirement in the new docs prior to run install_interactive.bat)


This is not quite clear.


Is the output the result of server.bat or install_interactive.bat ?


Best regards,


 


Szilard



ChemAxon 60ee1f1328

07-10-2009 10:48:34

Sorry I did not post the version : JChem 5.2.5.1


I have taken all your advice below and removed additional jar from PATH and CLASSPATH.


If I run server.bat start


C:\Program Files\ChemAxon\JChem\cartridge>"C:\Program Files\Java\jdk1.6.0_05\bin
\java.exe" -server -Xrs -XX:-OmitStackTraceInFastThrow -Dchemaxon.jchem.cartridg
e.config.file="C:\Program Files\ChemAxon\JChem\cartridge\\conf\jcart.properties"
 -Djava.util.logging.config.class=chemaxon.jchem.cartridge.util.LoggingConfigura
tor -Djava.awt.headless=true -classpath "C:\Program Files\ChemAxon\JChem\lib\jch
em.jar"  chemaxon.jchem.cartridge.server.Bootstrapper start
INFO: Server control process started
INFO: Using classpath: C:\Program Files\ChemAxon\JChem\lib\jchem.jar;
INFO: Server process start-ed.
java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
        at chemaxon.jchem.cartridge.rmi.impl.AdminImpl.main(AdminImpl.java:295)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.logging.LogFacto
ry
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
        ... 1 more
SEVERE: Server process exited with code: 1
INFO: Server shutdown thread started


 


If I run install-interactive.bat :


C:\Program Files\ChemAxon\JChem\cartridge>install_interact.bat
'install_interact.bat' is not recognized as an internal or external command,
operable program or batch file.

C:\Program Files\ChemAxon\JChem\cartridge>install-interact.bat

Name of the Oracle host. [localhost]:

Oracle listener port [1521]:

Name of the Oracle instance [mydb]: development

The host name of the JChem Server [localhost]:

The port at which the JChem Server accepts connections [1099]:

maximum memory allocated to JChem Server [700m]:
INFO: Checking JChem Server at localhost:1099...
java.lang.NoSuchMethodError: chemaxon.jchem.cartridge.rmi.client.RmiDirectory.lo
cate(Lchemaxon/jchem/cartridge/rmi/client/RmiServerDesc;I)Lchemaxon/jchem/cartri
dge/rmi/Directory;
        at chemaxon.jchem.cartridge.install.InstallUtil.checkJChemServer(Install
Util.java:131)
        at chemaxon.jchem.cartridge.install.InstallCmdLine.checkStartNewJChemSer
ver(InstallCmdLine.java:416)
        at chemaxon.jchem.cartridge.install.InstallCmdLine.getCheckJChemServerPa
ramsInteractively(InstallCmdLine.java:246)
        at chemaxon.jchem.cartridge.install.InstallCmdLine.getParamsInteractivel
y(InstallCmdLine.java:167)
        at chemaxon.jchem.cartridge.install.InstallCmdLine.install(InstallCmdLin
e.java:87)
        at chemaxon.jchem.cartridge.install.InstallCmdLine.main(InstallCmdLine.j
ava:682)


 


This is probably because the JChem server is not running due to issue atop?


However, I assume that having the JChem server 'up' is a pre-requisite of the install which does not appear to be in your instructions/documentation.


file:///C:/Program%20Files/ChemAxon/JChem/doc/admin/cartridge.html (default single host)


Also your JDK_5 reference Java SE I think (?) rather than EE which I happened to have installed on my XP machine so did not encounter other vista issue (that is underway).


I would ideally run all this on linux but these are two machines I have at home!


Best regards and thanks for your help,


Daniel.


 


 

ChemAxon aa7c50abf8

07-10-2009 17:19:06

Daniel,


I don't know how it happened, but it appears that two different JChem versions got mixed. The stack trace


java.lang.NoClassDefFoundError: org/apache/commons/logging/LogFactory
        at chemaxon.jchem.cartridge.rmi.impl.AdminImpl.main(AdminImpl.java:295)


is not consistent with JChem 5.2.5.1. The version from which this code comes is a JChem version before 5.1 (some of the 5.0.x versions).


This stack trace


java.lang.NoSuchMethodError: chemaxon.jchem.cartridge.rmi.client.RmiDirectory.lo
cate(Lchemaxon/jchem/cartridge/rmi/client/RmiServerDesc;I)Lchemaxon/jchem/cartri
dge/rmi/Directory;
        at chemaxon.jchem.cartridge.install.InstallUtil.checkJChemServer(Install
Util.java:131)


also indicates files from different JChem versions.



With 5.2.5.1 you don't have to pre-start JChem Server during installation, the installation process will start it for you. It is just that the installer doesn't reach the point where the server is started due to this other error.


I suggest to



  1. remove the C:\Program Files\ChemAxon\JChem\ directory

  2. download the last JChem version (the platform independent release) and

  3. retry the installation.


Regards,


Peter