starting jcman with an error

Hi,


I have a problem when I start jcman on a linux box, with suse 9.3, and java.1.4.2 sun I get following error:


./bin/jcman


java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver


at java.net.URLClassLoader$1.run(URLClassLoader.java:199)


at java.security.AccessController.doPrivileged(Native Method)


at java.net.URLClassLoader.findClass(URLClassLoader.java:187)


at java.lang.ClassLoader.loadClass(ClassLoader.java:289)


at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)


at java.lang.ClassLoader.loadClass(ClassLoader.java:235)


at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)


at java.lang.Class.forName0(Native Method)


at java.lang.Class.forName(Class.java:141)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:205)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemaxon.jchem.gui.Connector.go(Connector.java:64)


at chemaxon.jchem.gui.JChemFrame.connect(JChemFrame.java:561)


at chemaxon.jchem.JChemManager.init(JChemManager.java:89)


at chemaxon.jchem.JChemManager.main(JChemManager.java:106)








what am I doing wrong? How can I get rid of this error?





Regards,


Marek

Hi,





You should include the JDBC driver in your CLASSPATH environment variable.


The driver can be downloaded from the MySQL website:





http://dev.mysql.com/downloads/connector/j/3.1.html





After unpacking the package, you will find a .jar file, this is the actual driver file (e.g. "mysql-connector-java-3.1.12-bin.jar")





Best regards,





Szilard

PS:





Please see the following page for further information on installation:





http://www.chemaxon.com/jchem/doc/admin/prepscripts.html





Szilard

After installing JChem 3.1.3 I was able to start JChemManager with little difficulty and loaded an SDF file successfully. However, getting the cartridge installed and running took a little longer and in the process I followed your recommendations uninstalling the 1.4.2 JDK and downloading JDK 5.0 Update 6 and setting JAVA_HOME to C:\Program Files\Java, with the JVM at C:\Program Files\Java\jre1.5.0_06. The cartridge works well now with TomCat 5.0, I can run my substructure searches and display hits, but now I can no longer open the JChemManager GUI.





My CLASSPATH environmental seems to be set correctly





>echo %CLASSPATH% -> G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar





But after the login dialog box I get the following





java.lang.ClassNotFoundException: oracle.jdbc.driver.OracleDriver


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)


at java.lang.ClassLoader.loadClassInternal(Unknown Source)


at java.lang.Class.forName0(Native Method)


at java.lang.Class.forName(Unknown Source)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:2


05)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemaxon.jchem.gui.Connector.go(Connector.java:95)


at chemaxon.jchem.gui.JChemFrame.connect(JChemFrame.java:561)


at chemaxon.jchem.JChemManager.init(JChemManager.java:89)


at chemaxon.jchem.JChemManager.main(JChemManager.java:106)





What's missing?

Hi,





Some tips about the possible things I can think of:





- If you have just changed your CLASSPATH you should open a new command-line terminal for starting jcman (so changes can take effect)


- Are you sure the path is correct ?


- Is it on a network drive ? Is it connected ? You may also try to copy it to the local file system and use if from there.


- Is the .jar file intact (can you open it with WinZip or similar tool ?)





Let me know if this helps.





Szilard

> If you have just changed your CLASSPATH you should open a new command-line terminal for starting jcman (so changes can take effect)





No, the CLASSPATH env was set long ago





> Are you sure the path is correct ?


> Is it on a network drive ? Is it connected ? You may also try to copy it to the local file system and use if from there.





The file is local and it resides in the same path as set in the env





- Is the .jar file intact (can you open it with WinZip or similar tool ?)





Doesn't the cartridge use this same jdbc? The cartridge is working fine. How does JCHEMMGR find the JVM? Does it use JAVA_HOME?

Quote:

Doesn't the cartridge use this same jdbc?

No, it uses a copy.


Tomcat does not care about CLASSPATH, so you must have a copy in Tomcat's lib folder.


(usually under shared\lib )

Quote:

How does JCHEMMGR find the JVM? Does it use JAVA_HOME?

No, it only depends on the CLASSPATH.





Do you have read permission on the jar file ?

PS:





Please also paste here the complete output of

Code:

echo %CLASSPATH%

The entire contents of CLASSPATH are "G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar"





SYSTEM and USERS have read and execute permission on classes12.jar

This is not likely to make any difference, but could you, please, try using oracle.jdbc.OracleDriver as the driver class instead of oracle.jdbc.driver.OracleDriver?

>try using oracle.jdbc.OracleDriver as the driver class instead of oracle.jdbc.driver.OracleDriver?





Nope, that did not make any difference. I'm sorry I should have mentioned the DB and workstation are running on Win Server 2003. Marvin sketch works fine so the problem does not seem to affect all Java GUIs.

Please, could you try the following command on the command prompt:

Code:

jar tf G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar | %SystemRoot%\system32\find.exe /N "OracleDriver"

This command should return something like:

Code:

[163]oracle/jdbc/driver/OracleDriver.class [348]oracle/jdbc/OracleDriver.class

I only get back: 'jar' is not recognized as an internal or external command,


operable program or batch file.





I hate to flout my ignorance, but is that a 'PIPE' between classes12.jar and %SystemRoot%? I didn't know you could do that in Win.





I tried installing JChem on a different workstation, set the environmentals, and was able to open JChemMgr and load an SDF into the same DB without incident. I really suspect something happened during the JChem Cartridge installation. I made the same installations on both my Test and Production servers and can no longer open the Mgr GUI on either machine.

Quote:

I only get back: 'jar' is not recognized as an internal or external command, operable program or batch file.

Find the Java installation on your server. Let's assume it is installed in the %JAVA_HOME% directory. Modify the command accordingly:





%JAVA_HOME%\bin\jar tf G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar | %SystemRoot%\system32\find.exe /N "OracleDriver"





Actually, the jcman.bat script (which you probably use to start JChemManager) refers to the java runtime simply with "java", so an appropriate java.exe should be on your executable PATH. A jar.exe is usually also in %JAVA_HOME%\bin. So I would expect jar.exe to be also on your PATH. I wonder which java is found by jcman.bat. Please, could execute the following:

Code:

java -version

What does it return?

Quote:

I hate to flout my ignorance, but is that a 'PIPE' between classes12.jar and %SystemRoot%? I didn't know you could do that in Win.

Sure. Windows is crap, but tries hard catching up. :-)

>jar tf G:\oracle\product\10.1.0\db_1\jdbc\


lib\classes12.jar | %SystemRoot%\system32\find.exe /N "OracleDriver"





[122]oracle/jdbc/driver/OracleDriver.class


[129]oracle/jdbc/driver/OracleDriverExtension.class


[517]oracle/jdbc/OracleDriver.class





>java -version


java version "1.5.0_06"


Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-b05)


Java HotSpot(TM) Client VM (build 1.5.0_06-b05, mixed mode, sharing)





but my %Path% environmental includes no reference to


C:\Program Files\Java\jre1.5.0_06\bin





it does however include the following from the Oracle install


G:\Oracle\product\10.1.0\Client_1\jre\1.4.2\bin\client;


G:\Oracle\product\10.1.0\Client_1\jre\1.4.2\bin;





Conflict?

Quote:

but my %Path% environmental includes no reference to C:\Program Files\Java\jre1.5.0_06\bin

This is strange. How did you check your %Path%? In the command line, with SET PATH, or in the ControlPanel/System/Advanced/Environment settings?





Anyway, I suggest to edit the jcman.bat file so that it uses Sun Microsystems JDK (C:\Program Files\Java\jre1.5.0_06\bin) for sure. Does it make any difference?





If we're at editing jcman.bat...please, set the echo on (@echo on) just before java is started (at the end of the script) and post the output here. You are running the GUI version -- jcman.bat without command line parameters --, don't you?

>How did you check your %Path%? In the command line, with SET PATH, or in the ControlPanel/System/Advanced/Environment settings?





I don't see any difference between the two, here's the output for SET PATH





G:\Oracle\product\10.1.0\Client_1\bin;


G:\Oracle\product\10.1.0\Client_1\jre\1.4.2\bin\client;


G:\Oracle\product\10.1.0\Client_1\jre\1.4.2\bin;


C:\Program Files\ChemOffice2002\Common\DLLs;


C:\Perl\bin\;


C:\Perl\bin;


G:\oracle\product\10.1.0\db_1\bin;


G:\oracle\product\10.1.0\db_1\jre\1.4.2\bin\client;


G:\oracle\product\10.1.0\db_1\jre\1.4.2\bin;


C:\WINDOWS\system32;


C:\WINDOWS;


C:\WINDOWS\System32\Wbem;


C:\jchem\bin;


C:\jchem\bin





Heres JAVA_HOME


C:\Program Files\Java\jdk1.5.0_06





>Anyway, I suggest to edit the jcman.bat file





Okay, I'll be able happy to try, but I'm afraid you'll have to help me out a little bit. I guess I need to add a line like 'set=' but I need help with the rest of the syntax.





>You are running the GUI version -- jcman.bat without command line parameters


Yep.

Please, do the following:





1.) Save a copy of your current jcman.bat file.





2.) Insert at the beginning of line #156 in jcman.bat

Code:

"%JAVA_HOME%"\bin\

After the modification, this line should read as follows:

Code:

"%JAVA_HOME%"\bin\java %JAVA_OPTS% chemaxon.jchem.JChemManager

Note, the double quotes. They are required part of the command.





3.) Insert a new line immediately before line #156 and write the following in it:

Code:

@echo on

This will cause the exact command for starting the Java runtime with JChemManager to be displayed in the Command Propmt window where the jcman.bat has been executed.





4.) Run the modified jcman.bat.





5.) If the problem persists, copy the output of jcman.bat from the Command Prompt window and post it here.








PS:

Quote:

I don't see any difference between the two, here's the output for SET PATH

This may not be relevant in your case, but in general, the safe way of checking your path is to do it on the command line. In the Control Panel your full executable path is split into two parts: system path and user path. This may be the source of some confusion. (Not to mention that those tiny little editbox capsules are very hard to read.)

Thanks for the detailed instructions. I'm still getting the same error, but was able to obtain the following output:





C:\Documents and Settings\Administrator>"C:\Program Files\Java\jdk1.5.0_06"\bin\


java -client -Xmx200m -classpath "C:\jchem\lib\jchem.jar" chemaxon.jchem.JChemManager


java.lang.ClassNotFoundException: oracle.jdbc.driver.OracleDriver


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 sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)


at java.lang.ClassLoader.loadClass(ClassLoader.java:251)


at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)


at java.lang.Class.forName0(Native Method)


at java.lang.Class.forName(Class.java:164)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:205)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemaxon.jchem.gui.Connector.go(Connector.java:95)


at chemaxon.jchem.gui.JChemFrame.connect(JChemFrame.java:561)


at chemaxon.jchem.JChemManager.init(JChemManager.java:89)


at chemaxon.jchem.JChemManager.main(JChemManager.java:106)

Are your 100% sure that your CLASSPATH variable is set to G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar? Please, could you double check with SET CLASSPATH in the Command Prompt?

By the way, CLASSPATH is used only if JCHEMCLASSPATH is NOT set. Please, could you also check your JCHEMCLASSPATH?

I get the following:





C:\Documents and Settings\Administrator>set classpath


CLASSPATH=G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar





C:\Documents and Settings\Administrator>set JCHEMCLASSPATH


JCHEMCLASSPATH=C:\jchem\lib\jchem.jar

Please, either include G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar in your JCHEMCLASSPATH:

Code:

SET JCHEMCLASSPATH=C:\jchem\lib\jchem.jar;G:\oracle\product\10.1.0\db_1\jdbc\lib\classes12.jar

or unset JCHEMCLASSPATH:

Code:

SET JCHEMCLASSPATH=

As I wrote in my previous posting: CLASSPATH is used only, if JCHEMCLASSPATH is NOT set. If JCHEMCLASSPATH is set, it is used and CLASSPATH is not used. JCHEMCLASSPATH must therefore include either all Java libraries required or nothing.

Thanks, that fixed it. Whew!


I don't have any record in my notes of having explicitly created JCHEMCLASSPATH. Was it created by jchemstreams/install.bat?

Quote:

I don't have any record in my notes of having explicitly created JCHEMCLASSPATH. Was it created by jchemstreams/install.bat?

You mean cartridge/install.bat. No, it doesn't do anything like that.