ClassNotFoundException

[Hubert Pernegger]

hi,
my java environment is working properly, but nevertheless I got that error:

    
Caused by: java.lang.ClassNotFoundException: WSMPsrchClient not found in gnu.gcj.runtime.SystemClassLoader{urls=[file:/usr/java/jdk1.5.0_06/lib/dt.jar,
file:/usr/java/jdk1.5.0_06/lib/tools.jar],
parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}

the program compile without problems in eclipse, then I invoke a shell script that uses the above mentioned WSMPsrchClient, when I perform the shell script I get that error.

thanks for help

[ EJFH: Added newlines in long classpath to fix page formatting ]
[ May 15, 2006: Message edited by: Ernest Friedman-Hill ]

[Jesper de Jong]

Are you using a GNU Java environment?

Your system cannot find the class named WSMPsrchClient, most likely because you didn't include the directory or JAR file that contains it in the classpath.

[Ramen Chatterjee]

Just to add to Jesper's comment - check your project properties in Eclipse and see what jars are in your project that are missing when you run your script. Also, you could try printing the value of CLASSPATH from your script to check the paths/jars.

Regards

Ramen

[Ernest Friedman-Hill]

Also carefully check the shell script against the actual name of the class, because you may simply have misspelled it. Finally, the shell script uses an unqualified name for the class, but perhaps it is (as all classes should be) defined in a package, and you've left the package name off.

[Hubert Pernegger]

hi,
I have added the missing jar files to my project, and checked names, but I still get the same error....

my classpath evironment:

    
PATH=$PATH:$HOME/bin
 
JAVA_HOME=/usr/java/jdk1.5.0_06
PATH=${PATH}:${JAVA_HOME}/bin
CLASSPATH=${JAVA_HOME}/lib/dt.jar:${JAVA_HOME}/lib/tools.jar
 
CATALINA_HOME=/usr/local/jakarta-tomcat-5.0.28
 

 
export JAVA_HOME PATH CLASSPATH CATALINA_HOME
 

[Hubert Pernegger]

no, I'm not using a gnu environment....

[Ernest Friedman-Hill]

Well, this is the first time you're mentioning Tomcat, so of course that makes a difference -- is this a Web application? If so, the answers are going to be totally different, so let us know.

If it's not a Web application, then your CLASSPATH is quite wrong, far worse than just the default setting you'd get if CLASSPATH were entirely unset. You're telling Java that the only classes of interest will come from those two jars included in the JDK, which is surely not at all what you intend.

Anyway, let us know abot the Web application thing and we'll help you work this out.

[Hubert Pernegger]

no, sorry,
this program is not a web application....

ups, does that mean I have to add in the classpath all the jar files that are included in the project as well....

[Hubert Pernegger]

that's are a lot of jar files....

[Ernest Friedman-Hill]

Originally posted by Hubert Pernegger:
no, I'm not using a gnu environment....

It was a kind of rhetorical question: the known answer to which is "yes, you surely are." Whether you know it or not, rather than using the Sun JVM, you're using the GNU "gcj" toolchain: hence the "gnu.gcj.runtime.SystemClassLoader" in the error message.

[Hubert Pernegger]

ok, sorry, thanks for the explanation....

but do I have to add all the jar files from the project also into the classpath....

[Ernest Friedman-Hill]

Again, you need to tell us first if this is a Web application or not -- it matters tremendously. But honestly, the answer is "no" -- even if it's not a Web application, there are other better ways than setting CLASSPATH.

[Hubert Pernegger]

no it is not a webapplication....
it is a usual java application, that I invoke within a shell script with a few parameters....
and in eclipse I can compile it without any problems.....

but the shell script doesn't work (error mentioned in the first post)

[Ernest Friedman-Hill]

OK, cool, we're in the home stretch, then.

Right now you've got something like

java WSMPsrchClient

just edit the script so be something like

java -classpath /usr/wherever/jar1.jar:/usr/someplace/jar2.jar:/usr/another/jar3.jar

where jar1.jar, jar2.jar, etc, are all the jars your application needs. This is assuming everything is in a jar, of course; otherwise there's a sometimes confusing way of adding directories where classes may be found.

The -classpath switch overrides the environment variable.

[Hubert Pernegger]

hi,
I have done that as you proposed....but I still get the same error:

shell script:

    
#!/bin/sh
 
java -classpath /home/Hubert/installed/axis-1_3/lib/lib/activation.jar:/home/Hubert/installed/axis-1_3/lib/lib/axis.jar:/home/Hubert/installed/axis-1_3/lib/lib/commons-cli-1.0.jar:
/home/Hubert/installed/axis-1_3/lib/lib/commons-cli.jar:/home/Hubert/installed/axis-1_3/lib/lib/commons-discovery.jar:/home/Hubert/installed/axis-1_3/lib/lib/commons-logging.jar:
/home/Hubert/installed/axis-1_3/lib/lib/freefluo.jar:/home/Hubert/installed/axis-1_3/lib/lib/jaxrpc.jar:/home/Hubert/installed/axis-1_3/lib/lib/log4j-1.2.4.jar:
/home/Hubert/installed/axis-1_3/lib/lib/mail.jar:/home/Hubert/installed/axis-1_3/lib/lib/saaj.jar:/home/Hubert/installed/axis-1_3/lib/lib/servlet.jar:/home/Hubert/installed/axis-1_3/lib/lib/wsdl4j.jar:
/home/Hubert/installed/axis-1_3/lib/lib/xercesImpl.jar:/home/Hubert/installed/axis-1_3/lib/lib/xmlParserAPIs.jar:/home/Hubert/installed/axis-1_3/lib/lib/xmlrpc-2.0.jar:/home/Hubert/installed/axis-1_3/lib/lib/axis-ant.jar:
/home/Hubert/installed/axis-1_3/lib/lib/axis-schema.jar:/home/Hubert/installed/axis-1_3/lib/lib/jaxrpc.jar:/home/Hubert/installed/axis-1_3/lib/lib/wsdl4j-1.5.1.jar
 
exec < Permutat.txt
 
while read line
 do
  echo $line > input_$line.txt
 
  java WSMPsrchClient --matrix BLOSUM70 --gap 10 --annotation no --sort rank --alignments 200 --outfile $line.c.swiss6.xml --email [e-mail] --program mpsrch_ppa --database swissprot --sequence input_$line.txt
 
  rm input_$line.txt
 
 done
 

 

[Ernest Friedman-Hill]

You've got two different "java" lines there. You want to put that -classpath switch, with its long argument, on the second java command line (removing the first altogether.) Put it before the name of the class -- i.e.,

java -classpath /home/...:/home... WSMPsrchClient --matrix BLOSUM70 ...

[Hubert Pernegger]

ok,
now I get the this error:

    
Usage: gij [OPTION] ... CLASS [ARGS] ...
          to invoke CLASS.main, or
       gij -jar [OPTION] ... JARFILE [ARGS] ...
          to execute a jar file
Try `gij --help' for more information.
web_service_shell: line 11: /home/Hubert/installed/axis-1_3/lib/lib/commons-cli. jar:/home/Hubert/installed/axis-1_3/lib/lib/commons-discovery.jar:/home/Hubert/i nstalled/axis-1_3/lib/lib/commons-logging.jar:: No such file or directory
web_service_shell: line 12: /home/Hubert/installed/axis-1_3/lib/lib/freefluo.jar :/home/Hubert/installed/axis-1_3/lib/lib/jaxrpc.jar:/home/Hubert/installed/axis- 1_3/lib/lib/log4j-1.2.4.jar:: No such file or directory
web_service_shell: line 13: /home/Hubert/installed/axis-1_3/lib/lib/mail.jar:/ho me/Hubert/installed/axis-1_3/lib/lib/saaj.jar:/home/Hubert/installed/axis-1_3/li b/lib/servlet.jar:/home/Hubert/installed/axis-1_3/lib/lib/wsdl4j.jar:: No such f ile or directory
web_service_shell: line 14: /home/Hubert/installed/axis-1_3/lib/lib/xercesImpl.j ar:/home/Hubert/installed/axis-1_3/lib/lib/xmlParserAPIs.jar:/home/Hubert/instal led/axis-1_3/lib/lib/xmlrpc-2.0.jar:/home/Hubert/installed/axis-1_3/lib/lib/axis -ant.jar:: No such file or directory
web_service_shell: line 15: /home/Hubert/installed/axis-1_3/lib/lib/axis-schema. jar:/home/Hubert/installed/axis-1_3/lib/lib/jaxrpc.jar:/home/Hubert/installed/ax is-1_3/lib/lib/wsdl4j-1.5.1.jar: No such file or directory
web_service_shell: line 17: WSMPsrchClient: command not found
 

[Ernest Friedman-Hill]

Looks like you've got lots of extra newlines in there, breaking up the classpath. Please tell me you didn't do that because of the edit I did to your first post -- that was just so the formatting of this forum page wasn't all messed up by one enormous long line.

[Hubert Pernegger]

hi,
what do you mean...
it is all in one line java --classpath ......WSMPsrchClient.....

or what exactly do you mean....

[Ernest Friedman-Hill]

Yes, all on one line.

[Hubert Pernegger]

ok,
it was in one line...
I just guess there is something missing in the environment....

[Ernest Friedman-Hill]

Originally posted by Hubert Pernegger:
ok,
it was in one line...
I just guess there is something missing in the environment....

The error messages you recieved very clearly indicated that it was spread across multiple lines. Do you have this working yet?

[Hubert Pernegger]

hi,
ok I have put all in one line and I get the same error again that I have posted in the first post.

ok it seems I have both installed: /usr/java/jre1.5.0
and /usr/lib/jvm/java-1.4.1-gcj

in eclipse I'm using the jre1.5.0, but on the command line it seems that it is looking in /usr/lib/jvm/java-1.4.1-gcj