For what it's worth: There is a bug in the packaging dependencies of tomcat5.
The error above should be fixed if you install the package:
xml-commons-apis

The xml-commons package is installed, but the "apis" package is required and is
NOT installed. Not sure who to report this to at Fedora...but that fixed it for me.

Ack, sorry, I didn't read the error close enough, so I don't think your specific
error is related. Sorry for the noise.

Thanks for the feedback.  I just tried the recommendation and unfortunately, I
am still getting the problem described above.

Thanks anyways.

I upgraded to FC5 yeasterday and tried to reinstall Tomcat5.  Unfortunately, I'm
still getting the same problem.  Here is the message in the Tomcat Log:

Exception in thread "main" java.lang.NoClassDefFoundError:
org.apache.catalina.startup.Bootstrap
   at java.lang.Class.initializeClass (libgcj.so.7)
   at java.lang.Class.forName (libgcj.so.7)
   at gnu.java.lang.MainThread.run (libgcj.so.7)
Caused by: java.lang.ClassNotFoundException: javax.management.MBeanServer not
found in
gnu.gcj.runtime.SystemClassLoader{urls=[file:/usr/share/tomcat5/bin/bootstrap.jar,file:/usr/share/tomcat5/bin/commons-logging-api.jar,file:/usr/bin/build-classpath,file:/usr/bin/build-classpath],
parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}
   at java.net.URLClassLoader.findClass (libgcj.so.7)
   at java.lang.ClassLoader.loadClass (libgcj.so.7)
   at java.lang.ClassLoader.loadClass (libgcj.so.7)
   at java.lang.Class.initializeClass (libgcj.so.7)
   ...2 more

The classpath listed in the stack trace has the following entries:

file:/usr/share/tomcat5/bin/bootstrap.jar
file:/usr/share/tomcat5/bin/commons-logging-api.jar
file:/usr/bin/build-classpath
file:/usr/bin/build-classpath

Note the two file: urls referencing /usr/bin/build-classpath. This classpath is
generated by line 167 of /usr/bin/dtomcat5 which is this:

CLASSPATH="$CLASSPATH":"$CATALINA_HOME"/bin/bootstrap.jar:"$CATALINA_HOME"/bin/commons-logging-api.jar:`/usr/bin/build-\classpath
mx4j/mx4j-impl`:`/usr/bin/build-classpath mx4j/mx4j-jmx`

Note the two calls to /usr/bin/build-classpath, one with mx4j/mx4j-impl, and the
other with mx4j/mx4j-jmx. One of these should be returning
/usr/share/java/mx4j/mx4j-jmx.jar which contain the missing class. I have no
idea why in your case that is not happening. What happens if you manually run
the following command?

/usr/bin/build-classpath mx4j/mx4j-jmx

Also, could you post the output of this?:

rpm -V tomcat5 jpackage-utils

If I run the command /usr/bin/build-classpath mx4j/mx4j-jmx, I get the following:

/usr/share/java/mx4j/mx4j-jmx.jar

If I run rpm -V tomcat5 jpackage-utils, I get nothing, as below.

[root@atomic greg]# rpm -V tomcat5 jpackage-utils
[root@atomic greg]#

And yet both packages are indeed installed.

Thanks.

I'm still confused at the moment. Could you try the following commands as well
and send the output to me? (Please cut and paste for accuracy.)

sed 's@exec @exec /bin/echo @' /usr/bin/dtomcat5 > /tmp/dtomcat5
sh /tmp/dtomcat5 run

And for good measure:

rpm -qa tomcat5 jpackage-utils

Thanks

Hi Rafael.

Here is the output from the first:

[root@atomic greg]# sed 's@exec @exec /bin/echo @' /usr/bin/dtomcat5 > /tmp/dtomcat5
[root@atomic greg]# sh /tmp/dtomcat5 run
Using CATALINA_BASE:   /usr/share/tomcat5
Using CATALINA_HOME:   /usr/share/tomcat5
Using CATALINA_TMPDIR: /usr/share/tomcat5/temp
Using JRE_HOME:
/usr/lib/jvm/java/bin/java
-Djava.endorsed.dirs=/usr/share/tomcat5/common/endorsed -classpath
/usr/lib/jvm/java/lib/tools.jar:/usr/share/tomcat5/bin/bootstrap.jar:/usr/share/tomcat5/bin/commons-logging-api.jar:/usr/bin/build-classpath:
error: JVM_LIBDIR /usr/lib/jvm-exports/java does not exist or is not a
directory:/usr/bin/build-classpath: error: JVM_LIBDIR /usr/lib/jvm-exports/java
does not exist or is not a directory -Dcatalina.base=/usr/share/tomcat5
-Dcatalina.home=/usr/share/tomcat5 -Djava.io.tmpdir=/usr/share/tomcat5/temp
org.apache.catalina.startup.Bootstrap start
[root@atomic greg]#


And here is the output from the second:

[root@atomic greg]# rpm -qa tomcat5 jpackage-utils
jpackage-utils-1.6.6-1jpp_2rh
tomcat5-5.5.15-1jpp_6fc

Thanks.

I looked at the output above and noticed that the /usr/lib/jvm-exports/java did
not exist.  I created a symlink to the jre-gcj directory in the same jvm-exports
directory.  Now I get a new message in the logs. It appears to take longer to
run before crashing.  Also below is the output of the sed and sh commands above.
 They look clean now.

java.lang.NoClassDefFoundError: org.apache.catalina.core.StandardService
   at java.lang.Class.initializeClass (libgcj.so.7)
   at java.lang.Class.initializeClass (libgcj.so.7)
   at java.lang.Class.initializeClass (libgcj.so.7)
   at java.lang.Class.newInstance (libgcj.so.7)
   at org.apache.catalina.startup.Bootstrap.init (bootstrap.jar.so)
   at org.apache.catalina.startup.Bootstrap.main (bootstrap.jar.so)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.modeler.Registry
not found in
org.apache.catalina.loader.StandardClassLoader{urls=[file:/var/lib/tomcat5/server/classes/,file:/usr/share/tomcat5/server/lib/catalina-storeconfig.jar,file:/usr/share/tomcat5/server/lib/catalina-ant-jmx.jar,file:/usr/share/tomcat5/server/lib/catalina-cluster.jar,file:/usr/share/tomcat5/server/lib/catalina-optional.jar,file:/usr/share/tomcat5/server/lib/catalina.jar,file:/usr/share/tomcat5/server/lib/servlets-default.jar,file:/usr/share/tomcat5/server/lib/servlets-invoker.jar,file:/usr/share/tomcat5/server/lib/tomcat-jkstatus-ant.jar,file:/usr/share/tomcat5/server/lib/servlets-webdav.jar,file:/usr/share/tomcat5/server/lib/tomcat-ajp.jar,file:/usr/share/tomcat5/server/lib/tomcat-apr.jar,file:/usr/share/tomcat5/server/lib/tomcat-coyote.jar,file:/usr/share/tomcat5/server/lib/tomcat-http.jar,file:/usr/share/tomcat5/server/lib/tomcat-util.jar],
parent=org.apache.catalina.loader.StandardClassLoader{urls=[file:/var/lib/tomcat5/common/classes/,file:/usr/share/tomcat5/common/i18n/tomcat-i18n-en.jar,file:/usr/share/tomcat5/common/i18n/tomcat-i18n-es.jar,file:/usr/share/tomcat5/common/i18n/tomcat-i18n-fr.jar,file:/usr/share/tomcat5/common/i18n/tomcat-i18n-ja.jar,file:/usr/share/tomcat5/common/lib/naming-resources.jar,file:/usr/share/tomcat5/common/lib/naming-factory.jar],
parent=gnu.gcj.runtime.SystemClassLoader{urls=[file:/usr/share/tomcat5/bin/bootstrap.jar,file:/usr/share/tomcat5/bin/commons-logging-api.jar,file:/usr/share/java/mx4j/mx4j-impl.jar,file:/usr/share/java/mx4j/mx4j-jmx.jar],
parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}}}
   at java.net.URLClassLoader.findClass (libgcj.so.7)
   at java.lang.ClassLoader.loadClass (libgcj.so.7)
   at java.lang.ClassLoader.loadClass (libgcj.so.7)
   at java.lang.Class.initializeClass (libgcj.so.7)
   ...5 more


[root@atomic greg]# sed 's@exec @exec /bin/echo @' /usr/bin/dtomcat5 > /tmp/dtomcat5
[root@atomic greg]# sh /tmp/dtomcat5 run
Using CATALINA_BASE:   /usr/share/tomcat5
Using CATALINA_HOME:   /usr/share/tomcat5
Using CATALINA_TMPDIR: /usr/share/tomcat5/temp
Using JRE_HOME:
/usr/lib/jvm/java/bin/java
-Djava.endorsed.dirs=/usr/share/tomcat5/common/endorsed -classpath
/usr/lib/jvm/java/lib/tools.jar:/usr/share/tomcat5/bin/bootstrap.jar:/usr/share/tomcat5/bin/commons-logging-api.jar:/usr/share/java/mx4j/mx4j-impl.jar:/usr/share/java/mx4j/mx4j-jmx.jar
-Dcatalina.base=/usr/share/tomcat5 -Dcatalina.home=/usr/share/tomcat5
-Djava.io.tmpdir=/usr/share/tomcat5/temp org.apache.catalina.startup.Bootstrap start

I then noticed from the output above that org.apache.commons.modeler.Registry
appears to be missing.  After a search on Google, it appears to be part of the
jakarta-commons-modeler.i386 package.  From the text below, it looks like I have
it installed.

jakarta-commons-modeler.i386             1.1-4jpp_6fc           installed
Matched from:
jakarta-commons-modeler
[greg@atomic ~]$ rpm -V jakarta-commons-modeler.i386
[greg@atomic ~]$

It appears that the jakarta-commons-modeler jar is located in the directory
below.  Any idea why Tomcat5 is not seaching in this directory?


[greg@atomic ~]$ rpm -ql jakarta-commons-modeler.i386
/usr/lib/gcj/jakarta-commons-modeler
/usr/lib/gcj/jakarta-commons-modeler/jakarta-commons-modeler-1.1.jar.db
/usr/lib/gcj/jakarta-commons-modeler/jakarta-commons-modeler-1.1.jar.so
/usr/share/doc/jakarta-commons-modeler-1.1
/usr/share/doc/jakarta-commons-modeler-1.1/PROPOSAL.html
/usr/share/doc/jakarta-commons-modeler-1.1/RELEASE-NOTES.txt
/usr/share/doc/jakarta-commons-modeler-1.1/STATUS.html
/usr/share/java/commons-modeler-1.1.jar
/usr/share/java/commons-modeler.jar
/usr/share/java/jakarta-commons-modeler-1.1.jar
/usr/share/java/jakarta-commons-modeler.jar
[greg@atomic ~]$

Success, I've been able to fix it.  I have added the parameter
"/usr/share/java/jakarta-commons-modeler-1.1.jar" to the CLASSPATH settings in
the startup script /usr/bin/dtomcat5

I have attached the script below.

Therefore there are 2 problems that should be dealt with:

1. The file /etc/tomcat5/tomcat5.conf refers to the location of the JRE as
/usr/lib/jvm-exports/java.  This may not exist for many users, particulary those
that have upgraded from earlier releases of FC.  Should it not point to
/usr/lib/jvm-exports/jre-gcj instead?

2. We need to add another parameter
("/usr/share/java/jakarta-commons-modeler-1.1.jar") to the CLASSPATH settings in
the startup script /usr/bin/dtomcat5.  Please see the attached file below and
search for GJD.

Thanks.

Created attachment 127376 [details]
Modified Startup Script for Tomcat5

I'm glad you've been able to work around the problem, but I'm pretty sure the
issues you're seeing are problems with the upgrade, and you may run into more
problems down the line.

On a clean install /usr/lib/jvm-exports/java is a symbolic link to
/etc/alternatives/java_sdk_exports. Similarly the commons-modeler jar shouldn't
need to be in the CLASSPATH because it is linked to from
/usr/share/tomcat5/server/lib, and should be picked up by the catalina class loader.

I'm guessing if you run the following command:

ls /usr/share/tomcat5/server/lib

You'll have some missing or broken symbolic links relative to a clean fc5
install. Can you send me the output of the above command?

When I have a free machine I'm going to try to directly reproduce the problems
you've run into by testing the upgrade path you outlined in your initial report.

Thanks Rafael.

Here is the output to the ls command:

[root@atomic greg]# ls /usr/share/tomcat5/server/lib
[catalina-ant5].jar       [commons-fileupload].jar  servlets-invoker.jar
catalina-ant-jmx.jar      [commons-logging].jar     servlets-ssi.renametojar
catalina-cluster.jar      [commons-modeler].jar     servlets-webdav.jar
catalina.jar              [eclipse-ecj].jar         tomcat-ajp.jar
catalina-optional.jar     [jaas].jar                tomcat-apr.jar
catalina-storeconfig.jar  [mx4j][mx4j].jar          tomcat-coyote.jar
[commons-beanutils].jar   [regexp].jar              tomcat-http.jar
[commons-digester].jar    servlets-cgi.renametojar  tomcat-jkstatus-ant.jar
[commons-el].jar          servlets-default.jar      tomcat-util.jar
[root@atomic greg]#

Greg

Cannot reproduce in current releases . Closing.