Bug 238343

Having this error messages on RHEL 5.1 and tomcat5-5.5.23-0jpp.3.0.3.el5_1-x86_64

# service tomcat5 restart waiting for processes to exit                        
     [  OK  ]  
waiting for processes to exit  
waiting for processes to exit  
Starting tomcat5: /usr/bin/rebuild-jar-repository: error: could not find
jdbc-stdext Java extension for this JVM  
/usr/bin/rebuild-jar-repository: error: could not find jndi Java extension for
this JVM  
/usr/bin/rebuild-jar-repository: error: All detected jars were not found for
this jvm  
/usr/bin/rebuild-jar-repository: error: could not find jaas Java extension for
this JVM  
/usr/bin/rebuild-jar-repository: error: All detected jars were not found for
this jvm  
                                                          [  OK  ]  

tomcat5.conf

# tomcat5 service configuration file

# you could also override JAVA_HOME here
# Where your java installation lives
#JAVA_HOME="/usr/lib/jvm/java"
#JAVA_HOME="/usr/java/jdk1.5.0_14"
#JRE_HOME="/usr/java/jdk1.5.0_14/jre"
JAVA_HOME="/usr/java/jdk1.6.0_05"
JRE_HOME="/usr/java/jdk1.6.0_05/jre"

# alternatives --display java
java - status is manual.
link currently points to /usr/java/jdk1.6.0_05/bin/java
/usr/lib/jvm/jre-1.4.2-gcj/bin/java - priority 1420
slave keytool: /usr/lib/jvm/jre-1.4.2-gcj/bin/keytool
slave rmiregistry: /usr/lib/jvm/jre-1.4.2-gcj/bin/rmiregistry
slave jre_exports: /usr/lib/jvm-exports/jre-1.4.2-gcj
slave jre: /usr/lib/jvm/jre-1.4.2-gcj
/usr/java/jdk1.5.0_14/jre/bin/java - priority 1
slave keytool: (null)
slave rmiregistry: (null)
slave jre_exports: (null)
slave jre: (null)
/usr/java/jdk1.6.0_05/bin/java - priority 2
slave keytool: (null)
slave rmiregistry: (null)
slave jre_exports: (null)
slave jre: (null)
Current `best' version is /usr/lib/jvm/jre-1.4.2-gcj/bin/java. 

Can you post the output of:

ls -l /usr/lib/jvm-exports/java-1.4.2-gcj-1.4.2.0/

Missed this:

JAVA_HOME="/usr/java/jdk1.6.0_05"
JRE_HOME="/usr/java/jdk1.6.0_05/jre"

You'll need to retry against JPackage-style JDK packages.  For example
java-1.6.0-sun in the RHEL-5 Supplementary RHN channel.

In response to comment #1, those links exist for compatibility with other JVM
vendors/versions. A broken link in this case is harmless and the errors can be
safely ignored, but it should point to rt.jar of the currently selected JVM
alternative.

In response to comment #2, JAVA_HOME is being set to a JVM that does not look
like one that we support. You should be installing something like java-1.6.0-sun
that is JPackage-compatible and will provide the symlinks which should not be
broken.

If you are using a proper RPM package, you should not see errors with
rebuild-jar-repository. Can you post the output of:

$ ls -l /var/lib/tomcat5/common/lib
$ /usr/sbin/update-alternatives --display java | grep currently
$ /usr/sbin/update-alternatives --display javac | grep currently

Thanks Thomas and David for your replies.

I'll post the info as soon as I get it. Sorry, this a customer's system.
I think he hasn't installed the java-1.6.0-sun package from RHN. Have to confirm.

Requested info:

# ls -l /var/lib/tomcat5/common/lib
total 0
lrwxrwxrwx 1 root root 23 Apr 24 13:37 [ant].jar -> /usr/share/java/ant.jar
lrwxrwxrwx 1 root root 39 Apr 24 13:37 [commons-collections].jar ->
/usr/share/java/commons-collections.jar
lrwxrwxrwx 1 root root 32 Apr 24 13:37 [commons-dbcp].jar ->
/usr/share/java/commons-dbcp.jar
lrwxrwxrwx 1 root root 30 Apr 24 13:37 [commons-el].jar ->
/usr/share/java/commons-el.jar
lrwxrwxrwx 1 root root 39 Apr 24 13:37 [commons-logging-api].jar ->
/usr/share/java/commons-logging-api.jar
lrwxrwxrwx 1 root root 32 Apr 24 13:37 [commons-pool].jar ->
/usr/share/java/commons-pool.jar
lrwxrwxrwx 1 root root 23 Apr 24 13:37 [jaf].jar -> /usr/share/java/jaf.jar
lrwxrwxrwx 1 root root 36 Apr 24 13:37 [jasper5-compiler].jar ->
/usr/share/java/jasper5-compiler.jar
lrwxrwxrwx 1 root root 35 Apr 24 13:37 [jasper5-runtime].jar ->
/usr/share/java/jasper5-runtime.jar
lrwxrwxrwx 1 root root 28 Apr 24 13:37 [javamail].jar ->
/usr/share/java/javamail.jar
lrwxrwxrwx 1 root root 38 Apr 24 13:37 [jdbc-stdext].jar ->
/could/not/find/extension/for/this/jvm
lrwxrwxrwx 1 root root 44 Apr 11 14:19 jdbc-stdext.jar ->
/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre/lib/
lrwxrwxrwx 1 root root 27 Apr 10 18:12 jdtcore.jar -> /usr/share/java/jdtcore.jar
lrwxrwxrwx 1 root root 38 Apr 24 13:37 [jndi].jar ->
/could/not/find/extension/for/this/jvm
lrwxrwxrwx 1 root root 23 Apr 24 13:37 [jsp].jar -> /usr/share/java/jsp.jar
lrwxrwxrwx 1 root root 23 Apr 24 13:37 [jta].jar -> /usr/share/java/jta.jar
lrwxrwxrwx 1 root root 29 Apr 24 13:37 [mx4j][mx4j].jar ->
/usr/share/java/mx4j/mx4j.jar
lrwxrwxrwx 1 root root 42 Apr 10 18:12 naming-factory.jar ->
/usr/share/java/tomcat5/naming-factory.jar
lrwxrwxrwx 1 root root 44 Apr 10 18:12 naming-resources.jar ->
/usr/share/java/tomcat5/naming-resources.jar
lrwxrwxrwx 1 root root 27 Apr 24 13:37 [servlet].jar -> /usr/share/java/servlet.jar 

]# /usr/sbin/update-alternatives --display javac | grep currently
link currently points to /usr/lib/jvm/java-1.4.2-gcj/bin/javac

# /usr/sbin/update-alternatives --display java | grep currently
link currently points to /usr/java/jdk1.6.0_05/bin/java 

Thanks for the info. Can you also post the output of:

$ ls -lR /usr/lib/jvm-exports
$ rpm -qi `rpm -qf /usr/java/jdk1.6.0_05/bin/java`

I think what we have here is likely a Sun rpm that does not provide any of the
requisite links under /usr/lib/jvm-exports.

Note the links under /var/lib/tomcat5/common/lib that currently point somewhere
other than /usr/share/java:

lrwxrwxrwx 1 root root 38 Apr 24 13:37 [jdbc-stdext].jar ->
/could/not/find/extension/for/this/jvm
lrwxrwxrwx 1 root root 44 Apr 11 14:19 jdbc-stdext.jar ->
/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre/lib/
lrwxrwxrwx 1 root root 38 Apr 24 13:37 [jndi].jar ->
/could/not/find/extension/for/this/jvm

Tom, the one non-broken link is pointing to
/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre/lib (I assume to jdbc-stdext.jar which
is rt.jar---maybe this got cut off in the paste?). This is not the currently set
alternative for java. So am I correct in saying that to properly support
changing JAVA_HOME you would need:

(1) to make sure this same home is set as the java alternative at tomcat5
install-time
(2) that this java alternative must be a JPackage-compatible JDK in order to
provide the correct JVM exports

Again, I think that the missing JVM exports are are always harmless in practice
and that non-missing exports might actually break a situation like this where
JAVA_HOME is not set to the alternative used at build-jar-repository call-time
since I don't think it's possible to refresh that build-jar-repository at runtime.

I suggested customer to uninstall java-1.6.0-sun (if it is, as we suspect,
Sun's) and yum install Red Hat's java-1.6.0-sun pkg from RHN. 

These noted jars and tomcat5 package has been upgraded. This bug is no longer relevant.