I've never seen this show up as a build problem; it's (typically) a Tomcat warning that appears at webapp startup time. It's not a real problem or error... we don't actually recommend using APR, so every deployment logs this warning. The webapp should run just fine, despite the warning.

If LabKey Server is not responding to requests after startup then likely something else is going on. We'll need to see a full log to help further.

Adam

D:\jdk1.7.0_02\bin\java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:1616,suspend=y,server=n -Djava.endorsed.dirs=D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37/common/endorsed -Dcatalina.base=D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37/ -Dcatalina.home=D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37/ -Djava.io.tmpdir=D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37/temp -Ddevmode=true -ea -Dsun.io.useCanonCaches=false -Xmx768M -XX:MaxPermSize=1024M -classpath "D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37/bin/bootstrap.jar;C:\Users\Jalal\AppData\Roaming\JetBrains\IntelliJ IDEA Community Edition 12.1.3/lib/idea_rt.jar" -Dlabkey.externalModulesDir=D:\temp -javaagent:C:\Users\Jalal\.IdeaIC12\system\groovyHotSwap\gragent.jar -Dfile.encoding=UTF-8 org.apache.catalina.startup.Bootstrap start
Connected to the target VM, address: '127.0.0.1:1616', transport: 'socket'
Jul 31, 2013 12:06:22 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: D:\jdk1.7.0_02\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Users\Jalal\AppData\Roaming\JetBrains\IntelliJ IDEA Community Edition 12.1.3\bin\..\.\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Toshiba\Bluetooth Toshiba Stack\sys\;C:\Program Files (x86)\Toshiba\Bluetooth Toshiba Stack\sys\x64\;C:\Apache Ant\apache-ant-1.8.4\bin;D:\jdk1.7.0_02\bin;D:\apache-tomcat-6.0.37-windows-x64\apache-tomcat-6.0.37;D:\jdk1.7.0_02;D:\LabKey\external\ant\bin;D:\LabKey\external\bin;c:\users\jalal\appdata\roaming\jetbrains\intellij idea community edition 12.1.3\jre\jre\bin;.
Jul 31, 2013 12:06:23 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Jul 31, 2013 12:06:23 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 2104 ms
Jul 31, 2013 12:06:23 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Jul 31, 2013 12:06:23 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.37
Jul 31, 2013 12:06:23 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor labkey.xml
Jul 31, 2013 12:06:24 PM org.apache.catalina.loader.WebappLoader start
SEVERE: LifecycleException
java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:186)
    at org.apache.catalina.loader.WebappLoader.createClassLoader(WebappLoader.java:803)
    at org.apache.catalina.loader.WebappLoader.start(WebappLoader.java:661)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4575)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675)
    at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

Jul 31, 2013 12:06:24 PM org.apache.catalina.core.ContainerBase addChildInternal
SEVERE: ContainerBase.addChild: start:
LifecycleException: start: : java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader
    at org.apache.catalina.loader.WebappLoader.start(WebappLoader.java:709)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4575)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675)
    at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

Jul 31, 2013 12:06:24 PM org.apache.catalina.startup.HostConfig deployDescriptor
SEVERE: Error deploying configuration descriptor labkey.xml
java.lang.IllegalStateException: ContainerBase.addChild: start: LifecycleException: start: : java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:803)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
    at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675)
    at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

Jul 31, 2013 12:06:24 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory docs
Jul 31, 2013 12:06:24 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory examples
Jul 31, 2013 12:06:25 PM org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
Jul 31, 2013 12:06:25 PM org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
Jul 31, 2013 12:06:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory host-manager
Jul 31, 2013 12:06:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory manager
Jul 31, 2013 12:06:25 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory ROOT
Jul 31, 2013 12:06:26 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Jul 31, 2013 12:06:26 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Jul 31, 2013 12:06:26 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/87 config=null
Jul 31, 2013 12:06:26 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 2811 ms

Hello,

The error message "java.lang.ClassNotFoundException: org.labkey.bootstrap.LabkeyServerBootstrapClassLoader" indicates that the server isn't finding labkeyBootstrap.jar correctly. A successful Ant build should drop that file into TOMCAT_HOME/lib, which on your system is D:\apache-tomcat-6.0.37-windows-x64\lib. It is possible that the CATALINA_HOME environment variable is pointing at a different Tomcat installation?

Thanks,
Josh