That is just a warning and can be ignored. If the last message is "Ant build completed..." you should be fine.

Note that an IntelliJ ant integration bug causes the last line to report the wrong number of errors and warnings… in particular, it reports "one error" when no error actually occured. Again, this can be ignored.

I tried running the build target in IntelliJ and I get 1 warning without any errors as the Ant build is completed. However, when I try to run the project, I get this error.. Any help would be much appreciated.

C:jdk1.5.0_06binjava -ea -Xmx768M -Dsun.io.useCanonCaches=false -Djava.endorsed.dirs=C:apache-tomcat-5.5.17/common/endorsed -classpath C:jdk1.5.0_06/lib/tools.jar:C:apache-tomcat-5.5.17/bin/bootstrap.jar -Dcatalina.base=C:apache-tomcat-5.5.17 -Dcatalina.home=C:apache-tomcat-5.5.17 -Djava.io.tmpdir=C:apache-tomcat-5.5.17/temp -Dgroovy.cache=false -Dgroovy.root=C:C:CPAS1.4-4355-src/modules -Ddevmode=true -Didea.launcher.port=7534 "-Didea.launcher.bin.path=C:Program FilesJetBrainsIntelliJ IDEA 5.1bin" -Dfile.encoding=windows-1252 com.intellij.rt.execution.application.AppMain org.apache.catalina.startup.Bootstrap Start java.lang.NoClassDefFoundError: com/intellij/rt/execution/application/AppMain Exception in thread "main" Process finished with exit code 1

I just had this error. Josh at labkey sent me this info and it worked (since the West coast might not be awake for a while I'll forward it to you):

You'll need to add another JAR to your -classpath argument. On my machine it's C:/Program Files/JetBrains/IntelliJ IDEA 5.1/lib/idea_rt.jar.

Also, if you are on Windows you need to change the ":"s separator in the class path string to ";"s.

Bill

Which modules' classpath arguments in IntelliJ do I add this JAR to?

It should be added to the -classpath argument in your Debug Configuration. It doesn't need to be added to any module's classpath, which are not included in the debug profile.

I've managed to get things started but I've encountered another error.

Some other service is already using port 8080. Is the CPAS instance of Tomcat running already? Do you have another web server (IIS, Apache, another instance of Tomcat) installed and running on 8080? You'll need to shut down this service before IntelliJ can start the CPAS instance of Tomcat on this port. Either that, or change the port assigned to Tomcat in server.xml; see https://cpas.fhcrc.org/Wiki/home/help/1.5/page.view?name=configTo

Thanks for the help so far! =)