Which parsers do you using?

Can you please attach the scanned log file?

Which JDK are you using?

Used parsers can be find out attached "screen shot" picture. It mainly check warnings from the output of the console log, which is also attached as an zip file. The doxygen warnings log file semas to be empty, e.g. it's size is zero.

Here is the info of the used Java:
file.encoding UTF-8
file.encoding.pkg sun.io
file.separator /
java.awt.graphicsenv sun.awt.X11GraphicsEnvironment
java.awt.printerjob sun.print.PSPrinterJob
java.class.path /usr/share/hudson/slave.jar
java.class.version 50.0
java.endorsed.dirs /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/endorsed
java.ext.dirs /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/ext:/usr/java/packages/lib/ext
java.home /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre
java.io.tmpdir /tmp
java.library.path /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386/server:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../lib/i386::/opt/axis2c/lib:/usr/java/packages/lib/i386:/lib:/usr/lib
java.runtime.name OpenJDK Runtime Environment
java.runtime.version 1.6.0_0-b16
java.specification.name Java Platform API Specification
java.specification.vendor Sun Microsystems Inc.
java.specification.version 1.6
java.vendor Sun Microsystems Inc.
java.vendor.url http://java.sun.com/
java.vendor.url.bug http://java.sun.com/cgi-bin/bugreport.cgi
java.version 1.6.0_0
java.vm.info mixed mode
java.vm.name OpenJDK Server VM
java.vm.specification.name Java Virtual Machine Specification
java.vm.specification.vendor Sun Microsystems Inc.
java.vm.specification.version 1.0
java.vm.vendor Sun Microsystems Inc.
java.vm.version 14.0-b16
jna.platform.library.path /usr/lib:/lib
line.separator
os.arch i386
os.name Linux
os.version 2.6.18-194.3.1.el5
path.separator :
sun.arch.data.model 32
sun.boot.class.path /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/resources.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/rt.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/jsse.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/jce.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/charsets.jar:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/classes
sun.boot.library.path /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386
sun.cpu.endian little
sun.cpu.isalist
sun.io.unicode.encoding UnicodeLittle
sun.java.launcher SUN_STANDARD
sun.jnu.encoding UTF-8
sun.management.compiler HotSpot Tiered Compilers
sun.os.patch.level unknown
svnkit.ssh2.persistent false
user.country US
user.dir /root
user.home /root
user.language en
user.name root
user.timezone Europe/Helsinki
user.zoneinfo.dir /usr/share/javazi

This seems to be a JDK bug, see reference URL. The problematic parser is the Doxygen Parser. Until this is fixed you need to remove that parser.

Integrated in Hudson Plug-ins (Compile) #38
JENKINS-7178 Added test case that exposes JDK bug.

When I use same Warnings parser for a Doxygen log file, that has content it doesn't crash at all. But in my case the content of the Doxygen log file is empty (zero bytes)?

The problem is not the doxygen file. It's the console log. This logfile lets the doxygen parser fail.

Can someone please check if Jenkins running on JDK 7 solves this problem?

FreeBSD 9.1, OpenJDK 7. Same thing - getting java.lang.stackoverflow when trying to process Doxygen logs.

Ok, thanks for checking. I think the doxygen parser needs to be re-written in order to avoid that JDK bug.

This issue seems to be related to the size of the log (see also this comment in the linked ticket).
So there is a simple workaround: capture the stderr output of Doxygen in a file (or use the WARN_LOGFILE parameter in the Doxyfile) and let the warnings plugin run on that file.

It would make sense to re-implement the parser.