Hi Gandhi, I think the email from Jeff Painter may explain your situation. It's a question of your version of mysql being new. The crucial lines in your trace are:
org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) [INFO] [java] Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @61ca2dfa And this makes it sound like it is expecting a library version where certain classnames or accessibility has changed. Check Jeff's pull requests and see if that fixes your problem. Another quick trick is maven .... -fae (Fail at end) It will go through the rest of the build and only show failures then Peter On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan <gandhiraja...@gmail.com> wrote: > HI Peter, > > Thanks for the insights. I tried to debug from AppMain.java and it > eventually fails in > > "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.<init>(ObjectFactoryBind.java:43)" > > Attaching the complete stacktrace for reference: > > > [INFO] [java] invoking method > [INFO] [java] Exception in thread "main" > java.lang.ExceptionInInitializerError > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>(SingleElementNodeProperty.java:94) > [INFO] [java] at > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native > Method) > [INFO] [java] at > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) > [INFO] [java] at > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > [INFO] [java] at > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) > [INFO] [java] at > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:181) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:326) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:141) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1163) > [INFO] [java] at > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145) > [INFO] [java] at > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:236) > [INFO] [java] at > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > [INFO] [java] at > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) > [INFO] [java] at > > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > [INFO] [java] at > java.base/java.lang.reflect.Method.invoke(Method.java:568) > [INFO] [java] at > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:171) > [INFO] [java] at > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:129) > [INFO] [java] at > javax.xml.bind.ContextFinder.find(ContextFinder.java:307) > [INFO] [java] at > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:478) > [INFO] [java] at > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:435) > [INFO] [java] at > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:336) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.<init>(ObjectFactoryBind.java:43) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getObjectFactoryMapping(ObjectFactoryUtil.java:41) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJAXBElementBySrcXml(ObjectFactoryUtil.java:49) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getConnTypeBySrcXml(ObjectFactoryUtil.java:86) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJdbcTypeBySrcXml(ObjectFactoryUtil.java:64) > [INFO] [java] at > org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:80) > [INFO] [java] at > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > [INFO] [java] Caused by: > java.lang.reflect.InaccessibleObjectException: Unable to make protected > final java.lang.Class > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > java.lang.ClassFormatError accessible: module java.base does not "opens > java.lang" to unnamed module @61ca2dfa > [INFO] [java] at > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) > [INFO] [java] at > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) > [INFO] [java] at > java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199) > [INFO] [java] at > java.base/java.lang.reflect.Method.setAccessible(Method.java:193) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:177) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:172) > [INFO] [java] at > > java.base/java.security.AccessController.doPrivileged(AccessController.java:318) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.java:172) > [INFO] [java] ... 34 more > > On Mon, 29 Apr 2024 at 21:21, Peter Abramowitsch <pabramowit...@gmail.com> > wrote: > > > I think this is the class where Java is exiting with 1 > > /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java > > > > btw my environment is MacOS and I notice yours is Windows, so the root > > cause why this class is giving you trouble is something I wouldn't be > able > > to help you with. But some debug statements rather than asserts would > tell > > you, I think. > > > > Peter > > > > On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch < > > pabramowit...@gmail.com> > > wrote: > > > > > Hi Gandhi > > > This project is an odd one in the sense that when you tell it to skip > the > > > tests, it still goes through the effort in building up the db > environment > > > that the tests would use. But in any case, for me it does build either > > > way. In the attached log, I've run a maven clean before doing the > build > > > without tests. > > > > > > However, check my previous email about your issue. Whereas you'd > > narrowed > > > it down to a script, I found a line in your email which showed the > error > > > within that script's execution: A java program: jdl running as > App.Main > > > threw an assertion on one of the tasks connected with the mysql > database > > it > > > was trying to configure. You could put some debugging statements in > > there > > > to see which one. > > > > > > Peter > > > > > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan <gandhiraja...@gmail.com> > > > wrote: > > > > > >> Thanks for the insights Peter. I dint make it clear that I did ran the > > >> install on ytex module with test case execution toggled off. I used > the > > >> following command - "mvn -e clean install -Dmaven.test.skip=true" and > I > > >> still hit the same error. > > >> > > >> On digging deep, I could find that the build process is trying to > > execute > > >> "<ant antfile="build-setup.xml" dir="scripts" target="test.setup">" in > > >> build-main.xml which in turn is trying to invoke the following target > in > > >> build.setup.xml: > > >> > > >> <target name="test.setup" description="setup properties and database > for > > >> unit tests" > > >> depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > >> <ant dir="data" target="all" inheritAll="true"/> > > >> </target> > > >> > > >> Did you try running this on a fresh setup Peter? > > >> > > >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch < > > pabramowit...@gmail.com > > >> > > > >> wrote: > > >> > > >> > Hi Gandhi > > >> > Your error appears to be at this line > > >> > > > >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > >> Java > > >> > returned: 1 > > >> > > > >> > A test application being run here: AppMain is in charge of loading > a > > >> > temporary mysqldb that is used to test that part of ytex. For me > it > > is > > >> > working, but if you can find a way to run that surefire test in the > > >> > debugger, you can find out why it's failing on one of the > assertions. > > >> > Otherwise you can take this shortcut > > >> > > > >> > mvn <goal> -Dmaven.test.skip=true > > >> > > > >> > To build the project without running any tests. > > >> > > > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan < > gandhiraja...@gmail.com > > > > > >> > wrote: > > >> > > > >> > > Hi Sean, > > >> > > > > >> > > When I tried to build the complete ctakes suite, i get build > failure > > >> for > > >> > > ctakes-ytex module with the following error: > > >> > > > > >> > > [ERROR] Failed to execute goal > > >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > >> > > (generate-test-config) on project ctakes-ytex: An Ant > BuildException > > >> has > > >> > > occured: The following error occurred while executing this line: > > >> > > [ERROR] > > >> > > > > >> > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > > >> > The > > >> > > following error occurred while executing this line: > > >> > > [ERROR] > > >> > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > > >> > The > > >> > > following error occurred while executing this line: > > >> > > [ERROR] > > >> > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > > >> > The > > >> > > following error occurred while executing this line: > > >> > > [ERROR] > > >> > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > >> > Java > > >> > > returned: 1 > > >> > > [ERROR] around Ant part ...<ant antfile="build-setup.xml" > > >> dir="scripts" > > >> > > target="test.setup">... @ 5:70 in > > >> > > > > >> > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > >> > > > > >> > > Is this expected Sean? > > >> > > > > >> > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > >> > > <sean.fi...@childrens.harvard.edu.invalid> wrote: > > >> > > > > >> > > > Hi all, > > >> > > > > > >> > > > There is a candidate for version 5.1.0 of Apache cTAKES source > > code > > >> in > > >> > a > > >> > > > staging repository: > > >> > > > > > >> > > > > > >> > > > > >> > > > >> > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > >> > > > > > >> > > > The code is contained within the file: > > >> > > > ctakes-5.1.0-source-release.zip< > > >> > > > > > >> > > > > >> > > > >> > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > >> > > > > > > >> > > > > > >> > > > I welcome you all to test your favorite pipeline(s) and report > any > > >> > > issues. > > >> > > > I am calling a vote from the PMC to finish by 12:nn Eastern > time, > > >> next > > >> > > > Wednesday May 1. Please report any issues before that time. If > > any > > >> > > > 'road-block' issues are found they will need to be addressed > > before > > >> a > > >> > > > release. > > >> > > > > > >> > > > Thank you, > > >> > > > Sean > > >> > > > > > >> > > > > > >> > > > p.s. > > >> > > > > > >> > > > The 5.1.0 candidate is based upon the source code in the > > >> ctakes-5.1.0 > > >> > > tag: > > >> > > > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > >> > > > > > >> > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > >> > > > https://github.com/apache/ctakes/tree/5.1.0 > > >> > > > > > >> > > > The 5.1.0 branch is a copy of the main branch: > > >> > > > https://github.com/apache/ctakes/tree/main > > >> > > > The version number in the 5.1.0 branch is different, but there > are > > >> no > > >> > > code > > >> > > > differences between the two branches. > > >> > > > > > >> > > > > > >> > > > > > >> > > > > >> > > -- > > >> > > Regards, > > >> > > Gandhi > > >> > > > > >> > > "The best way to find urself is to lose urself in the service of > > >> others > > >> > > !!!" > > >> > > > > >> > > > >> > > >> > > >> -- > > >> Regards, > > >> Gandhi > > >> > > >> "The best way to find urself is to lose urself in the service of > others > > >> !!!" > > >> > > > > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of others > !!!" >
