java.security.PrivilegedActionException: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass

[bdklahn]

I'm trying to find some program which will convert all the ACSN2 SBGN-ML map files to GraphML, for ultimate loading into NetworkX.
With structured, standards-compliant, MLs, it should be pretty simple . . .
Nope.

java -jar ~/.m2/repository/fr/eisbm/ySBGN/1.0/ySBGN-1.0.jar 

** (java:21946): WARNING **: 18:00:01.109: AT-SPI: Could not obtain desktop path or name


** (java:21946): WARNING **: 18:00:01.639: atk-bridge: get_device_events_reply: unknown signature

** (java:21946): WARNING **: 18:00:01.639: atk-bridge: get_device_events_reply: unknown signature

** (java:21946): WARNING **: 18:00:01.639: atk-bridge: GetRegisteredEvents returned message with unknown signature

** (java:21946): WARNING **: 18:00:01.665: AT-SPI: Could not obtain desktop path or name


** (java:21946): WARNING **: 18:00:01.732: AT-SPI: Could not obtain desktop path or name



** (java:21946): WARNING **: 18:00:01.732: AT-SPI: Could not obtain desktop path or name

Convert button clicked, launch script
Apr 12, 2022 6:01:02 PM com.sun.xml.bind.v2.runtime.reflect.opt.Injector <clinit>
SEVERE: null
java.security.PrivilegedActionException: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass(java.lang.String,[B,int,int,java.lang.ClassLoader,java.security.ProtectionDomain)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:573)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.java:197)
        at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:81)
        at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:179)
        at com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:285)
        at com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>(SingleElementNodeProperty.java:94)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
        at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128)
        at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:181)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:514)
        at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:168)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:514)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:331)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:139)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1156)
        at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:165)
        at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:289)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:186)
        at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:146)
        at javax.xml.bind.ContextFinder.find(ContextFinder.java:350)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:446)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:409)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:313)
        at fr.eisbm.GRAPHML2SBGNML.Utils.readFromFile(Utils.java:37)
        at fr.eisbm.GRAPHML2SBGNML.SBGNML2GraphML.parseSBGNFile(SBGNML2GraphML.java:34)
        at fr.eisbm.GRAPHML2SBGNML.SBGNML2GraphML.convert(SBGNML2GraphML.java:23)
        at fr.eisbm.GRAPHML2SBGNML.App$2.call(App.java:204)
        at fr.eisbm.GRAPHML2SBGNML.App$2.call(App.java:196)
        at javafx.concurrent.Task$TaskCallable.call(Task.java:1425)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass(java.lang.String,[B,int,int,java.lang.ClassLoader,java.security.ProtectionDomain)
        at java.base/java.lang.Class.getMethod(Class.java:2227)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$3.run(Injector.java:201)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$3.run(Injector.java:197)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
        ... 38 more

> java --version
openjdk 17.0.2 2022-01-18
OpenJDK Runtime Environment (build 17.0.2+8-suse-4.1-x8664)
OpenJDK 64-Bit Server VM (build 17.0.2+8-suse-4.1-x8664, mixed mode)

It also fails with openjdk 11, etc., etc.

I'm running on OpenSUSE Tumbleweed, with openjfx 11.0.14-2.1 installed.

The jar in the repo wouldn't work, so I built with maven.
That createsySBGN-1.0.jar, despite the master branch I'm working on being 4 commits newer than . . .
commit 1c46b27 (tag: 1.1.2)

(maybe the pom hasn't been fully updated with a newer version number, or the tags aren't meant to match the jar version?)

It wouldn't build (or run??? . . . I can't recall . . . so many issues whenever I try to get any Java program to work right), with out this:

diff --git a/pom.xml b/pom.xml
index 5f7d553..c7e4ee8 100755
--- a/pom.xml
+++ b/pom.xml
@@ -116,6 +116,18 @@
             <mainClass>HelloFX</mainClass>
         </configuration>
     </plugin>
+            <plugin>
+                <groupId>org.jvnet.jaxb2.maven2</groupId>
+                <artifactId>maven-jaxb2-plugin</artifactId>
+                <version>0.14.0</version>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.glassfish.jaxb</groupId>
+                        <artifactId>jaxb-runtime</artifactId>
+                        <version>2.3.1</version>
+                   </dependency>
+               </dependencies>
+            </plugin>
        </plugins>
   </build>
   <version>1.0</version>

(which I found on the internet, as a fix for the error I was getting before)

Any idea how to get this to work? I've even gone so far as to try a Docker image with an old Java 8 in it. Of course I got the usual "DISPLAY not found", because it is an X11 application. I haven't gone so far as to fire up, say, and old Ubuntu VM with older stuff in it.

Does this really need to be a GUI application? It could easily be a CLI, with one; maybe two CL arguments.