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openworm / org.geppetto

Geppetto is an open-source platform to build web-based applications to visualize and simulate neuroscience data and models.
http://geppetto.org
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NeuroML Model bundle 1.0.1 fails #638

Closed clausagerskov closed 2 years ago

clausagerskov commented 2 years ago

NeuroML Model bundle 1.0.1 build fails:

[INFO] ---------------------< org.geppetto:model.neuroml >--------------------- [INFO] Building Geppetto NeuroML Model bundle 1.0.1 [1/13] [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] The POM for org.glassfish.jaxb:jaxb-runtime:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [WARNING] The POM for org.glassfish.jaxb:jaxb-xjc:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [WARNING] The POM for com.sun.xml.bind:jaxb-osgi:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details Downloading from org.geppetto-mvn-repo: https://raw.github.com/openworm/org.geppetto.maven/mvn-repo/org/geppetto/core/maven-metadata.xml Downloaded from org.geppetto-mvn-repo: https://raw.github.com/openworm/org.geppetto.maven/mvn-repo/org/geppetto/core/maven-metadata.xml (296 B at 302 B/s) Downloading from org.geppetto-mvn-repo: https://raw.github.com/openworm/org.geppetto.maven/mvn-repo/com/dropbox/core/dropbox-core-sdk/3.0.6-SNAPSHOT/maven-metadata.xml

is the initial warning that could be what leads to this build error:

Test set: org.geppetto.model.neuroml.test.LEMSConversionServiceTest

Tests run: 2, Failures: 0, Errors: 2, Skipped: 0, Time elapsed: 0.668 sec <<< FAILURE! - in org.geppetto.model.neuroml.test.LEMSConversionServiceTest testNeuron(org.geppetto.model.neuroml.test.LEMSConversionServiceTest) Time elapsed: 0.365 sec <<< ERROR! java.lang.ExceptionInInitializerError: null at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199) at java.base/java.lang.reflect.Method.setAccessible(Method.java:193) at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.getMethod(Injector.java:184) at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.access$000(Injector.java:69) at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:168) at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:165) at java.base/java.security.AccessController.doPrivileged(AccessController.java:318) at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.(Injector.java:164) at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:81) at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:179) at com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:285) at com.sun.xml.bind.v2.runtime.reflect.TransducedAccessor$CompositeTransducedAccessorImpl.(TransducedAccessor.java:235) at com.sun.xml.bind.v2.runtime.reflect.TransducedAccessor.get(TransducedAccessor.java:175) at com.sun.xml.bind.v2.runtime.property.AttributeProperty.(AttributeProperty.java:91) at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:108) at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:181) at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:503) at com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:320) at com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:139) at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1138) at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:162) at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:286) 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 org.neuroml.model.util.NeuroMLConverter.(NeuroMLConverter.java:73) at org.geppetto.model.neuroml.utils.OptimizedLEMSReader.readAllFormats(OptimizedLEMSReader.java:75) at org.geppetto.model.neuroml.utils.OptimizedLEMSReader.readAllFormats(OptimizedLEMSReader.java:67) at org.geppetto.model.neuroml.test.LEMSConversionServiceTest.createDomainModel(LEMSConversionServiceTest.java:219) at org.geppetto.model.neuroml.test.LEMSConversionServiceTest.testNeuron(LEMSConversionServiceTest.java:110)

clausagerskov commented 2 years ago

do you expect this build to only work with certain (old) versions of JRE and/or JDK?

clausagerskov commented 2 years ago

seems to not fail at that specific point with jdk8