Good morning. I installed knime 5.0.
as soon as I open the software the “error log” tab shows me a very long series of errors, which I show in the attached image
Uploading: image.png…
Uploading: Capture.PNG… / /
Looks like your screenshots didn’t upload. Can you try again? Also, actual log file itself (or an excerpt of it) is probably better than a screenshot if you still have that.
Could you help by providing a bit more detail about your experience, so we can narrow down what’s going on? That log file is pretty large 
Is KNIME failing to start, or running OK despite errors, or…? Are there errors that are easily reproducible?
for example:
eclipse.buildId=unknown
java.version=17.0.5
java.vendor=Eclipse Adoptium
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=en_US
Command-line arguments: -os win32 -ws win32 -arch x86_64 -data file:/C:/Users/19037080/knime-workspace/
org.eclipse.osgi
Error
Tue Mar 07 12:21:20 CET 2023
An error occurred while automatically activating bundle com.vernalis.knime.chem.mmp (88).
org.osgi.framework.BundleException: Exception in com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start() of bundle com.vernalis.knime.chem.mmp.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:839)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:767)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1032)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:371)
at org.eclipse.osgi.container.Module.doStart(Module.java:605)
at org.eclipse.osgi.container.Module.start(Module.java:468)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:513)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:570)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:335)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:397)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass0(BundleLoader.java:500)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:416)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:168)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:622)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:196)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:920)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:246)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:63)
at org.knime.core.node.extension.NodeFactoryExtension.createFactory(NodeFactoryExtension.java:184)
at org.knime.core.node.extension.NodeFactoryExtension.getFactory(NodeFactoryExtension.java:169)
at org.knime.core.node.extension.NodeFactoryExtension.isDeprecated(NodeFactoryExtension.java:126)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.base/java.util.Iterator.forEachRemaining(Unknown Source)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.count(Unknown Source)
at org.knime.core.node.extension.NodeFactoryExtensionManager.getInstance(NodeFactoryExtensionManager.java:126)
at org.knime.workbench.repository.RepositoryManager.readNodes(RepositoryManager.java:390)
at org.knime.workbench.repository.RepositoryManager.readRepository(RepositoryManager.java:176)
at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:559)
at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:572)
at org.knime.workbench.workflowcoach.ui.WorkflowCoachView$3.run(WorkflowCoachView.java:313)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Caused by: java.lang.UnsatisfiedLinkError: ‘long org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(java.lang.String)’
at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(Native Method)
at org.RDKit.RWMol.MolFromSmarts(RWMol.java:453)
at com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start(MatchedPairsMultipleCutsNodePlugin.java:91)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:818)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:810)
… 39 more
Root exception:
java.lang.UnsatisfiedLinkError: ‘long org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(java.lang.String)’
at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(Native Method)
at org.RDKit.RWMol.MolFromSmarts(RWMol.java:453)
at com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start(MatchedPairsMultipleCutsNodePlugin.java:91)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:818)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:810)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:767)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1032)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:371)
at org.eclipse.osgi.container.Module.doStart(Module.java:605)
at org.eclipse.osgi.container.Module.start(Module.java:468)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:513)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:570)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:335)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:397)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass0(BundleLoader.java:500)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:416)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:168)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:622)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:196)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:920)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:246)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:63)
at org.knime.core.node.extension.NodeFactoryExtension.createFactory(NodeFactoryExtension.java:184)
at org.knime.core.node.extension.NodeFactoryExtension.getFactory(NodeFactoryExtension.java:169)
at org.knime.core.node.extension.NodeFactoryExtension.isDeprecated(NodeFactoryExtension.java:126)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.base/java.util.Iterator.forEachRemaining(Unknown Source)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.count(Unknown Source)
at org.knime.core.node.extension.NodeFactoryExtensionManager.getInstance(NodeFactoryExtensionManager.java:126)
at org.knime.workbench.repository.RepositoryManager.readNodes(RepositoryManager.java:390)
at org.knime.workbench.repository.RepositoryManager.readRepository(RepositoryManager.java:176)
at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:559)
at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:572)
at org.knime.workbench.workflowcoach.ui.WorkflowCoachView$3.run(WorkflowCoachView.java:313)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Seems like something with the Vernalis extension and one of their nodes - but can you please describe what is actually happening? Is KNIME failing to start, or crashing, or something specific to the Vernalis nodes, or…?
Can you also try uploading your screenshots again please?
for example I can’t install some nodes like “EMPTY COLLECTION TO MISSING”, but also others from other collections.
most of the errors in the log refer to:
- org.eclipse.osgi.container
- org.eclipse.osgi.internal.framework
- org.eclipse.osgi.framework
- org.eclipse.pde.ui
- java.base/java.lang
- org.eclipse.ui.PlatformUI
and other…
In your case I would first try editing your knime.ini file to include the -clean parameter, and then restarting (don’t leave the -clean parameter in the .ini permanently, it increases startup time).
If that doesn’t help, perhaps something happened during installation of a particular extension. KNIME Version 5 is still a preview release. and doesn’t fully support all extensions yet. Maybe uninstall the Vernalis extension to see if that changes things?
hi, thanks for your patience.
yesterday via KNIME.INI I removed some errors.
Now it seems to me that this is left:
java.lang.ClassNotFoundException: org.knime.product.rcp.addons.ToolbarFixAddon cannot be found by org.knime.product_5.0.0.v202302221006
at org.eclipse.osgi.internal.loader.BundleLoader.generateException(BundleLoader.java:541)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass0(BundleLoader.java:536)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:416)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:168)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:622)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.createFromBundle(ReflectionContributionFactory.java:89)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.doCreate(ReflectionContributionFactory.java:60)
at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.create(ReflectionContributionFactory.java:37)
at org.eclipse.e4.ui.internal.workbench.swt.E4Application.createE4Workbench(E4Application.java:276)
at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:573)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:338)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:551)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:156)
at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:189)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:136)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:402)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:255)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:659)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:596)
at org.eclipse.equinox.launcher.Main.run(Main.java:1467)
This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.