Several nodes unavailable and uninstallable

[mwiegand]

I’d like to bring attention to this again as I am virtually unable to use Knime right now. I started on the Data Challenge S03E02 but restarting Knime does not resolve the issue anymore as it did before. Though, lots of updates were installed recently.

And apologize in advance but I have found several other any quite old posts so I feel inclined to “force” loop in all Knime Team members who touched the folowing.

July 2020 - Fun fact, I opened the first

Can't install Base Nodes

Good afternoon, Installation of the Base Nodes, String Manipulation, Rule Engine etc, does not work. Nothing happens when clicking on Next. [Bildschirmfoto 2020-07-28 um 18.18.52] Cheers Mike

June 2022

String Manipulation node disappeared - anyone else?

Dear Hive mind I have set up a work flow last week using the string manipulation node (amongst others). Opening the work flow today, the string manipulation node is missing with the following message: Node description for MISSING String Manipulation: " Placeholder node for missing “String Manipulation”. Node “String Manipulation” not available from extension “KNIME Javasnippet” (provided by “KNIME AG, Zurich, Switzerland”; plugin “org.knime.jsnippets” is not installed)" " Javasnippet exte…

Oct. 2022

Create a new Python Based KNIME Extension: Node not available from extension

Hi everyone, KNIME’s 4.6 update introduced the ability to create custom nodes using Python in VSCode, and I recently updated to version 4.6.3. I want to create some custom nodes using Python development, so I followed the KNIME documentation attached: Create a New Python based KNIME Extension Working through Tutorial 1, I completed all prerequisites: conda setup, basic.zip extracted, vscode set up, and KNIME Python Extension Development (Labs) installed. All the required text files config.yml…

April 2023

"column expressions" not available from extension

Hi Team, I am getting this error. While running it via batch file, I am getting this error. Can someone help me out? “column expressions” not available from extension “knime expressions” (provided by “knime ag, zurich, switzerland”; plugin “org.knime.expressions.base” is not installed) Apr 27, 2023 7:44:09 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (398) [org.apache.cxf.transport.http.HT…

@armingrudd // @carstenhaubold // @CarlWitt any idea what I could possibly do to identify the bug? As follows as much information I could gather:

All the following data can eb downloaded via this AWS S3-URL:

1. 240524 Knime - 77549 - Application Snapshot-1716581616820.apps
2. 240524 Knime - 77549 - Configuraation.txt
3. 240524 Knime - 77549 - Enabled Modules.txt
4. 240524 Knime - 77549 - Error Log.txt
5. 240524 Knime - 77549 - Installed Extensions.txt
6. 240524 Knime - 77549 - JVM Arguments.txt
7. 240524 Knime - 77549 - System Properties.txt
8. 240524 Knime - 77549 - Thread Dump.txt

In case it cuts a corner, let me know and we schedule a quick remote sessions. Many thanks in advance for having a look at this.

PS: And now another one raised the same issue:

Errors in Knime

I am getting errors for certain nodes e.g. missing column expressions, CSV readers. Status: Error: Node “Column Expressions” not available from extension “KNIME Expressions” (provided by “KNIME AG, Zurich, Switzerland”; plugin “org.knime.expressions.base” is not installed)

PPS: And another one

[KNIME AP 5.2.3] Missing core nodes on startup

Occasionally I have this pop up when I start KNIME AP, saying 'Errors due to missing node extensions (…) Do you want to search and install the required extensions? [image] I have these nodes installed already, and I haven’t done anything to alter core nodes, so this is unexpected and odd. I cannot reliably reproduce it. What I can say for the most recent time is: I had KNIME AP 5.2.3 open with at least 1 workflow open. My computer did a routine shutdown (unattended). I started my computer (…

PPPS: Albeit less detailed the symptoms are the same. Extension installed but nodes cannot be placed.

Node Missing from Node Repo - Big Query Connector

I’m using Knime 4.7 on my M1 Mac. After installing the Big Query Connector node, it’s not appearing in my node repository or showing up in workflows that I’m installing with that node present. When I check the installed extensions I see the Knime Big Query package installed, but I still can’t see the node in my repo, I can’t drag and drop it into my workspace, and I don’t know how to go about using this node. Has anyone else had the same issue with this node or any other extensions?

Even node developers seem to have experienced that behavior

Node missing

Hi there, We've developed several nodes (but I'm pretty new to the development) and now I have a strange problem and no one could solve it so far: A node is missing in the node repository. The jar-File is in the plugins- directory and there seems to be no problem with it. For other Knime applications the same jar does it's job... (copy / paste) If I export the plugin as directory instead of a jar, the node appears. Is there any explanation for this weird behaviour? Antje

There is even one dating back to 2018 showing the very same behavior

Missing node breaks Node connection.

Hi, Under the condition that KNIME Interactive R Statistics Integration is not installed, node connection between “Table to R” node in Metanode and “R to Table” node is broken. I think that Missing node breaks the connection. Original workflow: [1] Broken workflow: [2] Is this by design?

Since it happens continuously for me I will check if I had enabled the debug log level later on and try to check the Jar file respectively the extension folder for anything suspicious. Maybe the path length limit „issue“ plays a role but then it would be permanently since the beginning and not erratic.

Update
As follows my debug log level details and some more about the plugin directory:

240525 Knime - 77549 - Debug Log Level Error Log.txt (839.2 KB)
240525 Knime - 77549 - PLugin Directory CMD Details.txt (8.9 KB)
240525 Knime - 77549 - Debug Log Level Configuration.txt (854.7 KB)

This might be most impacting issue

!ENTRY org.eclipse.osgi 4 0 2024-05-25 12:32:55.590
!MESSAGE An error occurred while automatically activating bundle org.knime.jsnippets (869).
!STACK 0
org.osgi.framework.BundleException: Exception in org.knime.base.node.jsnippet.JavaSnippetActivator.start() of bundle org.knime.jsnippets.
	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.knime.bigdata.spark.node.StandardSparkNodeFactoryProvider.<init>(StandardSparkNodeFactoryProvider.java:215)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:204)
	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.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:74)
	at org.knime.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:46)
	at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getInstance(SparkNodeFactoryRegistry.java:62)
	at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getNodeIds(SparkNodeFactoryRegistry.java:114)
	at org.knime.bigdata.spark.core.node.SparkNodeSetFactory.getNodeFactoryIds(SparkNodeSetFactory.java:47)
	at org.knime.core.node.extension.NodeSetFactoryExtension.from(NodeSetFactoryExtension.java:296)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
	at java.base/java.util.Spliterators$ArraySpliterator.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.Nodes$CollectorTask.doLeaf(Unknown Source)
	at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Unknown Source)
	at java.base/java.util.stream.AbstractTask.compute(Unknown Source)
	at java.base/java.util.concurrent.CountedCompleter.exec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)
Caused by: java.lang.ExceptionInInitializerError
	at org.knime.knip.base.data.img.ImgPlusCellFactory.getDataType(ImgPlusCellFactory.java:116)
	at org.knime.core.data.DataTypeRegistry.availableDataTypes(DataTypeRegistry.java:227)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.parseAnnotations(DataCellToJavaConverterRegistry.java:481)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<init>(DataCellToJavaConverterRegistry.java:436)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<clinit>(DataCellToJavaConverterRegistry.java:427)
	at org.knime.base.node.jsnippet.JavaSnippet.cacheCustomTypeClasspaths(JavaSnippet.java:1262)
	at org.knime.base.node.jsnippet.JavaSnippetActivator.start(JavaSnippetActivator.java:68)
	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)
	... 43 more
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.lut.DefaultLUTService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:195)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:167)
	at org.scijava.Context.<init>(Context.java:281)
	at org.scijava.Context.<init>(Context.java:237)
	at org.scijava.Context.<init>(Context.java:213)
	at org.knime.knip.core.KNIPGateway.<init>(KNIPGateway.java:145)
	at org.knime.knip.core.KNIPGateway.getInstance(KNIPGateway.java:153)
	at org.knime.knip.core.KNIPGateway.cache(KNIPGateway.java:193)
	at org.knime.knip.base.data.img.ImgPlusCell.<clinit>(ImgPlusCell.java:120)
	... 54 more
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.DefaultDatasetService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 64 more
Caused by: java.lang.IllegalArgumentException: Invalid service: org.scijava.script.DefaultScriptService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 67 more
Caused by: java.lang.IllegalArgumentException: Invalid service: org.scijava.command.DefaultCommandService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 70 more
Caused by: java.util.ConcurrentModificationException
	at java.base/java.util.ArrayList$Itr.checkForComodification(Unknown Source)
	at java.base/java.util.ArrayList$Itr.next(Unknown Source)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:318)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 73 more
Root exception:
java.lang.ExceptionInInitializerError
	at org.knime.knip.base.data.img.ImgPlusCellFactory.getDataType(ImgPlusCellFactory.java:116)
	at org.knime.core.data.DataTypeRegistry.availableDataTypes(DataTypeRegistry.java:227)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.parseAnnotations(DataCellToJavaConverterRegistry.java:481)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<init>(DataCellToJavaConverterRegistry.java:436)
	at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<clinit>(DataCellToJavaConverterRegistry.java:427)
	at org.knime.base.node.jsnippet.JavaSnippet.cacheCustomTypeClasspaths(JavaSnippet.java:1262)
	at org.knime.base.node.jsnippet.JavaSnippetActivator.start(JavaSnippetActivator.java:68)
	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.knime.bigdata.spark.node.StandardSparkNodeFactoryProvider.<init>(StandardSparkNodeFactoryProvider.java:215)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Unknown Source)
	at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:204)
	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.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:74)
	at org.knime.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:46)
	at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getInstance(SparkNodeFactoryRegistry.java:62)
	at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getNodeIds(SparkNodeFactoryRegistry.java:114)
	at org.knime.bigdata.spark.core.node.SparkNodeSetFactory.getNodeFactoryIds(SparkNodeSetFactory.java:47)
	at org.knime.core.node.extension.NodeSetFactoryExtension.from(NodeSetFactoryExtension.java:296)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
	at java.base/java.util.Spliterators$ArraySpliterator.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.Nodes$CollectorTask.doLeaf(Unknown Source)
	at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Unknown Source)
	at java.base/java.util.stream.AbstractTask.compute(Unknown Source)
	at java.base/java.util.concurrent.CountedCompleter.exec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.lut.DefaultLUTService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:195)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:167)
	at org.scijava.Context.<init>(Context.java:281)
	at org.scijava.Context.<init>(Context.java:237)
	at org.scijava.Context.<init>(Context.java:213)
	at org.knime.knip.core.KNIPGateway.<init>(KNIPGateway.java:145)
	at org.knime.knip.core.KNIPGateway.getInstance(KNIPGateway.java:153)
	at org.knime.knip.core.KNIPGateway.cache(KNIPGateway.java:193)
	at org.knime.knip.base.data.img.ImgPlusCell.<clinit>(ImgPlusCell.java:120)
	... 54 more
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.DefaultDatasetService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 64 more
Caused by: java.lang.IllegalArgumentException: Invalid service: org.scijava.script.DefaultScriptService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 67 more
Caused by: java.lang.IllegalArgumentException: Invalid service: org.scijava.command.DefaultCommandService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 70 more
Caused by: java.util.ConcurrentModificationException
	at java.base/java.util.ArrayList$Itr.checkForComodification(Unknown Source)
	at java.base/java.util.ArrayList$Itr.next(Unknown Source)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:318)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	... 73 more

Best
Mike