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Merged
merged 7 commits into from
Oct 8, 2025
Merged

Install and use Knime smoothly #23

merged 7 commits into from
Oct 8, 2025
+211 −527

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guillaume-gricourt
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@guillaume-gricourt guillaume-gricourt commented Oct 6, 2025 •
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Simplify the use of Knime.
Remove arguments:

  • --kexec
  • --kver
  • --kplugins
  • --no-network

Use only:

  • --kinstall

Will search a Knime executable in the kinstall directory.
If no executable found, it will download Knime from Zenodo and install it.
If a knime executable is found, it will be used.

Knime can be installed through the command-line, before the use of Retropath2, with:
python -m retropath2_wrapper.kinme --kinstall <path> -kver {4.6.4,4.7.0}

Dependencies in the conda-recipes, can be removed:

    - nss-cos7-x86_64
    - atk-devel-cos7-x86_64
    - cups-devel-cos7-x86_64
    - xorg-libxcomposite
    - xorg-libxdamage
    - xorg-libxrandr
    - libxkbcommon-devel-cos7-x86_64
    - alsa-lib-devel-cos7-x86_64
    - libxshmfence-devel-cos7-x86_64
    - mesa-libgbm-cos7-x86_64
    - libdrm-cos7-x86_64

@tduigou
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tduigou commented Oct 6, 2025 •
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Some tests with error:

Command line:

python -m retropath2_wrapper test-rp2/sink.csv test-rp2/rules.csv test-rp2/rp2_out --source_name "Xylitol" --source_inchi "InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+" --log debug

First run :

  • raised a Knime / Eclipse popup window containing the following:
Java was started but returned exit code=13
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
-os macosx
-ws cocoa
-arch x86_64
-launcher /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
-name Knime
--launcher.library /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher.cocoa.macosx.x86_64_1.2.100.v20210209-1541/eclipse_11305.so
-startup /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
--launcher.overrideVmargs
-consoleLog
-application org.eclipse.equinox.p2.director
-repository jar:file:/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpri1e03wn/TrustedCommunityContributions_4.6_202212212136.zip!/,jar:file:/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpri1e03wn/org.knime.update.analytics-platform_4.6.4.zip!/
-bundlepool 
-destination /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/knime.py
-i org.knime.features.chem.types.feature.group,org.knime.features.datageneration.feature.group,org.knime.features.python.feature.group,org.rdkit.knime.feature.feature.group,org.eclipse.equinox.preferences
-vm /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/Eclipse/plugins/org.knime.binary.jre.macosx.x86_64_17.0.3.20220429/jre/Contents/Home/lib/libjli.dylib
-vmargs
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
  • however it ends with the good results

Second run with same command line (after removing the result dir test-rp2/rp2_out)

  • It ends without procuding result files, with error:
❯ python -m retropath2_wrapper test-rp2/sink.csv test-rp2/rules.csv test-rp2/rp2_out --source_name "Xylitol" --source_inchi "InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+" --log debug
<frozen runpy>:128: RuntimeWarning: 'retropath2_wrapper.__main__' found in sys.modules after import of package 'retropath2_wrapper', but prior to execution of 'retropath2_wrapper.__main__'; this may result in unpredictable behaviour
Configuration
 + retropath2_wrapper
     |--version: 3.4.2
 + KNIME
     |--path: /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
 + RetroPath2.0 workflow
     |--path: /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf

DEBUG    | 2025-10-06 15:54:49,198.198 __main__ - _cli(): args: Namespace(sink_file='/Users/tduigou/Downloads/test-rp2/sink.csv', rules_file='/Users/tduigou/Downloads/test-rp2/rules.csv', outdir='/Users/tduigou/Downloads/test-rp2/rp2_out', source_file='/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv', source_name='Xylitol', source_inchi='InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+', kinstall='/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper', rp2_version='r20250728', max_steps=3, topx=100, dmin=0, dmax=1000, mwmax_source=1000, msc_timeout=10, std_hydrogen='auto', log='debug', silent=False, quiet=False)
INFO     | 2025-10-06 15:54:49,198.198 RetroPath2 - sniff_rules(): Detect explicit hydrogens in reaction rules
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): sink_file: /Users/tduigou/Downloads/test-rp2/sink.csv
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): source_file: /Users/tduigou/Downloads/test-rp2/rp2_out/source.csv
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): rules_file: /Users/tduigou/Downloads/test-rp2/rules.csv
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): outdir: /Users/tduigou/Downloads/test-rp2/rp2_out
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): std_hydrogen: H added + Aromatized
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): rp2_version: None
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): max_steps: 3
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): topx: 100
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): dmin: 0
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): dmax: 1000
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): mwmax_source: 1000
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): msc_timeout: 10
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): knime: workflow: /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf
kinstall: /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper
kexec: /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
DEBUG    | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): rp2_params: {'max_steps': 3, 'topx': 100, 'dmin': 0, 'dmax': 1000, 'mwmax_source': 1000, 'std_hydrogen': 'H added + Aromatized'}
INFO     | 2025-10-06 15:54:49,199.199 RetroPath2 - check_input(): Checking input data
INFO     | 2025-10-06 15:54:49,199.199 RetroPath2 - check_inchi_from_file():    |- InChI
INFO     | 2025-10-06 15:54:49,199.199 RetroPath2 - check_src_in_sink_1():    |- Source in Sink (simple)
INFO     | 2025-10-06 15:54:49,199.199 RetroPath2 - retropath2(): Initializing
INFO     | 2025-10-06 15:54:49,200.200 RetroPath2 - format_files_for_knime():    |- Formatting files for KNIME
DEBUG    | 2025-10-06 15:54:49,200.200 RetroPath2 - retropath2(): {'sink': '/Users/tduigou/Downloads/test-rp2/sink.csv', 'source': '/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv', 'rules': '/Users/tduigou/Downloads/test-rp2/rules.csv', 'results': 'results.csv', 'src-in-sk': 'source-in-sink.csv', 'outdir': '/Users/tduigou/Downloads/test-rp2/rp2_out'}
INFO     | 2025-10-06 15:54:49,200.200 knime - call(): Running KNIME...Hydrogen: H added + Aromatized
DEBUG    | 2025-10-06 15:54:49,200.200 knime - call(): /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime -nosplash -nosave -reset -consoleLog --launcher.suppressErrors -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf -workflow.variable=input.dmin,"0",int -workflow.variable=input.dmax,"1000",int -workflow.variable=input.max-steps,"3",int -workflow.variable=input.topx,"100",int -workflow.variable=input.mwmax-source,"1000",int -workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String -workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String -workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String -workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String -workflow.variable=output.solutionfile,"results.csv",String -workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String -workflow.variable=input.std_mode,"H added + Aromatized",String -preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpwezam5xf.epfCompileCommand: exclude javax/swing/text/GlyphView.getBreakSpot bool exclude = true
Oct 06, 2025 3:54:51 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-frontend-jaxrs (417) [org.apache.cxf.jaxrs.JAXRSBindingFactory]
Oct 06, 2025 3:54:51 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http (421) [org.apache.cxf.transport.http.HTTPTransportFactory, org.apache.cxf.transport.http.HTTPWSDLExtensionLoader, org.apache.cxf.transport.http.policy.HTTPClientAssertionBuilder, org.apache.cxf.transport.http.policy.HTTPServerAssertionBuilder, org.apache.cxf.transport.http.policy.NoOpPolicyInterceptorProvider]
Oct 06, 2025 3:54:51 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (422) [org.apache.cxf.transport.http.HTTPConduitFactory, org.apache.cxf.transport.ConduitInitiator]
WARN 	 main Node	 No such file: "/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/rules.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/source.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/rules.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/source.csv"
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main WorkflowManager	 Workflow contains nodes with duplicate parameter name (will be made unique by appending node IDs): "single-selection"
WARN 	 main WorkflowManager	 Workflow contains nodes with duplicate parameter name (will be made unique by appending node IDs): "single-selection"
WARN 	 KNIME-Worker-6-Component Input 3:1081:0:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-6-Component Input 3:1081:0:1081 Node	 Errors overwriting node settings with flow variables: Unknown variable "rulesfile_path"
WARN 	 KNIME-Worker-15-Component Input 3:1081:0:938:0:865 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-8-Table Creator 3:1081:0:938:0:853:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-10-Table Creator 3:1081:0:938:0:855:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-17-Table Creator 3:1081:0:938:0:856:911:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-13-Table Creator 3:1081:0:938:0:854:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-2-CSV Reader (deprecated) 3:1081:0:938:0:741:480 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-7-String to Path (Variable) 3:1081:0:940:0:957 Node	 The node configuration changed and the table spec will be recalculated during execution.
WARN 	 KNIME-Worker-6-Table Creator 3:1081:0:938:0:741:795:792 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-6-Table Creator 3:1081:0:938:0:741:795:792 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-13-Table Validator 3:1081:0:938:0:741:767:761 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-8-CSV Reader (deprecated) 3:1081:0:938:0:741:794:481 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-14-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:795:793 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-14-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:795:793 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-0-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:794:793 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-17-Table Validator 3:1081:0:938:0:741:775:761 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-17-Table Validator 3:1081:0:938:0:741:775:761 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-6-Table Validator 3:1081:0:938:0:741:766:731 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-4-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-4-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-4-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-16-Delete Files (legacy) 3:1081:0:1083:0:966 DeleteFilesNodeModel	 File file:/Users/tduigou/Downloads/test-rp2/rp2_out/results.csv could not be deleted
WARN 	 KNIME-Worker-10-CSV Reader 3:1081:0:940:0:956 Node	 Pattern did not match any column name, leaving input unchanged
WARN 	 KNIME-Worker-3-Column Rename (Regex) 3:1081:0:940:0:955 Node	 Pattern did not match any column name, leaving input unchanged
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
Oct 06, 2025 3:55:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 417
Oct 06, 2025 3:55:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 421
Oct 06, 2025 3:55:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 422
Knime:
Java was started but returned exit code=4
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
-os macosx
-ws cocoa
-arch x86_64
-launcher /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
-name Knime
--launcher.library /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher.cocoa.macosx.x86_64_1.2.100.v20210209-1541/eclipse_11305.so
-startup /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
--launcher.overrideVmargs
-nosave
-reset
-consoleLog
-application org.knime.product.KNIME_BATCH_APPLICATION
-workflowFile=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf
-workflow.variable=input.dmin,"0",int
-workflow.variable=input.dmax,"1000",int
-workflow.variable=input.max-steps,"3",int
-workflow.variable=input.topx,"100",int
-workflow.variable=input.mwmax-source,"1000",int
-workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String
-workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String
-workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String
-workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String
-workflow.variable=output.solutionfile,"results.csv",String
-workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String
-workflow.variable=input.std_mode,"H added + Aromatized",String
-preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpwezam5xf.epf
-vm /Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/Eclipse/plugins/org.knime.binary.jre.macosx.x86_64_17.0.3.20220429/jre/Contents/Home/lib/libjli.dylib
-vmargs
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
DEBUG    | 2025-10-06 15:55:49,045.045 knime - call(): CompletedProcess(args=['/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime', '-nosplash', '-nosave', '-reset', '-consoleLog', '--launcher.suppressErrors', '-application', 'org.knime.product.KNIME_BATCH_APPLICATION', '-workflowFile=/Users/tduigou/code/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf', '-workflow.variable=input.dmin,"0",int', '-workflow.variable=input.dmax,"1000",int', '-workflow.variable=input.max-steps,"3",int', '-workflow.variable=input.topx,"100",int', '-workflow.variable=input.mwmax-source,"1000",int', '-workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String', '-workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String', '-workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String', '-workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String', '-workflow.variable=output.solutionfile,"results.csv",String', '-workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String', '-workflow.variable=input.std_mode,"H added + Aromatized",String', '-preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpwezam5xf.epf'], returncode=4)INFO     | 2025-10-06 15:55:49,045.045 knime - call():  OK
DEBUG    | 2025-10-06 15:55:49,045.045 RetroPath2 - check_src_in_sink_2(): src_in_sink_file: /Users/tduigou/Downloads/test-rp2/rp2_out/source-in-sink.csv
INFO     | 2025-10-06 15:55:49,045.045 RetroPath2 - check_src_in_sink_2():    |- Checking Source in Sink (advanced)
ERROR    | 2025-10-06 15:55:49,046.046 RetroPath2 - check_src_in_sink_2(): [Errno 2] No such file or directory: '/Users/tduigou/Downloads/test-rp2/rp2_out/source-in-sink.csv'
INFO     | 2025-10-06 15:55:49,046.046 __main__ - _cli():
ERROR    | 2025-10-06 15:55:49,046.046 __main__ - _cli(): The following error occured: 1
ERROR    | 2025-10-06 15:55:49,046.046 __main__ - _cli(): Exiting...

@tduigou
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tduigou commented Oct 6, 2025

@guillaume-gricourt, here an update:

  • retrying to install with the environment.yaml file provided in the repo: it fails with a "sink-in-source file not found", indicating the KNIME execution did not went well. This issue appears from the first execution (not second time like I mentionned before)
  • when setting the conda env without all "linux / x11 / ..." packages, installation is way more faster... but logs show that extensions are not available during execution.

@guillaume-gricourt
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guillaume-gricourt commented Oct 7, 2025 •
edited
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Ok, one plugin is absent org.rdkit.knime.nodes
Cant you attach the rules.csv file? because, I tested with the new worfklow combined with the old rules

@guillaume-gricourt
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guillaume-gricourt commented Oct 7, 2025 •
edited
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@tduigou Should work now

@tduigou
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tduigou commented Oct 7, 2025

Still the same issue :/

❯ python -m retropath2_wrapper /Users/tduigou/Downloads/test-rp2/sink.csv /Users/tduigou/Downloads/test-rp2/rules.csv /Users/tduigou/Downloads/test-rp2/rp2_out --source_name "Xylitol" --source_inchi "InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+" --log debug
<frozen runpy>:128: RuntimeWarning: 'retropath2_wrapper.__main__' found in sys.modules after import of package 'retropath2_wrapper', but prior to execution of 'retropath2_wrapper.__main__'; this may result in unpredictable behaviour
Configuration
 + retropath2_wrapper
     |--version: 3.4.2
 + KNIME
     |--path:
 + RetroPath2.0 workflow
     |--path: /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf

DEBUG    | 2025-10-07 13:22:31,599.599 __main__ - _cli(): args: Namespace(sink_file='/Users/tduigou/Downloads/test-rp2/sink.csv', rules_file='/Users/tduigou/Downloads/test-rp2/rules.csv', outdir='/Users/tduigou/Downloads/test-rp2/rp2_out', source_file='/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv', source_name='Xylitol', source_inchi='InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+', kinstall='/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper', rp2_version='r20250728', max_steps=3, topx=100, dmin=0, dmax=1000, mwmax_source=1000, msc_timeout=10, std_hydrogen='auto', log='debug', silent=False, quiet=False)
INFO     | 2025-10-07 13:22:31,599.599 RetroPath2 - sniff_rules(): Detect explicit hydrogens in reaction rules
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): sink_file: /Users/tduigou/Downloads/test-rp2/sink.csv
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): source_file: /Users/tduigou/Downloads/test-rp2/rp2_out/source.csv
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): rules_file: /Users/tduigou/Downloads/test-rp2/rules.csv
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): outdir: /Users/tduigou/Downloads/test-rp2/rp2_out
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): std_hydrogen: H added + Aromatized
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): rp2_version: None
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): max_steps: 3
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): topx: 100
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): dmin: 0
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): dmax: 1000
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): mwmax_source: 1000
DEBUG    | 2025-10-07 13:22:31,599.599 RetroPath2 - retropath2(): msc_timeout: 10
/dev/disk6          	GUID_partition_scheme
/dev/disk6s1        	Apple_HFS                      	/private/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpmu4a7dz8/KNIME
DEBUG    | 2025-10-07 13:23:37,283.283 misc - subprocess_call(): CompletedProcess(args=['hdiutil', 'mount', '-noverify', '/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpopax22qr', '-mountpoint', '/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpmu4a7dz8/KNIME'], returncode=0)
"/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpmu4a7dz8/KNIME" unmounted successfully.
DEBUG    | 2025-10-07 13:24:32,959.959 misc - subprocess_call(): CompletedProcess(args=['hdiutil', 'unmount', '/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmpmu4a7dz8/KNIME'], returncode=0)
CompileCommand: exclude javax/swing/text/GlyphView.getBreakSpot bool exclude = true
Oct 07, 2025 1:46:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-frontend-jaxrs (417) [org.apache.cxf.jaxrs.JAXRSBindingFactory]
Oct 07, 2025 1:46:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http (421) [org.apache.cxf.transport.http.HTTPTransportFactory, org.apache.cxf.transport.http.HTTPWSDLExtensionLoader, org.apache.cxf.transport.http.policy.HTTPClientAssertionBuilder, org.apache.cxf.transport.http.policy.HTTPServerAssertionBuilder, org.apache.cxf.transport.http.policy.NoOpPolicyInterceptorProvider]
Oct 07, 2025 1:46:47 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (422) [org.apache.cxf.transport.http.HTTPConduitFactory, org.apache.cxf.transport.ConduitInitiator]
The operation you've requested can not be performed because the folder /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/knime.py is read only.
Oct 07, 2025 1:46:49 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 417
Oct 07, 2025 1:46:49 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 421
Oct 07, 2025 1:46:49 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 422
DEBUG    | 2025-10-07 13:47:04,439.439 knime - install(): CompletedProcess(args=['/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime', '-nosplash', '-consoleLog', '-application', 'org.eclipse.equinox.p2.director', '-repository', 'jar:file:/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmplqxi7pqg/TrustedCommunityContributions_4.6_202212212136.zip!/,jar:file:/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmplqxi7pqg/org.knime.update.analytics-platform_4.6.4.zip!/', '-bundlepool', '', '-destination', '/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/knime.py', '-i', 'org.eclipse.equinox.preferences,org.knime.chem.base,org.knime.datageneration,org.knime.python.nodes,org.knime.features.chem.types.feature.group,org.knime.features.datageneration.feature.group,org.knime.features.python.feature.group,org.rdkit.knime.feature.feature.group,org.rdkit.knime.nodes'], returncode=13)
DEBUG    | 2025-10-07 13:47:04,593.593 RetroPath2 - retropath2(): knime: workflow: /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf
kinstall: /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper
kexec: /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
DEBUG    | 2025-10-07 13:47:04,593.593 RetroPath2 - retropath2(): rp2_params: {'max_steps': 3, 'topx': 100, 'dmin': 0, 'dmax': 1000, 'mwmax_source': 1000, 'std_hydrogen': 'H added + Aromatized'}
INFO     | 2025-10-07 13:47:04,593.593 RetroPath2 - check_input(): Checking input data
INFO     | 2025-10-07 13:47:04,593.593 RetroPath2 - check_inchi_from_file():    |- InChI
INFO     | 2025-10-07 13:47:04,594.594 RetroPath2 - check_src_in_sink_1():    |- Source in Sink (simple)
INFO     | 2025-10-07 13:47:04,597.597 RetroPath2 - retropath2(): Initializing
INFO     | 2025-10-07 13:47:04,597.597 RetroPath2 - format_files_for_knime():    |- Formatting files for KNIME
DEBUG    | 2025-10-07 13:47:04,597.597 RetroPath2 - retropath2(): {'sink': '/Users/tduigou/Downloads/test-rp2/sink.csv', 'source': '/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv', 'rules': '/Users/tduigou/Downloads/test-rp2/rules.csv', 'results': 'results.csv', 'src-in-sk': 'source-in-sink.csv', 'outdir': '/Users/tduigou/Downloads/test-rp2/rp2_out'}
INFO     | 2025-10-07 13:47:04,597.597 knime - call(): Running KNIME...Hydrogen: H added + Aromatized
DEBUG    | 2025-10-07 13:47:04,598.598 knime - call(): /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime -nosplash -nosave -reset -consoleLog --launcher.suppressErrors -application org.knime.product.KNIME_BATCH_APPLICATION -workflowFile=/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf -workflow.variable=input.dmin,"0",int -workflow.variable=input.dmax,"1000",int -workflow.variable=input.max-steps,"3",int -workflow.variable=input.topx,"100",int -workflow.variable=input.mwmax-source,"1000",int -workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String -workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String -workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String -workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String -workflow.variable=output.solutionfile,"results.csv",String -workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String -workflow.variable=input.std_mode,"H added + Aromatized",String -preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmp26wwbrlp.epfCompileCommand: exclude javax/swing/text/GlyphView.getBreakSpot bool exclude = true
Oct 07, 2025 1:47:06 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-frontend-jaxrs (417) [org.apache.cxf.jaxrs.JAXRSBindingFactory]
Oct 07, 2025 1:47:07 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http (421) [org.apache.cxf.transport.http.HTTPTransportFactory, org.apache.cxf.transport.http.HTTPWSDLExtensionLoader, org.apache.cxf.transport.http.policy.HTTPClientAssertionBuilder, org.apache.cxf.transport.http.policy.HTTPServerAssertionBuilder, org.apache.cxf.transport.http.policy.NoOpPolicyInterceptorProvider]
Oct 07, 2025 1:47:07 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (422) [org.apache.cxf.transport.http.HTTPConduitFactory, org.apache.cxf.transport.ConduitInitiator]
WARN 	 main Node	 No such file: "/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/rules.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/source.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/rules.csv"
WARN 	 main Node	 No such file: "/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/source.csv"
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
	at org.knime.core.data.DataType.load(DataType.java:657)
	at org.knime.core.node.config.Config.getDataType(Config.java:643)
	at org.knime.base.node.io.filereader.ColProperty.<init>(ColProperty.java:149)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.readColumnPropsFromConfig(TableCreator2NodeSettings.java:266)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeSettings.loadSettings(TableCreator2NodeSettings.java:199)
	at org.knime.base.node.io.tablecreator.TableCreator2NodeModel.validateSettings(TableCreator2NodeModel.java:220)
	at org.knime.core.node.Node.validateModelSettings(Node.java:692)
	at org.knime.core.node.workflow.FileNativeNodeContainerPersistor.loadNCAndWashModelSettings(FileNativeNodeContainerPersistor.java:211)
	at org.knime.core.node.workflow.FileSingleNodeContainerPersistor.loadNodeContainer(FileSingleNodeContainerPersistor.java:268)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8777)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.SubNodeContainer.performLoadContent(SubNodeContainer.java:1971)
	at org.knime.core.node.workflow.SingleNodeContainer.loadContent(SingleNodeContainer.java:867)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.postLoad(WorkflowManager.java:8793)
	at org.knime.core.node.workflow.WorkflowManager.loadContent(WorkflowManager.java:8679)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8543)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8464)
	at org.knime.core.node.workflow.WorkflowManager.load(WorkflowManager.java:8437)
	at org.knime.core.node.workflow.WorkflowManager.loadProject(WorkflowManager.java:8282)
	at org.knime.core.node.workflow.BatchExecutor.loadWorkflow(BatchExecutor.java:740)
	at org.knime.core.node.workflow.BatchExecutor.runOne(BatchExecutor.java:907)
	at org.knime.core.node.workflow.BatchExecutor.runAll(BatchExecutor.java:889)
	at org.knime.core.node.workflow.BatchExecutor.mainRun(BatchExecutor.java:671)
	at org.knime.product.headless.KNIMEBatchApplication.runBatchExecutor(KNIMEBatchApplication.java:127)
	at org.knime.product.headless.KNIMEBatchApplication.start(KNIMEBatchApplication.java:80)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:203)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:401)
	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:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1461)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main Node	 Node can't be executed - Node "RDKit From Molecule" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 main WorkflowManager	 Workflow contains nodes with duplicate parameter name (will be made unique by appending node IDs): "single-selection"
WARN 	 main WorkflowManager	 Workflow contains nodes with duplicate parameter name (will be made unique by appending node IDs): "single-selection"
WARN 	 KNIME-Worker-8-Component Input 3:1081:0:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-8-Component Input 3:1081:0:1081 Node	 Errors overwriting node settings with flow variables: Unknown variable "rulesfile_path"
WARN 	 KNIME-Worker-6-Component Input 3:1081:0:938:0:865 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-7-Table Creator 3:1081:0:938:0:853:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-10-Table Creator 3:1081:0:938:0:856:911:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-12-Table Creator 3:1081:0:938:0:855:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-13-Table Creator 3:1081:0:938:0:854:910:906 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-0-Table Creator 3:1081:0:938:0:741:795:792 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-9-CSV Reader (deprecated) 3:1081:0:938:0:741:480 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-0-Table Creator 3:1081:0:938:0:741:795:792 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-11-String to Path (Variable) 3:1081:0:940:0:957 Node	 The node configuration changed and the table spec will be recalculated during execution.
WARN 	 KNIME-Worker-6-CSV Reader (deprecated) 3:1081:0:938:0:741:794:481 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-7-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:795:793 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-12-Table Validator 3:1081:0:938:0:741:767:761 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-7-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:795:793 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-9-CASE Switch Data (End) (deprecated) 3:1081:0:938:0:741:794:793 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-8-Table Validator 3:1081:0:938:0:741:775:761 Node	 Node created an empty data table.
WARN 	 KNIME-Worker-8-Table Validator 3:1081:0:938:0:741:775:761 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-6-Table Validator 3:1081:0:938:0:741:766:731 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-16-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-16-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-16-Source, Sink (& Cofactor) 3:1081:0:938 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-0-Delete Files (legacy) 3:1081:0:1083:0:966 DeleteFilesNodeModel	 File file:/Users/tduigou/Downloads/test-rp2/rp2_out/results.csv could not be deleted
WARN 	 KNIME-Worker-10-CSV Reader 3:1081:0:940:0:956 Node	 Pattern did not match any column name, leaving input unchanged
WARN 	 KNIME-Worker-12-Column Rename (Regex) 3:1081:0:940:0:955 Node	 Pattern did not match any column name, leaving input unchanged
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
WARN 	 KNIME-Worker-5-Core 3:1081 Node	 Node can't be executed - Node "RDKit From InChI" not available from extension "RDKit Nodes Feature" (provided by "Novartis"; plugin "org.rdkit.knime.nodes" is not installed)
Oct 07, 2025 1:48:03 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 417
Oct 07, 2025 1:48:03 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 421
Oct 07, 2025 1:48:03 PM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 422
Knime:
Java was started but returned exit code=4
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
-os macosx
-ws cocoa
-arch x86_64
-launcher /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime
-name Knime
--launcher.library /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher.cocoa.macosx.x86_64_1.2.100.v20210209-1541/eclipse_11305.so
-startup /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
--launcher.overrideVmargs
-nosave
-reset
-consoleLog
-application org.knime.product.KNIME_BATCH_APPLICATION
-workflowFile=/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf
-workflow.variable=input.dmin,"0",int
-workflow.variable=input.dmax,"1000",int
-workflow.variable=input.max-steps,"3",int
-workflow.variable=input.topx,"100",int
-workflow.variable=input.mwmax-source,"1000",int
-workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String
-workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String
-workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String
-workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String
-workflow.variable=output.solutionfile,"results.csv",String
-workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String
-workflow.variable=input.std_mode,"H added + Aromatized",String
-preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmp26wwbrlp.epf
-vm /Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/Eclipse/plugins/org.knime.binary.jre.macosx.x86_64_17.0.3.20220429/jre/Contents/Home/lib/libjli.dylib
-vmargs
-server
-Dsun.java2d.d3d=false
-Dosgi.classloader.lock=classname
-XX:+UnlockDiagnosticVMOptions
-XX:+UseG1GC
-Dsun.net.client.defaultReadTimeout=0
-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot
-Dknime.xml.disable_external_entities=true
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.base/java.nio.channels=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
--add-opens=java.base/sun.nio=ALL-UNNAMED
--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
-Xmx2048m
-XstartOnFirstThread
-Xdock:icon=../Resources/knime_mac.icns
-Dorg.eclipse.swt.internal.carbon.smallFonts
-Dchromium.external_message_pump=true
-Darrow.enable_unsafe_memory_access=true
-Darrow.memory.debug.allocator=false
-Darrow.enable_null_check_for_get=false
--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.jgss.spi=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5.internal=ALL-UNNAMED
--add-exports=java.security.jgss/sun.security.krb5=ALL-UNNAMED
-Djava.class.path=/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS//../Eclipse/plugins/org.eclipse.equinox.launcher_1.6.100.v20201223-0822.jar
DEBUG    | 2025-10-07 13:48:04,728.728 knime - call(): CompletedProcess(args=['/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/KNIME_4.6.4.app/Contents/MacOS/knime', '-nosplash', '-nosave', '-reset', '-consoleLog', '--launcher.suppressErrors', '-application', 'org.knime.product.KNIME_BATCH_APPLICATION', '-workflowFile=/Users/tduigou/code/tmp/RetroPath2-wrapper/retropath2_wrapper/workflows/RetroPath2.0_r20250728.knwf', '-workflow.variable=input.dmin,"0",int', '-workflow.variable=input.dmax,"1000",int', '-workflow.variable=input.max-steps,"3",int', '-workflow.variable=input.topx,"100",int', '-workflow.variable=input.mwmax-source,"1000",int', '-workflow.variable=input.sourcefile,"/Users/tduigou/Downloads/test-rp2/rp2_out/source.csv",String', '-workflow.variable=input.sinkfile,"/Users/tduigou/Downloads/test-rp2/sink.csv",String', '-workflow.variable=input.rulesfile,"/Users/tduigou/Downloads/test-rp2/rules.csv",String', '-workflow.variable=output.dir,"/Users/tduigou/Downloads/test-rp2/rp2_out",String', '-workflow.variable=output.solutionfile,"results.csv",String', '-workflow.variable=output.sourceinsinkfile,"source-in-sink.csv",String', '-workflow.variable=input.std_mode,"H added + Aromatized",String', '-preferences=/var/folders/_4/1rd7r9d57nl35yy6w9cc_kb40000gn/T/tmp26wwbrlp.epf'], returncode=4)INFO     | 2025-10-07 13:48:04,728.728 knime - call():  OK
DEBUG    | 2025-10-07 13:48:04,728.728 RetroPath2 - check_src_in_sink_2(): src_in_sink_file: /Users/tduigou/Downloads/test-rp2/rp2_out/source-in-sink.csv
INFO     | 2025-10-07 13:48:04,728.728 RetroPath2 - check_src_in_sink_2():    |- Checking Source in Sink (advanced)
ERROR    | 2025-10-07 13:48:04,728.728 RetroPath2 - check_src_in_sink_2(): [Errno 2] No such file or directory: '/Users/tduigou/Downloads/test-rp2/rp2_out/source-in-sink.csv'
INFO     | 2025-10-07 13:48:04,728.728 __main__ - _cli():
ERROR    | 2025-10-07 13:48:04,729.729 __main__ - _cli(): The following error occured: 1
ERROR    | 2025-10-07 13:48:04,729.729 __main__ - _cli(): Exiting...

@guillaume-gricourt
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@tduigou can you try it ?

@tduigou
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tduigou commented Oct 7, 2025

Now it works 👍

@tduigou tduigou merged commit d6e1616 into master Oct 8, 2025
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@breakthewall breakthewall Awaiting requested review from breakthewall

@tduigou tduigou Awaiting requested review from tduigou

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@guillaume-gricourt @tduigou