Hello Everyone, I am currently not able to run R Snippets with the following error and I am not sure how to solve it. Please let me know if you have any suggestions/ideas how to resolve the issue. R cannot be initialized. XQuartz is required for the Cairo library on MacOS. Please download and install XQuartz from http://www.xquartz.org/ . KNIME log: 2020-07-17 13:00:24,094 : ERROR : KNIME-Worker-4-R Source (Workspace) 0:248 : : Node : R Source (Workspace) : 0:248 : Execute failed: XQuartz is required for the Cairo library on MacOS. Please download and install XQuartz from http://www.xquartz.org/ . org.knime.r.controller.IRController$RException: XQuartz is required for the Cairo library on MacOS. Please download and install XQuartz from http://www.xquartz.org/ . at org.knime.r.controller.RController.checkCairoOnMac(RController.java:406) at org.knime.r.controller.RController.initR(RController.java:329) at org.knime.r.controller.RController.initialize(RController.java:195) at org.knime.r.controller.RController.(RController.java:167) at org.knime.r.RSnippetNodeModel.executeInternal(RSnippetNodeModel.java:145) at org.knime.r.RSnippetNodeModel.execute(RSnippetNodeModel.java:136) at org.knime.core.node.NodeModel.executeModel(NodeModel.java:571) at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1236) at org.knime.core.node.Node.execute(Node.java:1016) at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:557) at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95) at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:218) at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:124) at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:334) at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:210) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123) at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246) R scripting extension is installed: KNIME R Scripting extension 4.0.0.v201906200740 de.mpicbg.tds.knime.scripting.r.feature.feature.group Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany I tested with R 3.6.1 and later upgraded to R 4.0.2: Path: /Library/Frameworks/R.framework/Resources or Path: /Library/Frameworks/R.framework/Versions/4.0/Resources Rserve and Cairo are installed: library(Rserve) library(Cairo) sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Cairo_1.5-13 Rserve_1.8-7 loaded via a namespace (and not attached): [1] compiler_4.0.2 tools_4.0.2 XQuartz is installed: XQuartz 2.7.11 (xorg-server 1.18.4) /opt/X11/bin/xquartz MacOS 10.15.5 KNIME 4.1.3

Rebuilding the Spotlight index for the whole drive did not fix the issue. Since it seems that the indexing in the “/Applications” directory was still disabled. Careful with “sudo mdutil -E”. It will cause each local store for the volumes indicated to be erased. The stores will be rebuilt if appropriate. To check the indexing status “sudo mdutil -s” can be used instead. user@MBP /Applications % sudo mdutil -E /Applications /System/Volumes/Data/Applications: 2020-07-23 10:40:51.171 mdutil[41004:1597023] mdutil disabling Spotlight: /System/Volumes/Data/Applications → kMDConfigSearchLevelFSSearchOnly Indexing disabled. Switching on indexing: user@MBP /Applications % sudo mdutil -i on /Applications /System/Volumes/Data/Applications: Indexing enabled. Now “mdls” reports the all metadata entries and the KNIME is able to confirm the R installation and runs without any issues. user@MBP Utilities % mdls XQuartz.app _kMDItemDisplayNameWithExtensions = “XQuartz.app” kMDItemAlternateNames = ( “XQuartz.app” ) kMDItemAppStoreCategory = “Utilities” kMDItemAppStoreCategoryType = “public.app-category.utilities” kMDItemCFBundleIdentifier = “org.macosforge.xquartz.X11” kMDItemContentCreationDate = 2016-09-26 07:41:50 +0000 kMDItemContentCreationDate_Ranking = 2016-09-26 00:00:00 +0000 kMDItemContentModificationDate = 2020-07-23 08:23:54 +0000 kMDItemContentModificationDate_Ranking = 2020-07-23 00:00:00 +0000 kMDItemContentType = “com.apple.application-bundle” kMDItemContentTypeTree = ( “com.apple.application-bundle”, “com.apple.application”, “public.executable”, “com.apple.localizable-name-bundle”, “com.apple.bundle”, “public.directory”, “public.item”, “com.apple.package” ) kMDItemCopyright = "© 2003-2016 Apple Inc. © 2003 XFree86 Project, Inc. © 2003-2016 X.org Foundation, Inc. " kMDItemDateAdded = 2020-06-21 08:35:01 +0000 kMDItemDateAdded_Ranking = 2020-06-21 00:00:00 +0000 kMDItemDisplayName = “XQuartz.app” kMDItemDocumentIdentifier = 0 kMDItemFSContentChangeDate = 2020-07-23 08:23:54 +0000 kMDItemFSCreationDate = 2016-09-26 07:41:50 +0000 kMDItemFSCreatorCode = “” kMDItemFSFinderFlags = 0 kMDItemFSHasCustomIcon = 0 kMDItemFSInvisible = 0 kMDItemFSIsExtensionHidden = 0 kMDItemFSIsStationery = 0 kMDItemFSLabel = 0 kMDItemFSName = “XQuartz.app” kMDItemFSNodeCount = 1 kMDItemFSOwnerGroupID = 0 kMDItemFSOwnerUserID = 0 kMDItemFSSize = 1 kMDItemFSTypeCode = “” kMDItemInterestingDate_Ranking = 2020-07-23 00:00:00 +0000 kMDItemKind = “Application” kMDItemLogicalSize = 7949322 kMDItemPhysicalSize = 8499200 kMDItemVersion = “2.7.11” I hope that this helps other people in the future! Cheers Oliver

R cannot be initialized - MacOS 10.15.5 - KNIME 4.1.3

KNIME Extensions

ipazin July 17, 2020, 11:49am 2

Hi there @oliveralka,

welcome to KNIME Community!

Have you checked this R Installation guide?
https://docs.knime.com/2020-07/r_installation_guide/index.html

And this topic can help as well:

Br,
Ivan

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