# R cannot be initialized - MacOS 10.15.5 - KNIME 4.1.3 **URL:** \ **Category:** KNIME Extensions\ **Tags:** scripting\ **Created:** [July 17, 2020, 11:30am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324 "2020-07-17T11:30:57Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![oliveralka](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/o/b4bc9f/32.png) [@oliveralka](https://forum.knime.com/u/oliveralka)\ **Post date:** [July 17, 2020, 11:30am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/1 "2020-07-17T11:30:57Z")
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/](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/](http://www.xquartz.org/). > org.knime.r.controller.IRController$RException: XQuartz is required for the Cairo library on MacOS. Please download and install XQuartz from [http://www.xquartz.org/](http://www.xquartz.org/). > at org.knime.r.controller.RController.checkCairoOnMac(RController.java:406) > at org.knime.r.controller.RController.initR(RController.java:329) > at org.knime.r.controller.RController.initialize(RController.java:195) > at org.knime.r.controller.RController.(RController.java:167) > at org.knime.r.RSnippetNodeModel.executeInternal(RSnippetNodeModel.java:145) > at org.knime.r.RSnippetNodeModel.execute(RSnippetNodeModel.java:136) > at org.knime.core.node.NodeModel.executeModel(NodeModel.java:571) > at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1236) > at org.knime.core.node.Node.execute(Node.java:1016) > at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:557) > at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95) > at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:218) > at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:124) > at org.knime.core.util.ThreadUtils$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 ---
**Author:** ![ipazin](https://forum-cdn.knime.com/user_avatar/forum.knime.com/ipazin/32/806_2.png) [@ipazin](https://forum.knime.com/u/ipazin)\ **Post date:** [July 17, 2020, 11:49am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/2 "2020-07-17T11:49:23Z")
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](https://docs.knime.com/2020-07/r_installation_guide/index.html) And this topic can help as well: > [@Install R alongside KNIME on Windows and MacOS](https://forum.knime.com/t/install-r-alongside-knime-on-windows-and-macos/13287): > > Over the last months I have collected a few entries about the installation of [R](https://www.r-project.org) alongside KNIME that contain some maybe useful hints how to overcome certain obstacles while installing them. I want to bring them together here. (If you are looking for a basic guide about how to install R in the first place you might look [here](https://medium.com/@GalarnykMichael/install-r-and-rstudio-on-windows-5f503f708027) or [here](https://www.dummies.com/programming/r/how-to-install-r/)). A few maybe unnecessary remarks upfront. Yes it takes some effort to get KNIME and R up and running but in the end you will be rewarded with the whole world of pos… Br, Ivan ---
**Author:** ![oliveralka](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/o/b4bc9f/32.png) [@oliveralka](https://forum.knime.com/u/oliveralka)\ **Post date:** [July 17, 2020, 12:05pm UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/3 "2020-07-17T12:05:51Z")
Hi Ivan, I went over the topics already and also did a test with installing the packages via your script: [https://bitbucket.org/KNIME/knime-r/src/master/org.knime.r/scripts/](https://bitbucket.org/KNIME/knime-r/src/master/org.knime.r/scripts/) Unfortunately, that did not solve the issue. Rserve and Cairo seem to work without any issue when called in R directly, but somehow in KNIME XQuartz is not recognized. The path to R.home is set as “/Library/Frameworks/R.framework/Versions/4.0/Resources”, which should be fine. Any ideas on how to narrow down the error? ---
**Author:** ![oliveralka](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/o/b4bc9f/32.png) [@oliveralka](https://forum.knime.com/u/oliveralka)\ **Post date:** [July 20, 2020, 2:25pm UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/4 "2020-07-20T14:25:08Z")
It seems that KNIME is checking the `kMDItemVersion` using `mdls`. > I downloaded and installed the current XQuartz 2.7.11 from [https://www.xquartz.org/](https://www.xquartz.org/), but it seems that no kMDItemVersion is available. ``` user@MBP Utilities % pwd /Applications/Utilities user@MBP Utilities % mdls XQuartz.app kMDItemFSContentChangeDate = 2020-07-17 08:17:51 +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 = "" user@MBP Utilities % mdls -name kMDItemVersion XQuartz.app kMDItemVersion = (null) ``` Which leads to the described issue above. I am actually not sure why this happens, since the right version seem to be annotated in the bundle: > ``` > user@MBP Utilities % plutil -p /Applications/Utilities/XQuartz.app/Contents/Info.plist | grep CFBundleShortVersionString > > "CFBundleShortVersionString" => "2.7.11 > > ``` Edit: Currently I think this is a specific issue on my system, since it works for other macOS 10.15.5 - I will take a look and post an update here. ---
**Author:** ![Mark\_Ortmann](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/m/bc79bd/32.png) [@Mark\_Ortmann](https://forum.knime.com/u/Mark_Ortmann)\ **Post date:** [July 21, 2020, 7:00am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/5 "2020-07-21T07:00:33Z")
Interesting. Have you tried an older version of Xquartz? Maybe you could try to install the same version someone who can use those nodes has installed? I would really much appreciated if you could keep us posted about your findings. Best Mark ---
**Author:** ![oliveralka](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/o/b4bc9f/32.png) [@oliveralka](https://forum.knime.com/u/oliveralka)\ **Post date:** [July 21, 2020, 7:04am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/6 "2020-07-21T07:04:39Z")
I have not found a fix yet - but it does not seem to be an XQuartz or KNIME issue but is related to a faulty Spotlight Index on MacOS. Checking the available metadata stored in the XQuartz app directory give the expected results: > user@MBP ~ % mdimport -t -d 3 /Applications/Utilities/XQuartz.app > Imported ‘/Applications/Utilities/XQuartz.app’ of type ‘com.apple.application-bundle’ with plugIn /System/Library/Spotlight/Application.mdimporter. > 31 attributes returned > { > “:MD:DeviceId” = 16777220; > “:MD:kMDItemPath” = “/Applications/Utilities/XQuartz.app”; > “\_kMDItemContentChangeDate” = “2020-07-17 08:17:51 +0000”; > “\_kMDItemCreationDate” = “2016-09-26 07:41:50 +0000”; > “\_kMDItemCreatorCode” = 0; > “\_kMDItemDisplayNameWithExtensions” = { > “” = “XQuartz.app”; > }; > “\_kMDItemFileName” = “XQuartz.app”; > “\_kMDItemFinderFlags” = 0; > “\_kMDItemFinderLabel” = 0; > “\_kMDItemFromImporter” = 1; > “\_kMDItemIsExtensionHidden” = 1; > “\_kMDItemIsFromImporter” = 1; > “\_kMDItemNodeCount” = 1; > “\_kMDItemOwnerGroupID” = 0; > “\_kMDItemOwnerUserID” = 0; > “\_kMDItemTypeCode” = 0; > “com\_apple\_metadata\_modtime” = “616666671.485049”; > kMDItemAlternateNames = ( > “XQuartz.app” > ); > kMDItemAppStoreCategory = { > “” = Utilities; > ar = “\U0627\U0644\U0623\U062f\U0648\U0627\U062a \U0627\U0644\U0645\U0633\U0627\U0639\U062f\U0629”; > ca = Utilitats; > cs = Utility; > da = “Hj\U00e6lpeprogrammer”; > de = Dienstprogramme; > el = “\U0392\U03bf\U03b7\U03b8\U03ae\U03bc\U03b1\U03c4\U03b1”; > en = Utilities; > “en\_AU” = Utilities; > “en\_GB” = Utilities; > es = Utilidades; > “es\_419” = Utilidades; > fi = “Lis\U00e4ohjelmat”; > fr = Utilitaires; > “fr\_CA” = Utilitaires; > he = “\U05db\U05dc\U05d9 \U05e2\U05d6\U05e8”; > hi = “\U092f\U0942\U091f\U093f\U0932\U093f\U091f\U0940”; > hr = “Uslu\U017eni programi”; > hu = “Seg\U00e9dprogramok”; > id = Utilitas; > it = Utility; > ja = “\U30e6\U30fc\U30c6\U30a3\U30ea\U30c6\U30a3”; > ko = “\Uc720\Ud2f8\Ub9ac\Ud2f0”; > ms = Kemudahan; > nl = “Hulpprogramma’s”; > no = “Verkt\U00f8y”; > pl = “Narz\U0119dzia”; > pt = “Utilit\U00e1rios”; > “pt\_PT” = “Utilit\U00e1rios”; > ro = Utilitare; > ru = “\U0423\U0442\U0438\U043b\U0438\U0442\U044b”; > sk = Utility; > sv = Verktyg; > th = “\U0e22\U0e39\U0e17\U0e34\U0e25\U0e34\U0e15\U0e35\U0e49”; > tr = “\U0130zlenceler”; > uk = “\U0423\U0442\U0438\U043b\U0456\U0442\U0438”; > vi = “Ti\U1ec7n \U00edch”; > “zh\_CN” = “\U5b9e\U7528\U5de5\U5177”; > “zh\_HK” = “\U5de5\U5177\U7a0b\U5f0f”; > “zh\_TW” = “\U5de5\U5177\U7a0b\U5f0f”; > }; > kMDItemAppStoreCategoryType = “public.app-category.utilities”; > kMDItemCFBundleIdentifier = “org.macosforge.xquartz.X11”; > kMDItemContentCreationDate = “2016-09-26 07:41:50 +0000”; > kMDItemContentModificationDate = “2020-07-17 08:17:51 +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 = { > “” = "\U00a9 2003-2016 Apple Inc. \U00a9 2003 XFree86 Project, Inc. \U00a9 2003-2016 [X.org](http://X.org) Foundation, Inc. "; > }; > kMDItemDateAdded = “2020-06-21 08:35:01 +0000”; > kMDItemDisplayName = { > “” = XQuartz; > }; > kMDItemDocumentIdentifier = 0; > kMDItemKind = { > “” = Application; > ar = “\U062a\U0637\U0628\U064a\U0642”; > ca = “Aplicaci\U00f3”; > cs = Aplikace; > da = Program; > de = Programm; > el = “\U0395\U03c6\U03b1\U03c1\U03bc\U03bf\U03b3\U03ae”; > en = Application; > “en\_AU” = Application; > “en\_GB” = Application; > es = “Aplicaci\U00f3n”; > “es\_419” = “Aplicaci\U00f3n”; > fi = Appi; > fr = Application; > “fr\_CA” = Application; > he = “\U05d9\U05d9\U05e9\U05d5\U05dd”; > hi = “\U0910\U092a\U094d\U0932\U093f\U0915\U0947\U0936\U0928”; > hr = Aplikacija; > hu = “Alkalmaz\U00e1s”; > id = Aplikasi; > it = Applicazione; > ja = “\U30a2\U30d7\U30ea\U30b1\U30fc\U30b7\U30e7\U30f3”; > ko = “\Uc751\Uc6a9 \Ud504\Ub85c\Uadf8\Ub7a8”; > ms = Aplikasi; > nl = App; > no = Program; > pl = aplikacja; > pt = Aplicativo; > “pt\_PT” = “Aplica\U00e7\U00e3o”; > ro = “Aplica\U021bie”; > ru = “\U041f\U0440\U043e\U0433\U0440\U0430\U043c\U043c\U0430”; > sk = “Aplik\U00e1cia”; > sv = Program; > th = “\U0e41\U0e2d\U0e1e\U0e1e\U0e25\U0e34\U0e40\U0e04\U0e0a\U0e31\U0e48\U0e19”; > tr = Uygulama; > uk = “\U041f\U0440\U043e\U0433\U0440\U0430\U043c\U0430”; > vi = “\U1ee8ng d\U1ee5ng”; > “zh\_CN” = “\U5e94\U7528\U7a0b\U5e8f”; > “zh\_HK” = “\U61c9\U7528\U7a0b\U5f0f”; > “zh\_TW” = “\U61c9\U7528\U7a0b\U5f0f”; > }; > kMDItemVersion = “2.7.11”; > } but the metadata is not available in mdls, since the index seems to be broken: > mdls -name kMDItemVersion /Applications/Utilities/XQuartz.app > kMDItemVersion = (null) I am currently trying to rebuild the index and see if all the metadata shows up. ---
**Author:** ![oliveralka](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/o/b4bc9f/32.png) [@oliveralka](https://forum.knime.com/u/oliveralka)\ **Post date:** [July 23, 2020, 8:53am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/7 "2020-07-23T08:53:56Z")
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](http://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 ---
**Author:** ![ipazin](https://forum-cdn.knime.com/user_avatar/forum.knime.com/ipazin/32/806_2.png) [@ipazin](https://forum.knime.com/u/ipazin)\ **Post date:** [July 23, 2020, 12:18pm UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/8 "2020-07-23T12:18:34Z")
Hi @oliveralka, glad you figured it out and it’s working now 👍 Br, Ivan ---
**Author:** ![Mark\_Ortmann](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/m/bc79bd/32.png) [@Mark\_Ortmann](https://forum.knime.com/u/Mark_Ortmann)\ **Post date:** [July 26, 2020, 9:44am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/9 "2020-07-26T09:44:51Z")
Awesome that you were able to fix the problem and thanks a lot for sharing your insides with us! Best Mark ---
**Author:** ![system](https://forum-cdn.knime.com/uploads/default/original/1X/ab3ccf34482a0329361734a18199390177204f15.png) [@system](https://forum.knime.com/u/system)\ **Post date:** [August 2, 2020, 9:44am UTC](https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/10 "2020-08-02T09:44:52Z")
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