R cannot be initialized - MacOS 10.15.5 - KNIME 4.1.3

[oliveralka]

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

[ipazin]

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:

Install R alongside KNIME on Windows and MacOS

Over the last months I have collected a few entries about the installation of R 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 or here). 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

[oliveralka]

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/

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?

[oliveralka]

It seems that KNIME is checking the kMDItemVersion using mdls.

knime/knime-r/blob/3075c8c3018977c85b7b84afda2d691c90e99fb6/org.knime.r/src/org/knime/r/controller/RCairoChecker.java#L123

I downloaded and installed the current XQuartz 2.7.11 from 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.

[Mark_Ortmann]

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

[oliveralka]

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 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.

[oliveralka]

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

[ipazin]

Hi @oliveralka,

glad you figured it out and it’s working now

Br,
Ivan

[Mark_Ortmann]

Awesome that you were able to fix the problem and thanks a lot for sharing your insides with us!

Best
Mark