I’ve installed newest R version 3.6.0 (R version 3.6.0 (2019-04-26) – “Planting of a Tree” Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)) and maintained the path to R Home and the R-Scripting in KNIME 4.0.0 preferences w/o getting errors. Furthermore I’ve installed RSERVE 1.8.6.
Nevertheless KNIME still shows R version 3.5.0:
"WARN R Predictor R Version 3.5.0 and Rserve <= 1.8-6 …
Is the R 3.5.0 the KNIME internal R version?
And if so how can I deactivate it?
Or is there something wrong in my settings?
What’s the entry in Preferences->KNIME->R->Path to R home <path>? What’s the output when you enter
<path>/bin/R --version on your console? What’s the output of a R Snippet node for the command version (just type version and then click eval selection).
If all the commands show 3.6.0, I’d like to ask you if it would be possible to share your workflow with us (using dummy data!)?
Looking forward to hearing from you
Mark
P.S. I understand correctly that your workflow can be executed without errors, but you see this warning message.
Output of R Snippet / Eval Script (R Predictor)
ERROR: Could not execute internal command.ERROR: R evaluation failed.: "sapply(ls(),function(a)class(get(a,envir=globalenv()))[1])"ERROR: R evaluation failed.: "sapply(ls(),function(a)class(get(a,envir=globalenv()))[1])“ERROR: eval failedERROR: Could not execute internal command.ERROR: R evaluation failed.: “library(‘Cairo’);options(device=‘png’,bitmapType=‘cairo’)
png(”/private/var/folders/_x/03t_39j54nv76jl3z64r836r0000gn/T/knime_03_OpenSourceVi11255/rtmp-dialog-11257/rsnippet-plot.png”,width=400.0,height=300.0)“ERROR: R evaluation failed.: “library(‘Cairo’);options(device=‘png’,bitmapType=‘cairo’)
png(”/private/var/folders/_x/03t_39j54nv76jl3z64r836r0000gn/T/knime_03_OpenSourceVi11255/rtmp-dialog-11257/rsnippet-plot.png”,width=400.0,height=300.0)"ERROR: eval failed> #Apply model, obtaining both prediction AND probabilities
knime.out <- cbind(knime.in, predict(knime.model, knime.in), predict(knime.model, knime.in, type=“raw”))
ERROR: Could not capture output of command.ERROR: R evaluation failed.: "knime.stdout.con<-textConnection(‘knime.stdout’,‘w’);knime.stderr.con<-textConnection(‘knime.stderr’,‘w’);sink(knime.stdout.con);sink(knime.stderr.con,type=‘message’)"ERROR: R evaluation failed.: "knime.stdout.con<-textConnection(‘knime.stdout’,‘w’);knime.stderr.con<-textConnection(‘knime.stderr’,‘w’);sink(knime.stdout.con);sink(knime.stderr.con,type=‘message’)"ERROR: voidEval failedERROR: Transferring the R script to R failed.ERROR: R evaluation failed.: "knime.tmp.script"ERROR: assign failedERROR: Could not capture output of command.ERROR: R evaluation failed.: "sink();sink(type=‘message’)
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse=’\n’), paste(knime.stderr,collapse=’\n’))
knime.output.ret"ERROR: R evaluation failed.: "sink();sink(type=‘message’)
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse=’\n’), paste(knime.stderr,collapse=’\n’))
knime.output.ret"ERROR: eval failedERROR: Could not cleanup after command execution.ERROR: R evaluation failed.: "rm(knime.tmp.ret,knime.output.ret,knime.stdout.con,knime.stderr.con,knime.stdout,knime.stderr)"ERROR: R evaluation failed.: "rm(knime.tmp.ret,knime.output.ret,knime.stdout.con,knime.stderr.con,knime.stdout,knime.stderr)"ERROR: voidEval failedERROR: Could not execute internal command.ERROR: R evaluation failed.: "dev.off()"ERROR: R evaluation failed.: "dev.off()"ERROR: eval failedERROR: Could not execute internal command.ERROR: R evaluation failed.: "ls()"ERROR: R evaluation failed.: "ls()"ERROR: eval failed
Workflow is: 03_OpenSourceVizAndModeling
from knime@hub.knime.com / 50_Applications / 28_Predicting_Departure_Delays
No, Workflow has errors in:
R Predictor (see above)
Column Appender: ERROR R Predictor 3:738:733 Execute failed: R evaluation failed.: “knime.out[1:11692,11]”
Could you please remove it. I’ll send you the script now. I hope that fixes your problems. Btw is this a fresh R installation or did you upgrade from a previous R version?
Dear Mark,
I’ve uninstalled Rserve and then entered:
install.packages(“Rserve”, , “http://www.rforge.net/”)
Warning in install.packages :
unable to access index for repository http://www.rforge.net/bin/macosx/el-capitan/contrib/3.6:
cannot open URL ‘http://www.rforge.net/bin/macosx/el-capitan/contrib/3.6/PACKAGES’
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘Rserve’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
.
.
. ld: library not found for -lssl
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [forward] Error 1
make: *** [all] Error 2 ERROR: compilation failed for package ‘Rserve’
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rserve’
Warning in install.packages :
installation of package ‘Rserve’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/_x/03t_39j54nv76jl3z64r836r0000gn/T/RtmpNfTJCT/downloaded_packages’
At the top right you should see a magnifying glass next to three stacked horizontal lines next to a circle with a D (it should also show a notification) . Click on the D and there you should see the message.
Btw. clicking on the D next to your post probably also works.
(it should also show a notification) . Click on the D and there you should see the message.