KNIME shows R version 3.5.0 although installed 3.6.0

I’ve installed newest R version 3.6.0 (R version 3.6.0 (2019-04-26) – “Planting of a Tree” Copyright © 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?

Thanks for help
Dieter

@dgoebel,

most importantly welcome to the community!

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.

Dear Mark,
thanks for reply.
R preferences: /Library/Frameworks/R.framework/Versions/3.6/Resources

(py37_knime) MacBook-Pro-3:~ dieterg$ /Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
R version 3.6.0 (2019-04-26) – “Planting of a Tree”
Copyright © 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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]”

Thanks for help
Dieter

@dgoebel,

first of all it seems like you don’t have Cairo installed. Could you also start R from the console and send me the output of

library(“Rserve”)
sessionInfo()<a class=“attachment”

Anyways, I’ll PM you an installation script that we use.

1 Like

Hi Mark,
my R 3.6 installation has CAIRO installed, but not the KNIME internal R.
That’s why I asked how to deactivate the KNIME internal R 3.5.0

Output from sessionInfo()

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

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
[6] methods base

other attached packages:
[1] Rserve_1.7-3.1

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0

@dgoebel,

the installed Rserve version is Rserve_1.7-3.1.

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?

remove.packges(“Rserve”)
install.packages (‘Rserve’,‘http://rforge.net/’,type='source’)

Can you check what the result of the install.packages command is, i.e., successful or failed :slight_smile:

1 Like

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’

my Mac OS XCODE is Version 10.2.1 (10E1001)

R is a new installation and not an upgrade

@dgoebel,

did you already try the script I sent you in a private messages?

Sorry, may my question is stupid, but where do I find your “private message”?
Thanks

At the top right you should see a magnifying glass next to three stacked horizontal lines next to a circle with a D :slight_smile: (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.

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