R cannot be initialized - MacOS 10.15.6 R 4.0.4 KNIME 4.3.2

Hi,
After following the R installation guide and trying everything I could find suggested here, I still cannot get R to initialize from KNIME on a new Mac.

MacOS 10.15.6
R 4.0.4
KNIME 4.3.2

KNIME R Scripting extension is installed: |4.0.0.v202009100739|de.mpicbg.tds.knime.scripting.r.feature.feature.group|Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany|

clang and GNU Fortran are freshly installed.

xQuartz: XQuartz 2.8.0_rc4 (xorg-server 1.19.7)

Rserve and Cairo are installed

sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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] Rserve_1.8-7 Cairo_1.5-12.2

loaded via a namespace (and not attached):
[1] compiler_4.0.4 tools_4.0.4

Rserve is running, Applications indexing is enabled (per a suggestion from a related query)

The path to R is correctly specified in the KNIME preferences, but the “R scripting” menu I expect from successful R-KNIME integrations on other Macs (different OS and KNIME versions) is missing here. Is this diagnostic?

Any ideas for what I am missing/doing wrong?

@kkhanson welcome to the KNIME forum.

You do not have the latest installation guide

https://docs.knime.com/latest/r_installation_guide/index.html

And it seems you have the community extension I would recommend using the official one.

Then you should check out my collection about installing R with KNIME

And you can check your versions especially of RServe which has to be at least 1.8.6

2 Likes

Thanks for the suggestions!

I do have both community and official R extensions installed — the community one works just fine as in past versions (of MacOS, R, KNIME), the official ones are the issue.

Uninstalling/reinstalling the Cairo and Rserve packages via Terminal rather than R Studio did not solve anything for me (all installed without errors), nor did stepping my version of Rserve back from 1.8-7 to 1.8-6.

I’d already followed the suggestions here: applications folder (where the R.app is) is indexed per the instructions, Spotlight index was rebuilt, and KNIME has access to the folder where R is stored (access removed and restored just in case). Xquartz is installed and functional (xclock, xcalc), and is callable from R via x11() (running R from terminal). The Cairo package is also functional in R from both RStudio and Terminal— I can generate the example plots in the Cairo documentation.

But I still cannot initialize R from within KNIME, and thus cannot even run an R Source (Table) node as in the check R package version workflow. I still receive the same “Execute failed: XQuartz is required for the Cairo library on MacOS.” error message.

Any further suggestions?