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A meta collection and article about R and KNIME

RKnimeInstallRserve1.8.6
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KNIME and R — installation across operating systems — some remarks (a newly condensed article) https://medium.com/p/dcf0efdc8ddf ---------------- A meta collection and article about R and KNIME R gives you the power to do a lot of great things combined with KNIME but to get R and KNIME together up and running can be a challenge. I came across a lot of questions about this over the year and wrote a summary article back in 2019 *1). I will try to give you the most helpful links and adress the most basic pitfalls. Most of this is related to Windows (10) and MacOS. Keep in mind you will need these components to get KNIME and R to work together - a working KNIME installation with R scripting nodes (the official version) https://hub.knime.com/knime/extensions/org.knime.features.r/latest - a working version of R - use the official guide and just install the binaries *1) or the Environment propagation *1a) or explore the possible challanges *1b) - R & KNIME will need RServe >=1.8.6 - there is *no* way around this. You *have* to make this work! And some other libraries like Cairo - compilation (if necessary) on Windows will need RTools *2) - compilation (if necessary) on MacOS will need Homebrew and some other tools possibly *3) - you have to configure the whole thing to make it work For starters follow the official installation guide - if that works you are done, perfect https://docs.knime.com/latest/r_installation_guide/index.html *1) On Windows or MacOS you might be able just to install the latest RServe binary version (1.8-10) with this commands: install.packages("Rserve", repos = "https://cran.r-project.org", type="win.binary") install.packages("Rserve", repos = "https://cran.r-project.org", type="mac.binary") see: https://forum.knime.com/t/r-integration-cannot-install-rserve/38785/2?u=mlauber71 --- you can install a specific package directly (check for the latest releases on: https://cran.r-project.org/package=Rserve) install.packages("https://cran.r-project.org/bin/windows/contrib/4.1/Rserve_1.8-10.zip", repos = NULL, type ="win.binary") install.packages("https://cran.r-project.org/bin/macosx/contrib/4.1/Rserve_1.8-10.tgz", repos = NULL, type ="mac.binary") --- on Windows you can also use the installr package: # install.packages("installr") library(installr) install.packages.zip("https://cran.r-project.org/bin/windows/contrib/4.1/Rserve_1.8-10.zip") ----------------------------------------------------------------------------------------------- *1a) the Conda Environment Propagation can be used to install a (typically slightly older) R version via Anaconda or Miniconda for KNIME https://hub.knime.com/mlauber71/spaces/Public/latest/kn_example_r_basic_knime_in_out_flow_variable~119aEydIH0oCdht8 => the benefit would be you are also set up for Python (https://kni.me/w/AvjrddXKOIoZYLV3) *1b) Install R alongside KNIME on Windows and MacOS (from 2019 but contains maybe useful links and explanations) https://forum.knime.com/t/install-r-alongside-knime-on-windows-and-macos/13287?u=mlauber71 If you want to see what you can do with KNIME and R you could explore my workspace and serach for workflows beginning with kn_example_r_<...> https://hub.knime.com/mlauber71/spaces/Public/latest/~sl4rYEzjFPm7a99a/ KNIME and R ggplot2 – „the beautiful Violin Plot that has it all“ https://forum.knime.com/t/knime-and-r-ggplot2-the-beautiful-violin-plot-that-has-it-all/38224 https://hub.knime.com/mlauber71/spaces/Public/latest/kn_example_r_violinplot_boxplot~DZP837sduxJ8yC-t ----------------------------------------------------------------------------------------------- If you still encounter problems these links about R and RServe 1.8.6 are most likely to help you on the way. *2) ------------------------- (only if your R is not up and running with the above points) RServe 1.8.6 on Windows https://forum.knime.com/t/compiling-rserve-1-8-6-on-windows-7-64bit/18318?u=mlauber71 https://forum.knime.com/t/how-i-finally-got-r-working-in-knime-on-windows-10/22491?u=mlauber71 If you (still) struggle to get RTools working on Windows you can follow this thread https://forum.knime.com/t/how-to-import-tables-from-docx-documents-via-r-snippet/19284/10?u=mlauber71 Using Rtools40 on Windows https://cran.r-project.org/bin/windows/Rtools/index.html Some more recent hints about R, RStudio and usage of admin rights and library path by noemireyes https://forum.knime.com/t/r-cannot-be-initialized/14836/15?u=mlauber71 *3) ------------------------- (only if your R is not up and running with the above points) RServe 1.8.6 on MacOSX => for Mac users please note there is a passage in the official guide about a script you will have to run to install "Homebrew". It is eays to miss that but it might be very vital: https://forum.knime.com/t/install-r-alongside-knime-on-windows-and-macos/13287/5?u=mlauber71 https://forum.knime.com/t/how-i-finally-got-r-working-in-knime-on-windows-10/22491/6?u=mlauber71 https://bitbucket.org/KNIME/knime-r/src/master/org.knime.r/scripts/ If you still encounter problems on MacOS refer to these articles: https://forum.knime.com/t/knime-r-integration-execute-failed-exception-occured-during-r-initialization/23016/6?u=mlauber71 https://forum.knime.com/t/installing-rserve-1-8-6-on-macos-10-15-catalina/20909/6?u=mlauber71 If you encounter problems with messages that R cannot find the XQuartz.app you might have to re-activate or rebuild your MacOSX Spotlight index for the folder https://forum.knime.com/t/r-cannot-be-initialized-macos-10-15-5-knime-4-1-3/25324/7?u=mlauber71 ----------------------------------------------------- If you want to ceck the status of your R installation you could use this node https://hub.knime.com/mlauber71/spaces/Public/latest/kn_example_r_check_version_of_package => if this produces unwanted or 'funny' results you will have to resort to some of the measures above ----------------------------------------------------- And then if you want to keep your R clean and updated here are two ways to do it. best to do it from RStudio or R GUI itself. 3 Methods to update R on RStudio (for Windows & Mac) https://www.linkedin.com/pulse/3-methods-update-r-rstudio-windows-mac-woratana-ngarmtrakulchol/ Updating R from R (on Windows) – using the {installr} package https://www.r-statistics.com/2013/03/updating-r-from-r-on-windows-using-the-installr-package/ ----------------------------------------------------- If you must you could start RServe outside of KNIME (in RStudio) - this is necessary for the Community nodes of R https://forum.knime.com/t/r-source-community-node-connection-error/13087/2?u=mlauber71 R Community nodes (I would *not* recommend using them in the first place) https://nodepit.com/category/community/r library(Rserve) library(RSclient) Rserve(port = 6311, debug = FALSE, args = “–vanilla”) # start the RServe(er) rsc <- RSconnect(port = 6311) # shutdown the server after you used it RSshutdown(rsc) -----------------------------------------------------

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