Execution Context is not working with installed packages

KNIME Business Hub
1

Hi there,

I have created an Execution context in KBH using Executor ImageBuilder workflow. I included R and python extensions which are required to execute the workflow, but I get the same error using other execution context without these packages.

  • ERROR R Snippet 4:741: Execute failed: Error in R code: Loading required package: robustlmm Error: could not find function “rlmer” Error: object ‘mdl’ not found Error: object ‘coeffs’ not found
    ** WARNING Column Appender 4:795:149:153: Table 1 is shorter than the selected table 0. Corresponding columns were filled using missing values.*
    ** ERROR R Snippet 4:765: Execute failed: Error in R code: Loading required package: robustlmm Loading required package: MASS Error: could not find function “rlmer” Error: object ‘mdl’ not found Error: object ‘mdl’ not found Error: object ‘mdl2’ not found Error: object ‘res’ not found*

Do we have to add any path or activate or export anything in the docker file?
Limited Extensions.txt (8.2 KB)

2

@lakshmi21 Thank your for your post. Based on the error messages from the R Snippet node your R code is referencing packages that are either missing or have missing dependencies. In your dockerfile you need to ensure that all necessary packages are being properly installed.

You may find it easier to use the Executor Image Builder app to assist you with building your custom executor image. The app will allow you to select range of configuration options including installing R and Python and it will generate a dockerfile for you. You can then modify that dockerfile as needed and allow the app to build the image or you can download the dockerfile and build the image yourself manually.

If you are still having issues after ensuring all of the required R packages are correctly installed please open a ticket with Customer Support for assistance troubleshooting the issue.

3

Hi Kevin,

Thanks for the details. It is surprising that some of the packages didn’t get installed with Dockerfile. When I manually checked by creating a container from that docker image, there are only half of them installed. Also, when I tried to install inside container the package got installed. It didn’t have any dependencies issue or compatible issue.

Maybe I am guessing I need to sort the order of the packages. Let me do it manually and then build the Docker image.

4

@lakshmi21 It is hard to say why some packages didn’t install via the Dockerfile. It could be for any number of reasons. Perhaps like you suspect the order of the packages may have contributed to some dependency issues, or maybe if you were installing a large number of packages the repository started throttling requests due to the volume. It could also be some connectivity issues were encounter, or maybe there is a proxy server in your environment that was causing some issues.

In any case I think re-ordering the packages so that dependencies are installed first is a good option to try. If that doesn’t resolve the situation I would try removing any unnecessary packages. If you are still finding that not all the packages are installing it you might have to install them to the container manually and then create a new image from the container once all the necessary packages are installed.

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