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Recently I upgraded my linux server-deployed shiny app's R from 3.3.3 to 3.4.1, and now instead of cluster plots i'm getting this error.

Didn't change nothing else and can't access server to try and debug it. All I have now is an error message:

Warning: Error in clusplot.default: object 'spannel' not found
Stack trace (innermost first):
    104: clusplot.default
    103: clusplot
    102: eval
    101: eval
    100: withProgress
     99: renderPlot
     89: <reactive:plotObj>
     78: plotObj
     77: origRenderFunc
     76: output$KM_plot
      1: runApp

As far as I understand, spannel is a C function, I know nothing about C, unfortunately.

here is briefly how it looks in server.R file: clusplot(KMData, KM$cluster)

Any ideas?

vladli
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1 Answers1

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The R upgrade messed up your libraries that are bound to shiny, compare the output of .libPaths() so they are in the correct directory. Also make sure never to run R as sudo as running it as root might crash your entire box

Pork Chop
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  • Sorry I didn't delete the question: I was getting a version of 'cluster' in R 3.4.1, but my cluster has been installed with R < 3.4.0. I deleted that version and got a newer version of 'cluster', which worked fine with R 3.4.1. Should I delete the question, by the way? Not sure what to do in such cases on SO. – vladli Jan 11 '18 at 18:08
  • its a common question https://stackoverflow.com/questions/15170399/changing-r-default-library-path-using-libpaths-in-rprofile-site-fails-to-work/23061822 – Pork Chop Jan 11 '18 at 18:38