file must be character string

Question

I am struggling with environmental asscocition analysis in R shiny package easyLG where I want to do landscape genomics analysis. The error appears as below:

 library("easyLG")
> easyLG_app()
Warning: Error in setwd: character argument expected
  119: setwd
  118: convertData [helper.R#7]
  117: <reactive:getData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#24]
  101: getData
  100: renderPrint [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#28]
   99: func
   83: origRenderFunc
   82: output$text1
    2: shiny::runApp
    1: easyLG_app
Warning: Error in setwd: character argument expected
  119: setwd
  118: convertData [helper.R#7]
  117: <reactive:getData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#24]
  101: getData
  100: renderPrint [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#28]
   99: func
   83: origRenderFunc
   82: output$text1
    2: shiny::runApp
    1: easyLG_app
Warning in dir.create("Data_conversion") :
  'Data_conversion' already exists
Warning: Error in if: missing value where TRUE/FALSE needed
  120: test_extension
  119: vcf2lfmm
  118: convertData [helper.R#11]
  117: <reactive:getData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#24]
  101: getData
  100: renderPrint [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#28]
   99: func
   83: origRenderFunc
   82: output$text1
    2: shiny::runApp
    1: easyLG_app
Warning in dir.create("Data_conversion") :
  'Data_conversion' already exists
Warning: Error in if: missing value where TRUE/FALSE needed
  120: test_extension
  119: vcf2lfmm
  118: convertData [helper.R#11]
  117: <reactive:getData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#24]
  101: getData
  100: renderPrint [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#28]
   99: func
   83: origRenderFunc
   82: output$text1
    2: shiny::runApp
    1: easyLG_app
Warning in dir.create("Data_conversion") :
  'Data_conversion' already exists
Warning: Error in read.table: 'file' must be a character string or connection
  118: stop
  117: read.table
  116: read.csv
  115: extractBiovar [helper.R#37]
  114: <reactive:getBioclimData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#67]
   98: getBioclimData
   97: renderDataTable [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#73]
   96: func
   83: origRenderFunc
   82: output$climTable
    2: shiny::runApp
    1: easyLG_app
Warning: Error in [[: subscript out of bounds
  121: .local
  120: stack
  118: .local
  117: stack
  115: extractBiovar [helper.R#40]
  114: <reactive:getBioclimData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#67]
   98: getBioclimData
   97: renderDataTable [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#73]
   96: func
   83: origRenderFunc
   82: output$climTable
    2: shiny::runApp
    1: easyLG_app
Warning: Error in [[: subscript out of bounds
  121: .local
  120: stack
  118: .local
  117: stack
  115: extractBiovar [helper.R#40]
  114: <reactive:getBioclimData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#67]
   98: getBioclimData
   97: renderDataTable [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#73]
   96: func
   83: origRenderFunc
   82: output$climTable
    2: shiny::runApp
    1: easyLG_app
Error in .local(.Object, ...) :

Warning: Error in .rasterObjectFromFile: Cannot create a RasterLayer object from this file.
  126: stop
  125: .rasterObjectFromFile
  124: .local
  123: raster
  121: .local
  120: stack
  118: .local
  117: stack
  115: extractBiovar [helper.R#40]
  114: <reactive:getBioclimData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#67]
   98: getBioclimData
   97: renderDataTable [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#73]
   96: func
   83: origRenderFunc
   82: output$climTable
    2: shiny::runApp
    1: easyLG_app
Warning: Error in [[: subscript out of bounds
  121: .local
  120: stack
  118: .local
  117: stack
  115: extractBiovar [helper.R#40]
  114: <reactive:getBioclimData> [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#67]
   98: getBioclimData
   97: renderDataTable [C:\Users\GD43514\Documents\R\R-3.6.3\library\easyLG\app/server.R#73]
   96: func
   83: origRenderFunc
   82: output$climTable
    2: shiny::runApp
    1: easyLG_app

it stands stuck after this and not responding any more.

can anyone help?

Comments

Hey @Girma,

Can you please provide your file.path? Because this kind of error occurs when something is wrong with your file.path.