Listening on http://127.0.0.1:41285
Loading required package: bfabricShiny

Attaching package: 'bfabricShiny'

The following object is masked from 'package:base':

    save

Loading required package: PKI
Loading required package: base64enc
Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(),  : 
  isFALSE(is.null(login)) is not TRUE
Error in `<reactive:user>`(...) : object 'u' not found
saving 'login and webservicepassword' ...
read bfabricposturl https://fgcz-c-072.uzh.ch:5000/.
Warning: Error in readLines: 'con' is not a connection
  123: <Anonymous>
  122: stop
  121: value[[3L]] [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#88]
  120: tryCatchOne
  119: tryCatchList
  118: tryCatch
  117: <reactive:readSampleList> [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#82]
  101: readSampleList
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#194]
   96: func
   83: renderFunc
   82: output$title
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#221]
   96: func
   83: renderFunc
   82: output$customerInfo
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#250]
   96: func
   83: renderFunc
   82: output$peptideList
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#268]
   96: func
   83: renderFunc
   82: output$parameterList
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#616]
   96: func
   83: renderFunc
   82: output$inputCustomText1
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#641]
   96: func
   83: renderFunc
   82: output$inputCustomText3
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#655]
   96: func
   83: renderFunc
   82: output$inputCustomText4
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#674]
   96: func
   83: renderFunc
   82: output$inputCustomText2
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#745]
   96: func
   83: renderFunc
   82: output$formula
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  144: <Anonymous>
  143: stop
  142: readSampleList
  135: <reactive:orderId> [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#49]
  119: orderId
  116: <reactive:reportFilename> [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#768]
  100: reportFilename
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#774]
   96: func
   83: renderFunc
   82: output$parameter
    1: runApp
Warning: Error in readLines: 'con' is not a connection
  106: <Anonymous>
  105: stop
  104: readSampleList
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#829]
   96: func
   83: renderFunc
   82: output$actionGenerateReportButton
    1: runApp
Warning: Error in [[: attempt to select less than one element in get1index
  100: aaa:::getOutputTable [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
saving 'login and webservicepassword' ...
Warning: Error in [[: attempt to select less than one element in get1index
  100: aaa:::getOutputTable [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
saving 'login and webservicepassword' ...
Warning: Error in fix.by: 'by' must specify a uniquely valid column
  105: stop
  104: fix.by
  103: merge.data.frame
  101: deriveAminoAcidFrequence
  100: aaa:::getOutputTable
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
saving 'login and webservicepassword' ...
Warning: Error in fix.by: 'by' must specify a uniquely valid column
  105: stop
  104: fix.by
  103: merge.data.frame
  101: deriveAminoAcidFrequence
  100: aaa:::getOutputTable
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
saving 'login and webservicepassword' ...
Warning: Error in fix.by: 'by' must specify a uniquely valid column
  105: stop
  104: fix.by
  103: merge.data.frame
  101: deriveAminoAcidFrequence
  100: aaa:::getOutputTable
   99: FUN [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#161]
   98: lapply
   97: renderUI [/usr/local/lib/R/site-library/aaa/shiny/aminoAcidAnalysis/server.R#116]
   96: func
   83: renderFunc
   82: output$outputKable
    1: runApp
saving 'login and webservicepassword' ...
generateReport


processing file: report.Rmd
output file: report.knit.md


Output created: aaa-report_Hagit_Elhawi_36833_20241120.pdf
bfabricUpload


Execution halted