Listening on http://127.0.0.1:45219 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save In function read_workflowid Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : isFALSE(is.null(login)) is not TRUE Error in ``(...) : object 'u' not found In function read_templatefile saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user nbionda Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_templatefile Warning: Error in $: $ operator is invalid for atomic vectors 123: 122: stop 121: read_workflowid 114: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#89] 98: read_templatefile 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#216] 96: func 83: renderFunc 82: output$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 365 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_templatefile Warning: Error in $: $ operator is invalid for atomic vectors 123: 122: stop 121: read_workflowid 114: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#89] 98: read_templatefile 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#216] 96: func 83: renderFunc 82: output$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3659 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#125] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#135] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_templatefile Warning: Error in $: $ operator is invalid for atomic vectors 123: 122: stop 121: read_workflowid 114: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#89] 98: read_templatefile 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#216] 96: func 83: renderFunc 82: output$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 36595 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 270 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 259 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 256 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 248 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 239 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 253 workflowtemplate step id 243 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 279 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 243 workflowtemplate step id 232 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 256 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 270 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 259 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 256 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 248 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 239 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 253 workflowtemplate step id 243 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 279 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 243 workflowtemplate step id 232 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 256 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 270 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 259 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 256 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 248 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 239 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 253 workflowtemplate step id 243 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 279 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 243 workflowtemplate step id 232 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 256 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 270 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 259 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 256 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 248 workflowtemplate step id 253 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 239 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 253 workflowtemplate step id 243 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 279 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 243 workflowtemplate step id 232 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 225 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 256 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 7305 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7305 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 230 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7305 Selected workflows ids: 7307 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7305 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 230 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7307 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 7305 Selected workflows ids: 7307 Selected workflows ids: 7316 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7305 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 230 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7307 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7316 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... Selected workflows ids: 7305 Selected workflows ids: 7307 Selected workflows ids: 7316 Selected workflows ids: 7317 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7305 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 230 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7307 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7316 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 7317 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7305 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 230 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7307 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7316 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7317 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36595.pdf bfabricUpload Execution halted