Listening on http://127.0.0.1:36593 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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 36 Warning in bfabricShiny::read(bf$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 = 36531 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 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 workflowtemplate step id 241 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 239 workflowtemplate step id 288 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 272 workflowtemplate step id 269 workflowtemplate step id 269 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 248 workflowtemplate step id 243 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 259 workflowtemplate step id 285 workflowtemplate step id 236 workflowtemplate step id 238 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 224 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 240 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 276 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 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 workflowtemplate step id 241 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 239 workflowtemplate step id 288 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 272 workflowtemplate step id 269 workflowtemplate step id 269 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 248 workflowtemplate step id 243 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 259 workflowtemplate step id 285 workflowtemplate step id 236 workflowtemplate step id 238 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 224 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 240 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 276 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation saving 'login and webservicepassword' ... Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = 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 workflowtemplate step id 241 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 239 workflowtemplate step id 288 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 272 workflowtemplate step id 269 workflowtemplate step id 269 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 248 workflowtemplate step id 243 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 259 workflowtemplate step id 285 workflowtemplate step id 236 workflowtemplate step id 238 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 224 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 240 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 276 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 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 workflowtemplate step id 241 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 260 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 279 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 239 workflowtemplate step id 288 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 266 workflowtemplate step id 225 workflowtemplate step id 272 workflowtemplate step id 269 workflowtemplate step id 269 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 248 workflowtemplate step id 243 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 259 workflowtemplate step id 285 workflowtemplate step id 236 workflowtemplate step id 238 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 307 workflowtemplate step id 224 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 240 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 276 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7257 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7257 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7257 Selected workflows ids: 7263 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7257 workflowtemplate step id 239 workflowtemplate step id 231 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 = 7263 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... Selected workflows ids: 7257 Selected workflows ids: 7263 Selected workflows ids: 7266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7257 workflowtemplate step id 239 workflowtemplate step id 231 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 = 7263 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 = 7266 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7257 Selected workflows ids: 7263 Selected workflows ids: 7266 Selected workflows ids: 7267 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7257 workflowtemplate step id 239 workflowtemplate step id 231 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 = 7263 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 = 7266 workflowtemplate step id 247 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 = 7267 workflowtemplate step id 256 workflowtemplate step id 256 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 = 7257 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7263 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7266 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7267 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36531.pdf bfabricUpload Execution halted