Listening on http://127.0.0.1:44293 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 schesnov 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 = 37132 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 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 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 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 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 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 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 283 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7676 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7676 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7676 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 289 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-37132.pdf bfabricUpload In function read_workflowid Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : isFALSE(is.null(login)) is not TRUE Error in ``(...) : object 'u' not found In function read_templatefile saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user schesnov Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 37 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 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 = 37177 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 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 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 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 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 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 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7703 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7703 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7703 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-37177.pdf bfabricUpload In function read_workflowid Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : isFALSE(is.null(login)) is not TRUE Error in ``(...) : object 'u' not found In function read_templatefile saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user wuethrich Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 37 Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. Warning: Error in $: $ operator is invalid for atomic vectors 121: append 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 = 37119 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 256 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 228 workflowtemplate step id 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 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 256 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 228 workflowtemplate step id 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 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 256 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 228 workflowtemplate step id 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 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 256 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 228 workflowtemplate step id 227 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 254 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 240 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 232 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 225 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 254 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 225 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 280 workflowtemplate step id 244 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 230 workflowtemplate step id 230 workflowtemplate step id 256 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 249 workflowtemplate step id 248 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 7666 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7666 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7666 Selected workflows ids: 7667 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7666 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7667 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: 7666 Selected workflows ids: 7667 Selected workflows ids: 7707 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7666 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7667 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 = 7707 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7666 Selected workflows ids: 7667 Selected workflows ids: 7707 Selected workflows ids: 7708 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7666 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7667 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 = 7707 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 7708 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 = 7666 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7667 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7707 workflowtemplate step id 250 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7708 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-37119.pdf bfabricUpload Execution halted