Listening on http://127.0.0.1:43377 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 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 [/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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 369 Warning in bfabricShiny::read(bf$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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3696 Warning in bfabricShiny::read(bf$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 = 36964 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 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 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 7565 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7565 Selected workflows ids: 7566 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 7565 Selected workflows ids: 7566 Selected workflows ids: 7567 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 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 = 7567 workflowtemplate step id 291 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7565 Selected workflows ids: 7566 Selected workflows ids: 7567 Selected workflows ids: 7568 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 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 = 7567 workflowtemplate step id 291 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 7568 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' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7567 workflowtemplate step id 291 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7568 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36964.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7567 workflowtemplate step id 291 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7568 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36964.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7565 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7566 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7567 workflowtemplate step id 291 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7568 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36964.pdf bfabricUpload In function read_workflowid Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : isFALSE(is.null(login)) is not TRUE Error in ``(...) : object 'u' not found In function read_templatefile saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user cfortes Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$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 = 36883 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 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 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_workflowid Bfabric query: workflow containerid = 368 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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 36833 Warning in bfabricShiny::read(bf$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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3688 Warning in bfabricShiny::read(bf$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 = 36883 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 7548 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7548 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7548 Selected workflows ids: 7549 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7548 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7549 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 7548 Selected workflows ids: 7549 Selected workflows ids: 7550 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7548 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7549 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 = 7550 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: 7548 Selected workflows ids: 7549 Selected workflows ids: 7550 Selected workflows ids: 7559 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7548 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7549 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 = 7550 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 = 7559 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 = 7548 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7549 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7550 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7559 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36883.pdf bfabricUpload In function read_workflowid Error in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : isFALSE(is.null(login)) is not TRUE Error in ``(...) : object 'u' not found In function read_templatefile saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user spfammatter Bfabric query: workflow containerid = 3 Warning in bfabricShiny::read(bf$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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 36 Warning in bfabricShiny::read(bf$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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3688 Warning in bfabricShiny::read(bf$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$textTemplate 1: runApp In function read_workflowid Warning in bfabricShiny::read(bf$login(), bf$webservicepassword(), posturl = posturl(), : query failed. In function read_templatefile In function read_workflowid Request started from user spfammatter Bfabric query: workflow containerid = 3688 Warning in bfabricShiny::read(bf$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 = 36884 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 291 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 254 workflowtemplate step id 277 workflowtemplate step id 278 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 289 workflowtemplate step id 243 workflowtemplate step id 227 workflowtemplate step id 272 workflowtemplate step id 256 workflowtemplate step id 231 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 226 workflowtemplate step id 248 workflowtemplate step id 232 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 225 workflowtemplate step id 225 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 247 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 273 workflowtemplate step id 257 workflowtemplate step id 244 workflowtemplate step id 257 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 290 workflowtemplate step id 259 workflowtemplate step id 256 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 232 workflowtemplate step id 232 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 250 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 244 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 227 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 266 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7554 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7554 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 7554 Selected workflows ids: 7561 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7554 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7561 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 7554 Selected workflows ids: 7561 Selected workflows ids: 7571 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7554 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7561 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7571 workflowtemplate step id 254 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7554 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7561 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7571 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36884.pdf bfabricUpload Execution halted