Listening on http://127.0.0.1:33835 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$textTemplate 1: runApp In function read_workflowid Bfabric query: workflow containerid = 37 Warning in bfabricShiny::read(bf$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 = 37227 In function read_templatefile Bfabric query: dataset id Selected workflows ids: In function read_steptemplateid Bfabric query: workflowstep workflowid = workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 248 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 256 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 231 workflowtemplate step id 228 workflowtemplate step id 254 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 266 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 307 workflowtemplate step id 244 workflowtemplate step id 236 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 272 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 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 248 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 256 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 231 workflowtemplate step id 228 workflowtemplate step id 254 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 266 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 307 workflowtemplate step id 244 workflowtemplate step id 236 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 272 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 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 248 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 256 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 231 workflowtemplate step id 228 workflowtemplate step id 254 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 266 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 307 workflowtemplate step id 244 workflowtemplate step id 236 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 272 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 247 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 247 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 247 workflowtemplate step id 272 workflowtemplate step id 245 workflowtemplate step id 239 workflowtemplate step id 256 workflowtemplate step id 266 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 231 workflowtemplate step id 244 workflowtemplate step id 230 workflowtemplate step id 247 workflowtemplate step id 256 workflowtemplate step id 247 workflowtemplate step id 231 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 workflowtemplate step id 248 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 256 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 244 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 226 workflowtemplate step id 231 workflowtemplate step id 228 workflowtemplate step id 254 workflowtemplate step id 248 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 266 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 239 workflowtemplate step id 272 workflowtemplate step id 241 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 243 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 307 workflowtemplate step id 244 workflowtemplate step id 236 workflowtemplate step id 266 workflowtemplate step id 239 workflowtemplate step id 254 workflowtemplate step id 250 workflowtemplate step id 254 workflowtemplate step id 243 workflowtemplate step id 272 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 7829 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7829 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: 7829 Selected workflows ids: 7830 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7829 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 = 7830 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... Selected workflows ids: 7829 Selected workflows ids: 7830 Selected workflows ids: 7839 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7829 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 = 7830 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7839 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7829 Selected workflows ids: 7830 Selected workflows ids: 7839 Selected workflows ids: 7840 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7829 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 = 7830 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7839 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 = 7840 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 = 7829 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7830 workflowtemplate step id 245 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7839 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7840 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-37227.pdf bfabricUpload Execution halted