Listening on http://127.0.0.1:41093 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save 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 = 3.527 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 35 Warning in bfabricShiny::read(bf$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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3527 Warning in bfabricShiny::read(bf$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_workflowid Bfabric query: workflow containerid = 35273 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 6244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6244 workflowtemplate step id 239 workflowtemplate step id 225 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6244 Selected workflows ids: 6259 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6244 workflowtemplate step id 239 workflowtemplate step id 225 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 6259 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6244 Selected workflows ids: 6259 Selected workflows ids: 6264 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6244 workflowtemplate step id 239 workflowtemplate step id 225 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 6259 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 6264 workflowtemplate step id 247 workflowtemplate step id 247 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 247 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 6244 Selected workflows ids: 6259 Selected workflows ids: 6264 Selected workflows ids: 6278 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6244 workflowtemplate step id 239 workflowtemplate step id 225 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 6259 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 6264 workflowtemplate step id 247 workflowtemplate step id 247 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 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 = 6278 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 6244 workflowtemplate step id 239 workflowtemplate step id 225 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6259 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6264 workflowtemplate step id 247 workflowtemplate step id 247 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 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6278 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-35273.pdf bfabricUpload Execution halted