Listening on http://127.0.0.1:43685 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 heinzmann Bfabric query: workflow containerid = 340 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 = 34029 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 5140 In function read_steptemplateid Bfabric query: workflowstep workflowid = 5140 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 5140 Selected workflows ids: 5172 In function read_steptemplateid Bfabric query: workflowstep workflowid = 5140 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 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 = 5172 workflowtemplate step id 266 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 5140 Selected workflows ids: 5172 Selected workflows ids: 5207 In function read_steptemplateid Bfabric query: workflowstep workflowid = 5140 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 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 = 5172 workflowtemplate step id 266 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 = 5207 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 5140 Selected workflows ids: 5172 Selected workflows ids: 5207 Selected workflows ids: 5238 In function read_steptemplateid Bfabric query: workflowstep workflowid = 5140 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 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 = 5172 workflowtemplate step id 266 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 = 5207 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 5238 workflowtemplate step id 259 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' ... In function read_workflowid Bfabric query: workflow containerid = 3029 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 = 35029 In function read_templatefile Bfabric query: dataset id Selected workflows ids: 5140 Selected workflows ids: 5172 Selected workflows ids: 5207 Selected workflows ids: 5238 In function read_steptemplateid Bfabric query: workflowstep workflowid = 5140 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 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 = 5172 workflowtemplate step id 266 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 = 5207 workflowtemplate step id 254 workflowtemplate step id 254 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 5238 workflowtemplate step id 259 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 6030 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6030 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6030 Selected workflows ids: 6046 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6030 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 = 6046 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6030 Selected workflows ids: 6046 Selected workflows ids: 6049 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6030 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 = 6046 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 = 6049 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: 6030 Selected workflows ids: 6046 Selected workflows ids: 6049 Selected workflows ids: 6050 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6030 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 = 6046 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 = 6049 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 = 6050 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 = 6030 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6046 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6049 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6050 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-35029.pdf bfabricUpload Execution halted