Listening on http://127.0.0.1:34299 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 wuethrich 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 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 352 Warning in bfabricShiny::read(bf$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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3528 Warning in bfabricShiny::read(bf$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 = 35281 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 6315 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6315 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6315 Selected workflows ids: 6316 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6315 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 = 6316 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6315 Selected workflows ids: 6316 Selected workflows ids: 6335 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6315 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 = 6316 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 = 6335 workflowtemplate step id 291 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... Selected workflows ids: 6315 Selected workflows ids: 6316 Selected workflows ids: 6335 Selected workflows ids: 6336 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6315 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 = 6316 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 = 6335 workflowtemplate step id 291 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 6336 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 = 6315 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6316 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6335 workflowtemplate step id 291 workflowtemplate step id 250 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6336 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-35281.pdf bfabricUpload saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user lkunz 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 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 = 35171 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 6212 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6212 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6212 Selected workflows ids: 6213 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6212 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 6213 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6212 Selected workflows ids: 6213 Selected workflows ids: 6322 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6212 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 6213 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 = 6322 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 = 6212 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6213 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6322 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-35171.pdf bfabricUpload Execution halted