Listening on http://127.0.0.1:33177 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 lkunz Bfabric query: workflow containerid = 33 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 337 Warning in bfabricShiny::read(bf$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 = 33786 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4919 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4919 workflowtemplate step id 239 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4919 Selected workflows ids: 4922 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4919 workflowtemplate step id 239 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 = 4922 workflowtemplate step id 244 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4919 Selected workflows ids: 4922 Selected workflows ids: 4939 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4919 workflowtemplate step id 239 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 = 4922 workflowtemplate step id 244 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 = 4939 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: 4919 Selected workflows ids: 4922 Selected workflows ids: 4939 Selected workflows ids: 4940 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4919 workflowtemplate step id 239 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 = 4922 workflowtemplate step id 244 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 = 4939 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 = 4940 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 = 4919 workflowtemplate step id 239 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4922 workflowtemplate step id 244 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4939 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4940 workflowtemplate step id 256 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33786.pdf bfabricUpload 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 = 33670 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4924 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4924 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 224 workflowtemplate step id 233 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4924 Selected workflows ids: 4925 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4924 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 224 workflowtemplate step id 233 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4925 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4924 Selected workflows ids: 4925 Selected workflows ids: 4946 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4924 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 224 workflowtemplate step id 233 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4925 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 = 4946 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 4924 Selected workflows ids: 4925 Selected workflows ids: 4946 Selected workflows ids: 4947 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4924 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 224 workflowtemplate step id 233 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4925 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 = 4946 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 = 4947 workflowtemplate step id 258 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 = 4924 workflowtemplate step id 272 workflowtemplate step id 239 workflowtemplate step id 224 workflowtemplate step id 233 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4925 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4946 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4947 workflowtemplate step id 258 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33670.pdf bfabricUpload Execution halted