Listening on http://127.0.0.1:35329 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 spfammatter Bfabric query: workflow containerid = 32 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 328 Warning in bfabricShiny::read(bf$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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3289 Warning in bfabricShiny::read(bf$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 = 32894 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4486 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4486 Selected workflows ids: 4505 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 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 = 4505 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4486 Selected workflows ids: 4505 Selected workflows ids: 4509 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 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 = 4505 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 = 4509 workflowtemplate step id 254 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 = 4486 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4505 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4509 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32894.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4505 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4509 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32894.pdf bfabricUpload bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4505 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4509 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32894.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4486 workflowtemplate step id 272 workflowtemplate step id 231 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4505 workflowtemplate step id 243 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4509 workflowtemplate step id 254 workflowtemplate step id 254 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32894.pdf bfabricUpload Execution halted