Listening on http://127.0.0.1:41503 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save saving 'login and webservicepassword' ... In function read_workflowid Request started from user wuethrich Bfabric query: workflow containerid = 3 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#122] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#132] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 31 Warning in bfabricShiny::read(bf$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#122] 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#122] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#132] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3155 Warning in bfabricShiny::read(bf$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#122] 120: [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#122] 104: read_workflowid 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#132] 96: func 83: renderFunc 82: output$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 31558 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3035 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3035 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3035 Selected workflows ids: 3036 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3035 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 = 3036 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 3035 Selected workflows ids: 3036 Selected workflows ids: 3040 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3035 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 = 3036 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 = 3040 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 3035 Selected workflows ids: 3036 Selected workflows ids: 3040 Selected workflows ids: 3041 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3035 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 = 3036 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 = 3040 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 = 3041 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 = 3035 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3036 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3040 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3041 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-31558.pdf bfabricUpload Execution halted