Listening on http://127.0.0.1:46227 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 cfortes Bfabric query: workflow containerid = 3375285 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3375 Warning in bfabricShiny::read(bf$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 = 33758 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4948 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4948 Selected workflows ids: 4955 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4948 Selected workflows ids: 4955 Selected workflows ids: 4968 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 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 = 4968 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 4948 Selected workflows ids: 4955 Selected workflows ids: 4968 Selected workflows ids: 4972 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 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 = 4968 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 = 4972 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 = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4968 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4972 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33758.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4968 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4972 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-33758.pdf bfabricUpload bfabricUpload In function read_workflowid Bfabric query: workflow containerid = 32420 In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4948 Selected workflows ids: 4955 Selected workflows ids: 4968 Selected workflows ids: 4972 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4948 workflowtemplate step id 239 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 4955 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 = 4968 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 = 4972 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 4949 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4949 Selected workflows ids: 4963 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4963 workflowtemplate step id 247 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: 4949 Selected workflows ids: 4963 Selected workflows ids: 4965 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4963 workflowtemplate step id 247 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 = 4965 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' ... Selected workflows ids: 4949 Selected workflows ids: 4963 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4963 workflowtemplate step id 247 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: 4949 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4949 Selected workflows ids: 4933 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4933 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4949 Selected workflows ids: 4933 Selected workflows ids: 4963 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4933 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 = 4963 workflowtemplate step id 247 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: 4949 Selected workflows ids: 4933 Selected workflows ids: 4963 Selected workflows ids: 4965 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4933 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 = 4963 workflowtemplate step id 247 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 = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 4949 Selected workflows ids: 4933 Selected workflows ids: 4963 Selected workflows ids: 4965 Selected workflows ids: 4931 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 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 = 4933 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 = 4963 workflowtemplate step id 247 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 = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results In function read_steptemplateid Bfabric query: workflowstep workflowid = 4931 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4933 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4963 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4931 workflowtemplate step id 230 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32420.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4933 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4963 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4931 workflowtemplate step id 230 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32420.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4933 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4963 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4931 workflowtemplate step id 230 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32420.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4949 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 239 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4933 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4963 workflowtemplate step id 247 workflowtemplate step id 247 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4965 workflowtemplate step id 256 workflowtemplate step id 256 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4931 workflowtemplate step id 230 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32420.pdf bfabricUpload Execution halted