Listening on http://127.0.0.1:33071 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 = 349 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 = 34974 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 6211 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6211 Selected workflows ids: 6216 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 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 = 6216 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6211 Selected workflows ids: 6216 Selected workflows ids: 6310 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 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 = 6216 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 = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 6211 Selected workflows ids: 6216 Selected workflows ids: 6310 Selected workflows ids: 6311 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 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 = 6216 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 = 6310 workflowtemplate step id 291 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 = 6311 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' ... Selected workflows ids: 6211 Selected workflows ids: 6216 Selected workflows ids: 6310 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 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 = 6216 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 = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 6211 Selected workflows ids: 6216 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 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 = 6216 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6211 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6216 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6216 Selected workflows ids: 6211 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 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 = 6211 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 6216 Selected workflows ids: 6211 Selected workflows ids: 6310 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 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 = 6211 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 = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 6216 Selected workflows ids: 6211 Selected workflows ids: 6310 Selected workflows ids: 6311 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 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 = 6211 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 = 6310 workflowtemplate step id 291 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 = 6311 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6311 workflowtemplate step id 256 processing file: report.Rmd Quitting from lines 81-95 (report.Rmd) Warning: Error in if: argument is of length zero 169: eval [#7] 168: eval 167: eval_with_user_handlers 162: evaluate_call 161: evaluate::evaluate 160: evaluate 157: eng_r 156: block_exec 155: call_block 154: process_group.block 151: process_file 150: knitr::knit 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6311 workflowtemplate step id 256 processing file: report.Rmd Quitting from lines 81-95 (report.Rmd) Warning: Error in if: argument is of length zero 169: eval [#7] 168: eval 167: eval_with_user_handlers 162: evaluate_call 161: evaluate::evaluate 160: evaluate 157: eng_r 156: block_exec 155: call_block 154: process_group.block 151: process_file 150: knitr::knit 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp 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 = 34974 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 6216 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 workflowtemplate step id 231 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 6216 Selected workflows ids: 6211 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 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 = 6211 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... Selected workflows ids: 6216 Selected workflows ids: 6211 Selected workflows ids: 6310 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 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 = 6211 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 = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 6216 Selected workflows ids: 6211 Selected workflows ids: 6310 Selected workflows ids: 6311 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6216 workflowtemplate step id 240 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 = 6211 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 = 6310 workflowtemplate step id 291 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 = 6311 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 = 6216 workflowtemplate step id 240 workflowtemplate step id 231 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6211 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6310 workflowtemplate step id 291 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 6311 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-34974.pdf bfabricUpload Execution halted