Listening on http://127.0.0.1:46281 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 schesnov Bfabric query: workflow containerid = 3203 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 32038 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3478 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3478 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3478 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32038.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3478 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32038.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3478 workflowtemplate step id 277 workflowtemplate step id 276 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32038.pdf bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user wuethrich Bfabric query: workflow containerid = 320 Warning in bfabricShiny::read(bf$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 = 32040 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3467 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 workflowtemplate step id 230 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3467 Selected workflows ids: 3468 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 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 = 3468 workflowtemplate step id 226 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3467 Selected workflows ids: 3468 Selected workflows ids: 3469 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 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 = 3468 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 = 3469 workflowtemplate step id 244 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 3467 Selected workflows ids: 3468 Selected workflows ids: 3469 Selected workflows ids: 3480 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 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 = 3468 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 = 3469 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 = 3480 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 3467 Selected workflows ids: 3468 Selected workflows ids: 3469 Selected workflows ids: 3480 Selected workflows ids: 3481 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 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 = 3468 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 = 3469 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 = 3480 workflowtemplate step id 250 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 3481 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' ... saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3467 workflowtemplate step id 230 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3468 workflowtemplate step id 226 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3469 workflowtemplate step id 244 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3480 workflowtemplate step id 250 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3481 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32040.pdf bfabricUpload bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user schesnov Bfabric query: workflow containerid = 320 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 3204 Warning in bfabricShiny::read(bf$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 = 32043 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3482 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3482 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3482 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32043.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3482 workflowtemplate step id 277 workflowtemplate step id 280 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32043.pdf bfabricUpload 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 = 32035 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3433 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3433 workflowtemplate step id 224 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3433 Selected workflows ids: 3483 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3433 workflowtemplate step id 224 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 = 3483 workflowtemplate step id 266 workflowtemplate step id 269 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 3433 Selected workflows ids: 3483 Selected workflows ids: 3456 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3433 workflowtemplate step id 224 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 = 3483 workflowtemplate step id 266 workflowtemplate step id 269 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 3456 workflowtemplate step id 247 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 3433 Selected workflows ids: 3483 Selected workflows ids: 3456 Selected workflows ids: 3461 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3433 workflowtemplate step id 224 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 = 3483 workflowtemplate step id 266 workflowtemplate step id 269 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 3456 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 = 3461 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 = 3433 workflowtemplate step id 224 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3483 workflowtemplate step id 266 workflowtemplate step id 269 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3456 workflowtemplate step id 247 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3461 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32035.pdf bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user schesnov 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 320 Warning in bfabricShiny::read(bf$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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 32044 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3484 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3484 workflowtemplate step id 277 workflowtemplate step id 279 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user schesnov Bfabric query: workflow containerid = 320 Warning in bfabricShiny::read(bf$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 = 32044 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3485 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3485 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 275 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 61 workflowtemplate name: Analysis procedure: Purified Biomolecules saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3485 workflowtemplate step id 277 workflowtemplate step id 279 workflowtemplate step id 275 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32044.pdf bfabricUpload Execution halted