Listening on http://127.0.0.1:44679 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 paolo Bfabric query: workflow containerid = 33171 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4412 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4412 Selected workflows ids: 4418 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 workflowtemplate step id 256 workflowtemplate step id 256 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 Selected workflows ids: 4444 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 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 = 4444 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 Selected workflows ids: 4444 Selected workflows ids: 4445 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 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 = 4444 workflowtemplate step id 231 workflowtemplate step id 225 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 = 4445 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 Selected workflows ids: 4444 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 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 = 4444 workflowtemplate step id 231 workflowtemplate step id 225 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 Selected workflows ids: 4444 Selected workflows ids: 4445 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 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 = 4444 workflowtemplate step id 231 workflowtemplate step id 225 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 = 4445 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... In function read_templatefile In function read_workflowid Bfabric query: workflow containerid = 32743 Bfabric query: dataset id Selected workflows ids: 4412 Selected workflows ids: 4418 Selected workflows ids: 4419 Selected workflows ids: 4420 Selected workflows ids: 4444 Selected workflows ids: 4445 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4412 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 231 workflowtemplate step id 231 workflowtemplate step id 239 workflowtemplate step id 232 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 = 4418 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 4419 workflowtemplate step id 254 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 = 4420 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 = 4444 workflowtemplate step id 231 workflowtemplate step id 225 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 = 4445 workflowtemplate step id 243 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 4453 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 260 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 260 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.131 ...Acknowledgment Policy}\newline \newlineIt is Warning: Error in : LaTeX failed to compile /tmp/RtmpU98qfk/fgcz_order_report-32743.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-32743.log for more info. 157: stop 156: show_latex_error 155: on_error 153: run_engine 152: latexmk_emu 151: tinytex::latexmk 150: latexmk 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$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 260 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.118 ...Acknowledgment Policy}\newline \newlineIt is Warning: Error in : LaTeX failed to compile /tmp/RtmpU98qfk/fgcz_order_report-32743.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-32743.log for more info. 157: stop 156: show_latex_error 155: on_error 153: run_engine 152: latexmk_emu 151: tinytex::latexmk 150: latexmk 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user paolo Bfabric query: workflow containerid = 32743 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4453 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 260 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 260 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32743.pdf bfabricUpload saving 'login and webservicepassword' ... In function read_workflowid read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Request started from user paolo Bfabric query: workflow containerid = 32743 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 4453 In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 257 workflowtemplate step id 256 workflowtemplate step id 259 workflowtemplate step id 260 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 60 workflowtemplate name: Proteomics Results saving 'login and webservicepassword' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 4453 workflowtemplate step id 257 workflowtemplate step id 256 workflowtemplate step id 259 workflowtemplate step id 260 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-32743.pdf bfabricUpload Execution halted