Listening on http://127.0.0.1:43741 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 antdit Bfabric query: workflow containerid = 31893 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 3585 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 workflowtemplate step id 232 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation Selected workflows ids: 3585 Selected workflows ids: 3611 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 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 = 3611 workflowtemplate step id 245 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition Selected workflows ids: 3585 Selected workflows ids: 3611 Selected workflows ids: 3612 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 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 = 3611 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 = 3612 workflowtemplate step id 249 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 3585 Selected workflows ids: 3611 Selected workflows ids: 3612 Selected workflows ids: 3613 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 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 = 3611 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 = 3612 workflowtemplate step id 249 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 3613 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 = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3611 workflowtemplate step id 245 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3612 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3613 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.189 ...newline - UP000029965\newline \newlineThe following Warning: Error in : LaTeX failed to compile /tmp/RtmpA9XNbU/fgcz_order_report-31893.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-31893.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$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3611 workflowtemplate step id 245 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3612 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3613 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.176 ...newline - UP000029965\newline \newlineThe following Warning: Error in : LaTeX failed to compile /tmp/RtmpA9XNbU/fgcz_order_report-31893.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-31893.log for more info. 157: stop 156: show_latex_error 155: on_error 153: run_engine 152: latexmk_emu 151: tinytex::latexmk 150: latexmk 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3611 workflowtemplate step id 245 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3612 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3613 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! Undefined control sequence. l.176 ...newline - UP000029965\newline \newlineThe following Warning: Error in : LaTeX failed to compile /tmp/RtmpA9XNbU/fgcz_order_report-31893.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-31893.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 = 3585 workflowtemplate step id 241 workflowtemplate step id 234 workflowtemplate step id 239 workflowtemplate step id 232 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3611 workflowtemplate step id 245 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3612 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 3613 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-31893.pdf bfabricUpload Execution halted