Listening on http://127.0.0.1:43435 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 pgehrig Bfabric query: workflow containerid = 3 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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 36 Warning in bfabricShiny::read(bf$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$workflow 1: runApp In function read_workflowid Bfabric query: workflow containerid = 364 Warning in bfabricShiny::read(bf$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 = 36411 saving 'login and webservicepassword' ... In function read_templatefile Bfabric query: dataset id Selected workflows ids: 7160 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation saving 'login and webservicepassword' ... Selected workflows ids: 7160 Selected workflows ids: 7177 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation saving 'login and webservicepassword' ... Selected workflows ids: 7160 Selected workflows ids: 7177 Selected workflows ids: 7178 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition saving 'login and webservicepassword' ... Selected workflows ids: 7160 Selected workflows ids: 7177 Selected workflows ids: 7178 Selected workflows ids: 7215 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis saving 'login and webservicepassword' ... Selected workflows ids: 7160 Selected workflows ids: 7177 Selected workflows ids: 7178 Selected workflows ids: 7215 Selected workflows ids: 7206 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 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 = 7206 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis Selected workflows ids: 7160 Selected workflows ids: 7177 Selected workflows ids: 7178 Selected workflows ids: 7215 Selected workflows ids: 7206 Selected workflows ids: 7216 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 57 workflowtemplate name: Proteomics Sample Preparation In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 58 workflowtemplate name: Proteomics Data acquisition In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 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 = 7206 workflowtemplate step id 254 In function read_workflowtemplate Bfabric query: workflowtemplate workflowtemplateid = 59 workflowtemplate name: Proteomics Data analysis In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 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' ... generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! LaTeX Error: There's no line here to end. Warning: Error in : LaTeX failed to compile /tmp/RtmpAxwqbv/fgcz_order_report-36411.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-36411.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 = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! LaTeX Error: There's no line here to end. Warning: Error in : LaTeX failed to compile /tmp/RtmpAxwqbv/fgcz_order_report-36411.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-36411.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$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! LaTeX Error: There's no line here to end. Warning: Error in : LaTeX failed to compile /tmp/RtmpAxwqbv/fgcz_order_report-36411.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-36411.log for more info. 157: stop 156: show_latex_error 155: on_error 153: run_engine 152: latexmk_emu 151: tinytex::latexmk 150: latexmk 149: rmarkdown::render 148: eventReactiveValueFunc [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#330] 104: report 97: renderUI [/usr/local/lib/R/site-library/oreport/shiny/order_report/server.R#343] 96: func 83: renderFunc 82: output$downloadReportButton 1: runApp generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md ! LaTeX Error: There's no line here to end. Warning: Error in : LaTeX failed to compile /tmp/RtmpAxwqbv/fgcz_order_report-36411.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See fgcz_order_report-36411.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 = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36411.pdf bfabricUpload generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36411.pdf generateReport In function read_steptemplateid Bfabric query: workflowstep workflowid = 7160 workflowtemplate step id 239 workflowtemplate step id 240 workflowtemplate step id 228 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7177 workflowtemplate step id 239 workflowtemplate step id 224 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7178 workflowtemplate step id 245 workflowtemplate step id 266 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7215 workflowtemplate step id 249 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7206 workflowtemplate step id 254 In function read_steptemplateid Bfabric query: workflowstep workflowid = 7216 workflowtemplate step id 256 processing file: report.Rmd output file: report.knit.md Output created: fgcz_order_report-36411.pdf bfabricUpload Execution halted