Listening on http://127.0.0.1:45121 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. DEBUG XXX https://fgcz-c-072.uzh.ch:5002/ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ bfabricConnectionWorking TRUE DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_002_S488912_NegativeCTRL_negative_control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_006_S488914_mGFP-BAZ2A-dTAM_DropletPellet_mutant.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_004_S488913_mGFP-BAZ2A-WT_DropletPellet_WT.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 89808 output$tic.basepeak <- renderPlot({ #rows are 89808 output$download 2... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. ggsave to file /tmp/Rtmpa06Lc5/rawDiag-1a9ab5d4e7223.pdf generated pdf /tmp/Rtmpa06Lc5/rawDiag-1a9ab5d4e7223.pdf bfabricShiny::uploadResource ... DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ The current plot is available as workunit 287695 #rows are 89808 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation ideoms with `aes()` Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 89808 output$download 2... DEBUG renderPlot plotQCs #rows are 89808 output$download 2... ggsave to file /tmp/Rtmpa06Lc5/rawDiag-1a9ab422bd0e8.pdf Warning: Error in +: non-numeric argument to binary operator 1: runApp #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. DEBUG XXX https://fgcz-c-072.uzh.ch:5002/ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ bfabricConnectionWorking TRUE DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ 'empdegree' found. saving 'login and webservicepassword' ... DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ saving 'login and webservicepassword' ... DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ saving 'login and webservicepassword' ... DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ DEBUG XXX lkunz 8c0bdb7b0b024f45f4dee85768359b48 https://fgcz-c-072.uzh.ch:5002/ executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_006_S488914_mGFP-BAZ2A-dTAM_DropletPellet_mutant.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_004_S488913_mGFP-BAZ2A-WT_DropletPellet_WT.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31303/Proteomics/QEXACTIVEHF_2/mungo_20230331/20230331_002_S488912_NegativeCTRL_negative_control.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 89808 output$tic.basepeak <- renderPlot({ #rows are 89808 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 87 rows containing missing values (`geom_line()`). #rows are 89808 output$download 2... #rows are 89808 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... #rows are 89808 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 89808 output$download 2... DEBUG renderPlot plotQCs #rows are 89808 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp saving 'login and webservicepassword' ... Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp Execution halted