Listening on http://127.0.0.1:33805 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$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31567/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31567_002_S500571_C1_14_7K.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31567/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31567_006_S500573_C3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31567/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31567_008_S500574_S1_14_7K.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31567/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31567_004_S500572_C2_Control.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 77101 output$tic.basepeak <- renderPlot({ #rows are 77101 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d37a288fc1.pdf generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d37a288fc1.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288649 #rows are 77101 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 77101 output$download 2... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d350828dea.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d350828dea.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288650 #rows are 77101 output$download 1... #rows are 77101 output$download 2... #rows are 77101 output$download 2... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d3ea38d76.pdf generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d3ea38d76.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288652 #rows are 77101 output$download 1... Warning: The select input "bfabric8-workunit" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. #rows are 77101 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31628/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31628_002_S503026_MEAGFPtripsin_Wild_Type__WT_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31628/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31628_006_S503028_MEAGFPalpha_Wild_Type__WT_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31628/Proteomics/QEXACTIVE_1/analytic_20230503/20230503_C31628_004_S503027_MEAGFPaspN_Wild_Type__WT_.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 56711 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 56711 output$download 2... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d37aa74214.pdf generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d37aa74214.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288663 #rows are 56711 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 56711 output$download 2... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d333419451.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d333419451.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288664 #rows are 56711 output$download 1... #rows are 56711 output$download 2... #rows are 56711 output$download 2... ggsave to file /tmp/RtmpwegNmH/rawDiag-38e3d33f23c766.pdf generated pdf /tmp/RtmpwegNmH/rawDiag-38e3d33f23c766.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288665 #rows are 56711 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 56711 output$download 1... 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$tableXICAUC 1: runApp Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 56711 output$download 2... #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Execution halted