Listening on http://127.0.0.1:34469 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$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_proteomeDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 1850207 output$tic.basepeak <- renderPlot({ #rows are 1850207 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 319 rows containing missing values (`geom_line()`). #rows are 1850207 output$download 2... #rows are 1850207 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 1850207 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_proteomeDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 2018428 output$tic.basepeak <- renderPlot({ #rows are 2018428 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_phoshoDDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_phoshoDDA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 353983 output$tic.basepeak <- renderPlot({ #rows are 353983 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 353983 output$download 2... #rows are 353983 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 353983 output$download 2... #rows are 353983 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... #rows are 353983 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 353983 output$download 2... DEBUG renderPlot plotQCs #rows are 353983 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$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$tableInfo 1: runApp #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_phoshoDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 1090962 output$tic.basepeak <- renderPlot({ #rows are 1090962 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$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") 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: '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: '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 1090962 output$download 2... DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_phoshoDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_phoshoDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 1090962 Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... saving 'login and webservicepassword' ... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... #rows are 1090962 output$download 2... DEBUG renderPlot plotQCs #rows are 1090962 output$download 2... DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_proteomeDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 2018428 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 2018428 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_010_S525049_siC_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_015_S525052_siG_I2_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_014_S525043_siC_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_016_S525042_siC_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_008_S525048_siC_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_004_S525051_siG_I1_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_002_S525053_siG_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_003_S525045_siG_C1_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_009_S525044_siC_C3_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_005_S525046_siG_C2_Untreated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_013_S525050_siC_I3_Treated_proteomeDIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29033/Proteomics/EXPLORIS_1/radhika_20230619/20230619_007_S525047_siG_C3_Untreated_proteomeDIA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 2018428 output$scan.frequency <- renderPlot Warning: Removed 348 rows containing missing values (`geom_line()`). #rows are 2018428 output$download 2... saving 'login and webservicepassword' ... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... Warning: Computation failed in `stat_binhex()` Caused by error in `if (diff(ybnds) <= 0) ...`: ! missing value where TRUE/FALSE needed #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... #rows are 2018428 output$download 2... #rows are 2018428 output$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") 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: '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: '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 2018428 output$download 2... DEBUG renderPlot plotQCs #rows are 2018428 output$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: '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: '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: '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