Listening on http://127.0.0.1:33351 Attaching package: 'shinydashboard' The following object is masked from 'package:graphics': box Loading required package: readr Loading required package: reshape2 Loading required package: lattice Loading required package: rawDiag Loading required package: rawrr Loading required package: ggnewscale fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-02 19:30:27.497262 | timeMax: 2024-11-01 18:30:27.499123 | timeDiff: 5184000.00186133 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 input timeRange: 7776000 | timeMin: 2024-09-02 17:30:27.497 | timeMax: 2024-11-01 17:30:27.499 | timeDiff: 5184000.00200009 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 0 nrow dataFiltered(): 0 Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 13 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 558 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 558 Loading required package: ggh4x Loading required package: ggplot2 Attaching package: 'ggh4x' The following object is masked from 'package:ggplot2': guide_axis_logticks using 'ggh4x' package ... nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? NA p36647/Proteomics/TIMSTOF_1/mtuchel_20241029_/zip/20241029_007_autoQC03dia_S1-A9_1_10720.d.zip NA p36647/Proteomics/TIMSTOF_1/mtuchel_20241029_/zip/20241029_007_autoQC03dia_S1-A9_1_10720.d.zip plotClick: fn has changed to /srv/www/htdocs//p36647/Proteomics/TIMSTOF_1/mtuchel_20241029_/zip/20241029_007_autoQC03dia_S1-A9_1_10720.d.zip plotClick: NA plotClick: fn has changed to /srv/www/htdocs//p36721/Proteomics/TIMSTOF_1/saenz_20241029_/zip/20241029_001_autoQC03dia_S1-A1_1_10712.d.zip p36721/Proteomics/TIMSTOF_1/saenz_20241029_/zip/20241029_001_autoQC03dia_S1-A1_1_10712.d.zip plotClick: fn has changed to /srv/www/htdocs//p36647/Proteomics/TIMSTOF_1/mtuchel_20241031_/zip/20241031_001_autoQC03dia_S1-A1_1_10721.d.zip p36647/Proteomics/TIMSTOF_1/mtuchel_20241031_/zip/20241031_001_autoQC03dia_S1-A1_1_10721.d.zip NA plotClick: fn has changed to /srv/www/htdocs//p36647/Proteomics/TIMSTOF_1/mtuchel_20241031_/zip/20241031_012r_autoQC03dia_S1-A12_1_10736.d.zip p36647/Proteomics/TIMSTOF_1/mtuchel_20241031_/zip/20241031_012r_autoQC03dia_S1-A12_1_10736.d.zip NA p36492/Proteomics/TIMSTOF_1/analytic_20241031/zip/20241031_003_autoQC03dia_S1-B2_1_10738.d.zip p36647/Proteomics/TIMSTOF_1/mtuchel_20241031_/zip/20241031_012r_autoQC03dia_S1-A12_1_10736.d.zip p36721/Proteomics/TIMSTOF_1/saenz_20241029_/zip/20241029_001_autoQC03dia_S1-A1_1_10712.d.zip NA fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-05 17:23:46.89161 | timeMax: 2024-11-04 16:23:46.892593 | timeDiff: 5184000.00098324 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1120 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1120 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-05 15:23:46.892 | timeMax: 2024-11-04 15:23:46.893 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1120 using 'ggh4x' package ... Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 143 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 360 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 143 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_002_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_003_autoQC03dia.raw NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730733820260521000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-05 17:57:32.267193 | timeMax: 2024-11-04 16:57:32.267772 | timeDiff: 5184000.00057864 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1120 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1120 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-05 15:57:32.267 | timeMax: 2024-11-04 15:57:32.268 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1120 using 'ggh4x' package ... Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 143 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 360 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 143 using 'ggh4x' package ... NA p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_002_autoQC03dda.raw p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_003_autoQC03dia.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730735848392186000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-07 10:34:25.944515 | timeMax: 2024-11-06 09:34:25.945097 | timeDiff: 5184000.00058246 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1168 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-07 08:34:25.945 | timeMax: 2024-11-06 08:34:25.945 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 364 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 216 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... NA NA p3000/Proteomics/FUSION_2/chiawei_20241104/20241104_003_autoQC03dia.raw NA nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 338 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... NA nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730882062159062000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-07 17:09:12.85457 | timeMax: 2024-11-06 16:09:12.855226 | timeDiff: 5184000.00065589 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 0 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$autoQC03-DDA-ui 1: runApp reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$autoQC03-DIA-ui 1: runApp nFacets: 4 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 364 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 216 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-07 15:09:12.85457 | timeMax: 2024-11-06 15:09:12.85523 | timeDiff: 5184000.00065994 nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-07 15:09:12.855 | timeMax: 2024-11-06 15:09:12.855 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw p3000/Proteomics/FUSION_2/chiawei_20241104/20241104_003_autoQC03dia.raw NA p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730905749058881000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning: Error in if: missing value where TRUE/FALSE needed 1: runApp input timeRange: 1209600 | timeMin: 2024-10-30 16:40:38.237936 | timeMax: 2024-11-06 16:40:38.237985 | timeDiff: 604800.000048876 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730907638232548000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 13:10:51.464722 | timeMax: 2024-11-07 12:10:51.465654 | timeDiff: 5184000.00093246 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 0 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$autoQC03-DDA-ui 1: runApp reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$autoQC03-DIA-ui 1: runApp nFacets: 4 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 364 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 216 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-08 11:10:51.46472 | timeMax: 2024-11-07 11:10:51.46565 | timeDiff: 5184000.00092983 nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-08 11:10:51.465 | timeMax: 2024-11-07 11:10:51.466 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw NA p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw nrow dataFiltered(): 216 using 'ggh4x' package ... NA p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw nrow dataFiltered(): 342 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 338 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... NA nrow dataFiltered(): 216 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_1/pgehrig_20241008_autoQC/20241011_05_autoQC03dia_flex.raw nFacets: 0 nrow dataFiltered(): 0 nFacets: 1 nrow dataFiltered(): 54 using 'ggh4x' package ... nrow dataFiltered(): 54 using 'ggh4x' package ... Warning: Error in graphics::plot.new: figure margins too large 104: graphics::plot.new 101: startPNG 100: plotPNG 99: resizeSavedPlot 97: func 95: f 94: Reduce 85: do 84: hybrid_chain 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 336 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 336 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values or values outside the scale range (`geom_point()`). NA nFacets: 4 nrow dataFiltered(): 1072 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_point()`). nFacets: 1 Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 288 using 'ggh4x' package ... nrow dataFiltered(): 208 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/spfammatter_20241029/20241029_007_autoQC03dda.raw nrow dataFiltered(): 288 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/roschi_20241031/20241021_004_autoQC03dia.raw NA nrow dataFiltered(): 288 using 'ggh4x' package ... nrow dataFiltered(): 288 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/roschi_20241031/20241021_004_autoQC03dia.raw p3000/Proteomics/EXPLORIS_1/lkunz_20240930/20240930_003_autoQC03dia.raw nFacets: 1 nrow dataFiltered(): 143 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 360 using 'ggh4x' package ... NA p36765/Proteomics/EXPLORIS_2/analytic_20241105/20241105_C36765_025_autoQC03dia.raw NA p36765/Proteomics/EXPLORIS_2/analytic_20241105/20241105_C36765_025_autoQC03dia.raw p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_003_autoQC03dia.raw NA nFacets: 1 nrow dataFiltered(): 299 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 0 nrow dataFiltered(): 0 p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_005_autoQC03dda.raw nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... NA p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw p36513/Proteomics/FUSION_2/josephinekempis_20241031/20241031_004_autoQC03dda.raw p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241104_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA nFacets: 0 nrow dataFiltered(): 0 nFacets: 1 nrow dataFiltered(): 0 Warning: Error in graphics::plot.new: figure margins too large 104: graphics::plot.new 101: startPNG 100: plotPNG 99: resizeSavedPlot 97: func 95: f 94: Reduce 85: do 84: hybrid_chain 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp Warning: Error in graphics::plot.new: figure margins too large 104: graphics::plot.new 101: startPNG 100: plotPNG 99: resizeSavedPlot 97: func 95: f 94: Reduce 85: do 84: hybrid_chain 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 4 Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw NA p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw NA p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw NA nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 364 using 'ggh4x' package ... p36752/Proteomics/FUSION_2/analytic_20241101/20241031_C36752_005_autoQC03dda.raw NA nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... nrow dataFiltered(): 342 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 13:23:42.276523 | timeMax: 2024-11-07 12:23:42.277448 | timeDiff: 5184000.00092459 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 11:23:42.277 | timeMax: 2024-11-07 11:23:42.277 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1296 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730977847878327000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1092 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 342 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 342 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw nrow dataFiltered(): 342 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 364 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw p26109/Proteomics/FUSION_2/roschi_20241105_Noemi_training/20241105_018_autoQC03dia.raw NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730482215746929000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730978616513988000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Execution halted Warning messages: 1: agg could not write to the given file 2: agg could not write to the given file 3: agg could not write to the given file 4: agg could not write to the given file 5: agg could not write to the given file