Listening on http://127.0.0.1:46857 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 15:03:04.311925 | timeMax: 2024-11-07 14:03:04.312517 | timeDiff: 5184000.00059199 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 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$__autoQC01__-plot 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 15:03:09.10905 | timeMax: 2024-11-07 14:03:09.109638 | timeDiff: 5184000.00058842 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 13:03:04.312 | timeMax: 2024-11-07 13:03:04.313 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1184 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 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 ... nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 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$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 13:03:09.109 | timeMax: 2024-11-07 13:03:09.11 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1184 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). NA nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_002_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.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_1730984585233827000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 17:14:42.80088 | timeMax: 2024-11-07 16:14:42.801676 | timeDiff: 5184000.00079536 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1072 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$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-08 15:14:42.801 | timeMax: 2024-11-07 15:14:42.802 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1072 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1072 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_point()`). p25334/Proteomics/EXPLORIS_1/dlesli_20241030_SuSu155/20241101_029_autoQC01.raw 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(): 221 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 288 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 288 using 'ggh4x' package ... nrow dataFiltered(): 221 using 'ggh4x' package ... NA p3000/Proteomics/EXPLORIS_1/antdit_20241107/20241107_003_autoQC03dda.raw nrow dataFiltered(): 221 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 221 using 'ggh4x' package ... NA p3000/Proteomics/EXPLORIS_1/antdit_20241107/20241107_003_autoQC03dda.raw input timeRange: 7776000 | timeMin: 2024-08-09 15:14:56.07046 | timeMax: 2024-11-07 15:14:42.802 | timeDiff: 7775986.7315402 nFacets: 1 nrow dataFiltered(): 403 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-08-09 18:15:21.802974 | timeMax: 2024-11-07 15:14:42.802 | timeDiff: 7772360.99902582 nFacets: 1 nrow dataFiltered(): 403 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 403 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-08-09 16:15:21.803 | timeMax: 2024-11-07 15:14:42.802 | timeDiff: 7772360.99900007 nFacets: 1 nrow dataFiltered(): 403 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-08-09 16:15:21.803 | timeMax: 2024-11-07 16:15:24.314064 | timeDiff: 7772402.51106429 nFacets: 1 nrow dataFiltered(): 403 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 403 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-08-09 16:15:21.803 | timeMax: 2024-11-07 15:15:24.314 | timeDiff: 7772402.51099992 nrow dataFiltered(): 403 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 1248 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$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 846 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-02-27 15:15:25.828 | timeMax: 2024-11-07 15:15:24.314 | timeDiff: 21945598.4859998 nrow dataFiltered(): 1248 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1287 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 900 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-02-17 15:15:25.828 | timeMax: 2024-11-07 15:15:24.314 | timeDiff: 22809598.4859998 nFacets: 1 nrow dataFiltered(): 1677 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1062 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-15 15:15:33.927 | timeMax: 2024-11-07 15:15:24.314 | timeDiff: 30931190.3869998 nrow dataFiltered(): 1677 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 1677 using 'ggh4x' package ... NA p33354/Proteomics/EXPLORIS_1/tomasfranziska_20240422/20240422_033_autoQC03dda.raw p34853/Proteomics/EXPLORIS_1/tobiasko_20240409_ubiProbes/20240409_017_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_1/lkunz_20241007/20241007_002_autoQC03dda.raw p3000/Proteomics/EXPLORIS_1/lkunz_20240930/20240930_002_autoQC03dda.raw p3000/Proteomics/EXPLORIS_1/lkunz_20240923/20240923_002_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_1/lkunz_20240930/20240930_002_autoQC03dda.raw NA nrow dataFiltered(): 1062 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 1062 using 'ggh4x' package ... p23412/Proteomics/EXPLORIS_1/gillet_20240416/20240416_013_autoQC03dia.raw NA nFacets: 1 nrow dataFiltered(): 1495 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 2160 using 'ggh4x' package ... nrow dataFiltered(): 2160 using 'ggh4x' package ... nrow dataFiltered(): 1495 using 'ggh4x' package ... nrow dataFiltered(): 1495 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 1495 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/lkunz_20241104/20241104_002_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_2/analytic_20240617/20240617_004_autoQC03dda.raw p3000/Proteomics/EXPLORIS_2/analytic_20240716/20240716_003_autoQC03dda.raw p36084/Proteomics/EXPLORIS_2/analytic_20240910/20240910_C36084_015_autoQC03dda.raw NA nFacets: 1 nrow dataFiltered(): 1677 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1062 using 'ggh4x' package ... nrow dataFiltered(): 1677 using 'ggh4x' package ... nrow dataFiltered(): 1677 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 1677 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730992478347626000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-09 09:11:20.409243 | timeMax: 2024-11-08 08:11:20.40985 | timeDiff: 5184000.00060654 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$rawDiag: FALSE nrow dataFiltered(): 1184 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-09 07:11:20.409 | timeMax: 2024-11-08 07:11:20.41 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731049876871759000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-09 13:11:52.834662 | timeMax: 2024-11-08 12:11:52.835295 | timeDiff: 5184000.000633 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-09 11:11:52.835 | timeMax: 2024-11-08 11:11:52.835 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw NA Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1092 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 1092 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw NA p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw vals$rawrr: TRUE NA p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw Plotting chromatograms ... Read 22032 items NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. Plotting .missing() ... Read 22032 items Warning: Error in hist.default: 'x' must be numeric 171: stop 170: hist.default 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotTools 1: runApp plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. Plotting .missing() ... Read 22032 items Warning: Error in hist.default: 'x' must be numeric 171: stop 170: hist.default 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotTools 1: runApp NA plotClick: plotClick: p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_004_autoQC03dia.raw p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw plotClick: plotClick: Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw Plotting chromatograms ... Read 22032 items NA p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw NA p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_autoQC03dia.raw plotClick: NA p3000/Proteomics/LUMOS_2/roschi_20241108/20241108_002_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_1731064309188660000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-09 15:01:17.545842 | timeMax: 2024-11-08 14:01:17.54658 | timeDiff: 5184000.00073814 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 768 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 768 using 'ggh4x' package ... Warning: Removed 37 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_line()`). input timeRange: 7776000 | timeMin: 2024-09-09 13:01:17.546 | timeMax: 2024-11-08 13:01:17.547 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 768 using 'ggh4x' package ... Warning: Removed 37 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_line()`). NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw NA Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 312 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 0 nrow dataFiltered(): 0 nrow dataFiltered(): 312 using 'ggh4x' package ... p36785/Proteomics/QEXACTIVE_1/analytic_20241107/20241107_C36785_011_autoQC03dda.raw NA p36785/Proteomics/QEXACTIVE_1/analytic_20241107/20241107_C36785_011_autoQC03dda.raw nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) autoQC01 module APEX wide nrow: 282612 autoQC01 module APEX long nrow: 0 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 autoQC01 module APEX long nrow: 888 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 p36764/Proteomics/EXPLORIS_2/analytic_20241106/20241106_C36764_001_autoQC01.raw p36765/Proteomics/EXPLORIS_2/analytic_20241105/20241105_C36765_024_autoQC01.raw NA p36764/Proteomics/EXPLORIS_2/analytic_20241106/20241106_C36764_001_autoQC01.raw nFacets: 4 nrow dataFiltered(): 1040 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_point()`). NA p25334/Proteomics/EXPLORIS_1/dlesli_20241030_SuSu155/20241101_029_autoQC01.raw p25334/Proteomics/EXPLORIS_1/dlesli_20241030_SuSu155/20241101_001_autoQC01.raw p25334/Proteomics/EXPLORIS_1/dlesli_20241030_SuSu155/20241101_029_autoQC01.raw nFacets: 4 nrow dataFiltered(): 768 using 'ggh4x' package ... Warning: Removed 37 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_line()`). NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_001_autoQC01.raw p36735/Proteomics/QEXACTIVE_1/analytic_20241030/20241030_C36735_063_autoQC01.raw p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-09 15:21:04.157076 | timeMax: 2024-11-08 14:21:04.157691 | timeDiff: 5184000.00061512 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-09 13:21:04.157 | timeMax: 2024-11-08 13:21:04.158 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731072060627830000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning: Error in if: missing value where TRUE/FALSE needed 1: runApp input timeRange: 1209600 | timeMin: 2024-11-01 14:56:50.9827 | timeMax: 2024-11-08 14:56:50.982751 | timeDiff: 604800.00005126 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731074210976987000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-10 09:37:21.163187 | timeMax: 2024-11-09 08:37:21.163764 | timeDiff: 5184000.00057721 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 221 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 306 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 306 using 'ggh4x' package ... nrow dataFiltered(): 221 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-10 07:37:21.16319 | timeMax: 2024-11-09 07:37:21.16376 | timeDiff: 5184000.00057006 nFacets: 1 nrow dataFiltered(): 221 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-10 07:37:21.163 | timeMax: 2024-11-09 07:37:21.164 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 221 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning: Error in if: missing value where TRUE/FALSE needed 1: runApp input timeRange: 1209600 | timeMin: 2024-11-02 09:08:05.764705 | timeMax: 2024-11-09 09:08:05.764768 | timeDiff: 604800.000062704 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731139685751811000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-10 10:08:25.193255 | timeMax: 2024-11-09 09:08:25.194723 | timeDiff: 5184000.00146866 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 input timeRange: 7776000 | timeMin: 2024-09-10 08:08:25.193 | timeMax: 2024-11-09 08:08:25.195 | timeDiff: 5184000.00199986 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p3000/Proteomics/LUMOS_2/cfortes_20241104_autoQC/20241104_002_autoQC01.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.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_1731139696880119000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-11 18:02:59.07114 | timeMax: 2024-11-10 17:02:59.071741 | timeDiff: 5184000.00060105 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 752 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 752 using 'ggh4x' package ... Warning: Removed 36 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 3 rows containing missing values or values outside the scale range (`geom_line()`). input timeRange: 7776000 | timeMin: 2024-09-11 16:02:59.071 | timeMax: 2024-11-10 16:02:59.072 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 752 using 'ggh4x' package ... Warning: Removed 36 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 3 rows containing missing values or values outside the scale range (`geom_line()`). NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 325 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 0 nrow dataFiltered(): 0 nrow dataFiltered(): 325 using 'ggh4x' package ... NA p36853/Proteomics/QEXACTIVE_1/analytic_20241108/20241108_C36853_009_autoQC03dda.raw NA Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) autoQC01 module APEX wide nrow: 282612 autoQC01 module APEX long nrow: 0 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 autoQC01 module APEX long nrow: 564 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 34 rows containing missing values or values outside the scale range (`geom_point()`). p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw NA p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731254575614622000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 09:13:34.021503 | timeMax: 2024-11-11 08:13:34.022074 | timeDiff: 5184000.00057125 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1088 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1088 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-12 07:13:34.022 | timeMax: 2024-11-11 07:13:34.022 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1088 using 'ggh4x' package ... NA fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 10:25:03.043541 | timeMax: 2024-11-11 09:25:03.044114 | timeDiff: 5184000.00057316 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 130 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$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$autoQC03-DIA-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 08:25:03.04354 | timeMax: 2024-11-11 08:25:03.04411 | timeDiff: 5184000.00057006 nFacets: 1 nrow dataFiltered(): 130 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 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$autoQC03-DIA-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 08:25:03.044 | timeMax: 2024-11-11 08:25:03.044 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 130 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 130 using 'ggh4x' package ... NA nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1088 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1088 using 'ggh4x' package ... NA nFacets: 4 nrow dataFiltered(): 272 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_006_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241105_005_autoQC01.raw nFacets: 4 nrow dataFiltered(): 1088 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 130 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... p36834/Proteomics/EXPLORIS_2/fottner_20241108/20241108_007_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p36834/Proteomics/EXPLORIS_2/fottner_20241108/20241108_007_autoQC03dia.raw NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731313499577801000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 11:37:08.244608 | timeMax: 2024-11-11 10:37:08.245185 | timeDiff: 5184000.0005765 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-12 09:37:08.245 | timeMax: 2024-11-11 09:37:08.245 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731317824749373000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731309210566101000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731137837683436000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 17:45:13.094506 | timeMax: 2024-11-11 16:45:13.095087 | timeDiff: 5184000.00058103 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$rawDiag: FALSE nrow dataFiltered(): 256 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 15:45:13.095 | timeMax: 2024-11-11 15:45:13.095 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 256 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 256 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 17:45:17.880111 | timeMax: 2024-11-11 16:45:17.880688 | timeDiff: 5184000.00057745 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$rawDiag: FALSE nrow dataFiltered(): 256 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-12 15:45:17.88 | timeMax: 2024-11-11 15:45:17.881 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1152 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2024-09-12 15:45:17.88 | timeMax: 2024-11-11 16:45:35.796275 | timeDiff: 5184017.91627526 nFacets: 4 nrow dataFiltered(): 1152 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2024-09-12 15:45:17.88 | timeMax: 2024-11-11 15:45:35.796 | timeDiff: 5184017.91599989 nFacets: 4 nrow dataFiltered(): 1152 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:36.96702 | timeMax: 2024-11-11 15:45:35.796 | timeDiff: 63071998.82898 nFacets: 4 nrow dataFiltered(): 17200 using 'ggh4x' package ... Warning: Removed 110 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:40.369153 | timeMax: 2024-11-11 15:45:35.796 | timeDiff: 63071995.426847 nFacets: 4 nrow dataFiltered(): 15632 using 'ggh4x' package ... Warning: Removed 109 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:36.96702 | timeMax: 2024-08-22 15:45:36.967 | timeDiff: 56073599.99998 nFacets: 4 nrow dataFiltered(): 15632 using 'ggh4x' package ... Warning: Removed 109 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:42.557112 | timeMax: 2024-08-22 15:45:36.967 | timeDiff: 56073594.4098883 nFacets: 4 nrow dataFiltered(): 15632 using 'ggh4x' package ... Warning: Removed 109 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:42.557 | timeMax: 2024-08-22 15:45:36.967 | timeDiff: 56073594.4100001 nFacets: 4 nrow dataFiltered(): 15632 using 'ggh4x' package ... Warning: Removed 109 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:44.459265 | timeMax: 2024-08-22 15:45:36.967 | timeDiff: 56073592.507735 nFacets: 4 nrow dataFiltered(): 11792 using 'ggh4x' package ... Warning: Removed 102 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:42.557 | timeMax: 2024-03-26 15:45:42.181 | timeDiff: 43199999.6240001 nFacets: 4 nrow dataFiltered(): 11792 using 'ggh4x' package ... Warning: Removed 102 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:46.826326 | timeMax: 2024-03-26 15:45:42.181 | timeDiff: 43199995.3546743 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:44.459 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004799.8879998 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:48.869487 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004795.4775126 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:48.869 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004795.4779999 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:50.680415 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004793.6665852 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:50.68 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004793.6669998 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:52.522535 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004791.824465 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:52.523 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004791.8239999 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:54.346983 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004790.0000165 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:54.347 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004790 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:56.224968 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004788.1220315 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:45:56.225 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004788.122 nFacets: 4 nrow dataFiltered(): 8992 using 'ggh4x' package ... Warning: Removed 81 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:45:58.096315 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004786.2506847 Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 3 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(): 3380 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 144 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 3380 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 15:45:58.09632 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004786.2506797 nFacets: 3 nrow dataFiltered(): 3380 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 17:45:59.419079 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33001184.9279208 nFacets: 3 nrow dataFiltered(): 3380 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 15:45:58.096 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33004786.2509999 nFacets: 3 nrow dataFiltered(): 3380 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 17:46:00.644849 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33001183.7021506 nFacets: 3 nrow dataFiltered(): 3380 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 16:46:00.645 | timeMax: 2023-11-29 15:45:44.347 | timeDiff: 33001183.7019999 nFacets: 3 nrow dataFiltered(): 3380 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2024-09-12 15:45:13.095 | timeMax: 2024-11-11 16:46:05.7048 | timeDiff: 5184052.6098001 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2024-09-12 15:45:13.095 | timeMax: 2024-11-11 15:46:05.705 | timeDiff: 5184052.6099999 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 15:46:06.87307 | timeMax: 2024-11-11 15:46:05.705 | timeDiff: 63071998.8319299 nFacets: 4 nrow dataFiltered(): 16256 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:46:09.809277 | timeMax: 2024-11-11 15:46:05.705 | timeDiff: 63071995.8957229 nFacets: 4 nrow dataFiltered(): 16256 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:46:09.809 | timeMax: 2024-11-11 15:46:05.705 | timeDiff: 63071995.8959999 nFacets: 4 nrow dataFiltered(): 16256 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:46:11.801501 | timeMax: 2024-11-11 15:46:05.705 | timeDiff: 63071993.9034989 nFacets: 4 nrow dataFiltered(): 9488 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:46:09.809 | timeMax: 2023-11-19 15:46:09.494 | timeDiff: 32140799.6849999 nFacets: 4 nrow dataFiltered(): 9488 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:46:13.939762 | timeMax: 2023-11-19 15:46:09.494 | timeDiff: 32140795.5542383 nFacets: 4 nrow dataFiltered(): 9488 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 15:46:13.94 | timeMax: 2023-11-19 15:46:09.494 | timeDiff: 32140795.5539999 nFacets: 4 nrow dataFiltered(): 9488 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-12 16:46:15.870114 | timeMax: 2023-11-19 15:46:09.494 | timeDiff: 32140793.6238859 nFacets: 4 nrow dataFiltered(): 16000 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-26 15:46:13.567 | timeMax: 2024-11-11 15:46:13.56728 | timeDiff: 61862400.0002801 nFacets: 4 nrow dataFiltered(): 16000 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 63072000 | timeMin: 2022-11-26 15:46:13.567 | timeMax: 2024-11-11 15:46:13.567 | timeDiff: 61862400 Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 5 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(): 11089 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 1476 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 1476 using 'ggh4x' package ... nrow dataFiltered(): 11089 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? input timeRange: 63072000 | timeMin: 2022-11-12 15:46:19.52853 | timeMax: 2024-11-11 15:46:13.567 | timeDiff: 63071994.0384698 nFacets: 5 nrow dataFiltered(): 11297 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 17:46:22.695388 | timeMax: 2024-11-11 15:46:13.567 | timeDiff: 63068390.8716118 nFacets: 5 nrow dataFiltered(): 11297 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 16:46:22.695 | timeMax: 2024-11-11 15:46:13.567 | timeDiff: 63068390.872 nFacets: 5 nrow dataFiltered(): 11297 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 63072000 | timeMin: 2022-11-12 16:46:22.695 | timeMax: 2023-11-25 15:46:25.045 | timeDiff: 32655602.3500001 nFacets: 5 nrow dataFiltered(): 7475 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 72 using 'ggh4x' package ... NA p32987/Proteomics/LUMOS_2/vismi_20231006/20231006_006_autoQC4L.raw NA NA p3000/Proteomics/LUMOS_1/pgehrig_20220311_RapiFluor/20230125_16_autoQC4L.raw p30484/Proteomics/LUMOS_1/analytic_20230127/20230127_C30484_013_autoQC4L.raw NA p30640/Proteomics/LUMOS_1/analytic_20230131/20230131_C30640_005_autoQC4L.raw NA p29369/Proteomics/LUMOS_1/moslu_20231030_20231030_pretrial/20231030_013_autoQC4L.raw NA NA p3000/Proteomics/LUMOS_1/pgehrig_20240422_autoQC/20240711_05_autoQC03dda.raw 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 17:51:45.531891 | timeMax: 2024-11-11 16:51:45.532486 | timeDiff: 5184000.00059533 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 256 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(): 256 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-12 15:51:45.532 | timeMax: 2024-11-11 15:51:45.532 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-09-12 15:51:45.532 | timeMax: 2024-11-11 16:51:50.109502 | timeDiff: 5184004.57750154 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2024-09-12 15:51:45.532 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 5184004.57799983 nFacets: 4 nrow dataFiltered(): 256 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 15:51:51.2377 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535998.8722999 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 16:51:55.402301 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535994.7076991 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 15:51:55.402 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535994.7079999 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 16:51:57.230101 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535992.8798988 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 15:51:57.23 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535992.8799999 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 16:51:59.008748 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535991.1012518 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 15:51:59.009 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535991.1009998 nFacets: 4 nrow dataFiltered(): 6896 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2023-11-12 16:52:00.78056 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535989.3294404 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$rawDiag: FALSE nrow dataFiltered(): 3926 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 1476 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 1476 using 'ggh4x' package ... nrow dataFiltered(): 3926 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 15:52:00.78056 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535989.3294399 nFacets: 4 nrow dataFiltered(): 3926 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 17:52:02.267322 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31532387.8426781 nFacets: 4 nrow dataFiltered(): 3926 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 15:52:00.781 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31535989.329 nFacets: 4 nrow dataFiltered(): 3926 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 17:52:03.665814 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31532386.4441862 nFacets: 4 nrow dataFiltered(): 3926 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 16:52:03.666 | timeMax: 2024-11-11 15:51:50.11 | timeDiff: 31532386.444 nFacets: 4 nrow dataFiltered(): 3926 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1476 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-12 17:52:09.706511 | timeMax: 2024-11-11 16:52:09.707114 | timeDiff: 5184000.00060368 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$rawDiag: FALSE nrow dataFiltered(): 1184 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-12 15:52:09.707 | timeMax: 2024-11-11 15:52:09.707 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2024-09-12 15:52:09.707 | timeMax: 2024-11-11 16:52:16.448484 | timeDiff: 5184006.74148417 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 31536000 | timeMin: 2024-09-12 15:52:09.707 | timeMax: 2024-11-11 15:52:16.448 | timeDiff: 5184006.74099994 nFacets: 4 nrow dataFiltered(): 1184 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 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1014 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(): 1014 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 15:52:18.71166 | timeMax: 2024-11-11 15:52:16.448 | timeDiff: 31535997.73634 nFacets: 5 nrow dataFiltered(): 3523 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1800 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 17:52:22.324885 | timeMax: 2024-11-11 15:52:16.448 | timeDiff: 31532394.1231148 nFacets: 5 nrow dataFiltered(): 3523 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1800 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-11-12 16:52:22.325 | timeMax: 2024-11-11 15:52:16.448 | timeDiff: 31532394.1229999 nFacets: 5 nrow dataFiltered(): 3523 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1800 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731340326232910000.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_1731339914457321000.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_1731339909624721000.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_1731340302076702000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-13 09:53:16.896159 | timeMax: 2024-11-12 08:53:16.896743 | timeDiff: 5184000.00058365 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__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: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 195 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 306 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 306 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-13 07:53:16.89616 | timeMax: 2024-11-12 07:53:16.89674 | timeDiff: 5184000.00058007 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-13 07:53:16.896 | timeMax: 2024-11-12 07:53:16.897 | timeDiff: 5184000.00100017 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... nrow dataFiltered(): 195 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 195 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_003_autoQC03dda.raw p36678/Proteomics/EXPLORIS_1/analytic_20241108/20241108_C36678_011_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241107/20241107_003_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_003_autoQC03dda.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_004_autoQC03dia.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_004_autoQC03dia.raw NA nrow dataFiltered(): 306 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 306 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_004_autoQC03dia.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241107/20241107_004_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_1731397993433586000.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$__autoQC01__-ui 1: runApp Warning: Error in if: missing value where TRUE/FALSE needed 1: runApp input timeRange: 1209600 | timeMin: 2024-11-05 09:30:46.312834 | timeMax: 2024-11-12 09:30:46.312879 | timeDiff: 604800.000044584 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__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_1731400246307517000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-13 15:38:31.839189 | timeMax: 2024-11-12 14:38:31.83978 | timeDiff: 5184000.00059056 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1136 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$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-13 13:38:31.839 | timeMax: 2024-11-12 13:38:31.84 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1136 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1136 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_013_autoQC01.raw 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(): 1040 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(): 1040 using 'ggh4x' package ... vals$rawrr: TRUE p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw plotClick: Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731418708332778000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-13 16:11:54.464751 | timeMax: 2024-11-12 15:11:54.465456 | timeDiff: 5184000.00070453 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$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(): 378 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 378 using 'ggh4x' package ... nrow dataFiltered(): 143 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-13 14:11:54.46475 | timeMax: 2024-11-12 14:11:54.46546 | timeDiff: 5184000.00071001 nFacets: 1 nrow dataFiltered(): 143 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 378 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-13 14:11:54.465 | timeMax: 2024-11-12 14:11:54.465 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 143 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 378 using 'ggh4x' package ... NA nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1072 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1072 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_point()`). vals$rawrr: TRUE NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_001_autoQC01.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_002_autoQC01.raw p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_001_autoQC01.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_004_autoQC03dia.raw NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731420710947022000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 09:15:00.774917 | timeMax: 2024-11-13 08:15:00.775508 | timeDiff: 5184000.00059175 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$rawDiag: FALSE nrow dataFiltered(): 688 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 688 using 'ggh4x' package ... Warning: Removed 36 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 12 rows containing missing values or values outside the scale range (`geom_line()`). input timeRange: 7776000 | timeMin: 2024-09-14 07:15:00.775 | timeMax: 2024-11-13 07:15:00.776 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 688 using 'ggh4x' package ... Warning: Removed 36 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 12 rows containing missing values or values outside the scale range (`geom_line()`). p36853/Proteomics/QEXACTIVE_1/analytic_20241108/20241108_C36853_008_autoQC01.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731070873531643000.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 p36811/Proteomics/QEXACTIVE_1/analytic_20241105/20241105_C36811_004_autoQC01.raw 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(): 273 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 0 nrow dataFiltered(): 0 nrow dataFiltered(): 273 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 09:29:02.552735 | timeMax: 2024-11-13 08:29:02.553766 | timeDiff: 5184000.00103021 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$rawDiag: FALSE nrow dataFiltered(): 1136 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 07:29:02.553 | timeMax: 2024-11-13 07:29:02.554 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1136 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1136 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 10:48:07.121404 | timeMax: 2024-11-13 09:48:07.122345 | timeDiff: 5184000.00094128 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$rawDiag: FALSE nrow dataFiltered(): 1040 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$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$autoQC03-DIA-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 08:48:07.1214 | timeMax: 2024-11-13 08:48:07.12235 | timeDiff: 5184000.00095034 nFacets: 4 nrow dataFiltered(): 1040 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 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$autoQC03-DIA-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 08:48:07.121 | timeMax: 2024-11-13 08:48:07.122 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1040 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 1040 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1730984579774618000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731482936015844000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731487680231326000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-14 15:19:51.714154 | timeMax: 2024-11-13 14:19:51.714737 | timeDiff: 5184000.00058222 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$rawDiag: FALSE nrow dataFiltered(): 1136 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1136 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-14 13:19:51.714 | timeMax: 2024-11-13 13:19:51.715 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1136 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1088 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). vals$rawrr: TRUE p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. NA plotClick: fn has changed to /srv/www/htdocs//p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_002_autoQC01.raw p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_002_autoQC01.raw Reading raw file: /srv/www/htdocs//p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_002_autoQC01.raw Plotting chromatograms ... Read 22032 items plotClick: Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731503988264072000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 09:10:20.571431 | timeMax: 2024-11-14 08:10:20.572014 | timeDiff: 5184000.00058222 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 156 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 396 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 396 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 07:10:20.57143 | timeMax: 2024-11-14 07:10:20.57201 | timeDiff: 5184000.00058007 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 396 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 07:10:20.571 | timeMax: 2024-11-14 07:10:20.572 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 396 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 09:31:12.014268 | timeMax: 2024-11-14 08:31:12.014856 | timeDiff: 5184000.0005877 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731569468566165000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 09:55:41.535529 | timeMax: 2024-11-14 08:55:41.536118 | timeDiff: 5184000.00058842 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 195 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 324 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 324 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 07:55:41.53553 | timeMax: 2024-11-14 07:55:41.53612 | timeDiff: 5184000.00059009 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 324 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 07:55:41.536 | timeMax: 2024-11-14 07:55:41.536 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 324 using 'ggh4x' package ... NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_026_autoQC03dda.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731570938048596000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 14:09:37.913083 | timeMax: 2024-11-14 13:09:37.914446 | timeDiff: 5184000.00136304 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$rawDiag: FALSE nrow dataFiltered(): 1136 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 12:09:37.913 | timeMax: 2024-11-14 12:09:37.914 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1136 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1136 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 240 using 'ggh4x' package ... NA vals$rawrr: TRUE p3000/Proteomics/LUMOS_1/pgehrig_20241008_autoQC/20241011_06_autoQC01_flex.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731586171566040000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 17:26:48.612565 | timeMax: 2024-11-14 16:26:48.613791 | timeDiff: 5184000.00122643 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1072 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1072 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-15 15:26:48.613 | timeMax: 2024-11-14 15:26:48.614 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1072 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_004_autoQC01.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_004_autoQC01.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_004_autoQC01.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_004_autoQC01.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_001_autoQC01.raw NA Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 416 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 198 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 198 using 'ggh4x' package ... nrow dataFiltered(): 416 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-15 17:57:09.847116 | timeMax: 2024-11-14 16:57:09.847704 | timeDiff: 5184000.00058866 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 156 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 396 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 396 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 15:57:09.84712 | timeMax: 2024-11-14 15:57:09.8477 | timeDiff: 5184000.00057983 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 396 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-15 15:57:09.847 | timeMax: 2024-11-14 15:57:09.848 | timeDiff: 5184000.00100017 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 396 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 324 using 'ggh4x' package ... vals$rawrr: TRUE p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw NA p3000/Proteomics/EXPLORIS_1/antdit_20241111/20241111_004_autoQC03dia.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_026_autoQC03dda.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_026_autoQC03dda.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw NA p25334/Proteomics/EXPLORIS_1/dlesli_20241112_SuSu155/20241112_027_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731599826289957000.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 NA nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 360 using 'ggh4x' package ... p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA p3000/Proteomics/LUMOS_2/cfortes_20241105_autoQC/20241104_003_autoQC03dda.raw NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA nFacets: 4 nrow dataFiltered(): 416 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 198 using 'ggh4x' package ... p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_005_autoQC03dda.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_005_autoQC03dda.raw p36873/Proteomics/FUSION_2/adelizliang_20241111/20241111_005_autoQC03dia.raw p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_005_autoQC03dda.raw NA p36908/Proteomics/FUSION_2/adelizliang_20241113/20241113_005_autoQC03dda.raw NA nFacets: 4 nrow dataFiltered(): 338 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 162 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 416 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 198 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731598003816396000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-19 09:58:32.353743 | timeMax: 2024-11-18 08:58:32.35432 | timeDiff: 5184000.00057745 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__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: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 195 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 306 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 306 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-19 07:58:32.35374 | timeMax: 2024-11-18 07:58:32.35432 | timeDiff: 5184000.00058007 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-19 07:58:32.354 | timeMax: 2024-11-18 07:58:32.354 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 306 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731916708937337000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-19 10:27:15.819998 | timeMax: 2024-11-18 09:27:15.820578 | timeDiff: 5184000.00057983 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1152 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1152 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-19 08:27:15.82 | timeMax: 2024-11-18 08:27:15.821 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1152 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1408 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241116_027_autoQC01.raw Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1040 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 324 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 324 using 'ggh4x' package ... nrow dataFiltered(): 1040 using 'ggh4x' package ... p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241108_DLP252/20241111_015_autoQC03dia.raw NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731918432334367000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-19 14:51:42.47641 | timeMax: 2024-11-18 13:51:42.477003 | timeDiff: 5184000.00059319 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 ... input timeRange: 7776000 | timeMin: 2024-09-19 12:51:42.476 | timeMax: 2024-11-18 12:51:42.477 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1408 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_029_autoQC01.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_029_autoQC01.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_029_autoQC01.raw 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(): 1040 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 324 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 324 using 'ggh4x' package ... nrow dataFiltered(): 1040 using 'ggh4x' package ... vals$rawrr: TRUE NA p36862/Proteomics/LUMOS_2/analytic_20241113/20241113_C36862_021_autoQC03dda.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731934299047614000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-19 15:28:39.993851 | timeMax: 2024-11-18 14:28:39.994434 | timeDiff: 5184000.00058293 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$autoQC03-DIA-ui 1: runApp nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 156 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 378 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 378 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-19 13:28:39.99385 | timeMax: 2024-11-18 13:28:39.99443 | timeDiff: 5184000.00057983 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 378 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-09-19 13:28:39.994 | timeMax: 2024-11-18 13:28:39.994 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 378 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 324 using 'ggh4x' package ... NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw NA plotClick: fn has changed to /srv/www/htdocs//NA vals$rawrr: TRUE Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw NA p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw p25334/Proteomics/LUMOS_2/dlesli_20241114_DLP252/20241119_030_autoQC03dda.raw NA plotClick: Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731936516484564000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-20 12:51:55.273887 | timeMax: 2024-11-19 11:51:55.274462 | timeDiff: 5184000.0005753 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 992 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$__autoQC01__-plot 1: runApp nrow dataFiltered(): 992 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-20 10:51:55.274 | timeMax: 2024-11-19 10:51:55.274 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 992 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values or values outside the scale range (`geom_point()`). p36964/Proteomics/FUSION_2/adelizliang_20241119/20241119_001_autoQC01.raw p36964/Proteomics/FUSION_2/adelizliang_20241119/20241119_001_autoQC01.raw p36964/Proteomics/FUSION_2/adelizliang_20241119/20241119_001_autoQC01.raw p36968/Proteomics/FUSION_2/damontruffer_20241118/20241118_001_autoQC01.raw Reading /scratch/DIAQC/qc/dump/comet.RData ... nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 416 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 180 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$autoQC03-DIA-plot 1: runApp nrow dataFiltered(): 180 using 'ggh4x' package ... nrow dataFiltered(): 416 using 'ggh4x' package ... p36907/Proteomics/FUSION_2/aeberle_20241115/20241115_005_autoQC03dda.raw NA p36907/Proteomics/FUSION_2/aeberle_20241115/20241115_005_autoQC03dda.raw fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-20 12:53:55.421386 | timeMax: 2024-11-19 11:53:55.421964 | timeDiff: 5184000.0005784 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$rawDiag: FALSE nrow dataFiltered(): 704 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 704 using 'ggh4x' package ... Warning: Removed 39 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_line()`). input timeRange: 7776000 | timeMin: 2024-09-20 10:53:55.421 | timeMax: 2024-11-19 10:53:55.422 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 704 using 'ggh4x' package ... Warning: Removed 39 rows containing missing values or values outside the scale range (`geom_point()`). Warning: Removed 13 rows containing missing values or values outside the scale range (`geom_line()`). NA 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(): 247 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 0 nrow dataFiltered(): 0 nrow dataFiltered(): 247 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731482097322204000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp p36883/Proteomics/QEXACTIVE_1/analytic_20241115/20241115_C36883_007_autoQC03dda.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1732013631964220000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1731568217108965000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ... nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-09-22 10:00:08.134989 | timeMax: 2024-11-21 09:00:08.135577 | timeDiff: 5184000.00058842 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$rawDiag: FALSE nrow dataFiltered(): 1392 Warning: Error in .ggplot: !is.null(variables) is not TRUE 173: 172: stop 171: stopifnot 170: .ggplot 169: ggplot2FUN 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-plot 1: runApp nrow dataFiltered(): 1392 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-09-22 08:00:08.135 | timeMax: 2024-11-21 08:00:08.136 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1392 using 'ggh4x' package ... Warning: Removed 1 row containing missing values or values outside the scale range (`geom_point()`). p36677/Proteomics/LUMOS_2/analytic_20241120/20241120_C36677_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p36677/Proteomics/LUMOS_2/analytic_20241120/20241120_C36677_001_autoQC01.raw p36677/Proteomics/LUMOS_2/analytic_20241120/20241120_C36677_001_autoQC01.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1732176004632419000.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_1732013511747224000.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