Listening on http://127.0.0.1:43091 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 Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 07:53:20.026722 | timeMax: 2024-03-14 07:53:20.027311 | timeDiff: 5184000.00058842 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 06:53:20.027 | timeMax: 2024-03-14 06:53:20.027 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 07:55:19.563774 | timeMax: 2024-03-14 07:55:19.56435 | timeDiff: 5184000.00057626 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2024-01-14 06:55:19.564 | timeMax: 2024-03-14 06:55:19.564 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1824 using 'ggh4x' package ... Warning: Removed 45 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX wide nrow: 262977 autoQC01 module APEX long nrow: 1368 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 66 rows containing missing values (`geom_point()`). NA p34501/Proteomics/QEXACTIVE_1/analytic_20240313/20240313_C34501_001_autoQC01.raw p34558/Proteomics/QEXACTIVE_1/analytic_20240313/20240313_C34558_001_autoQC01.raw p34501/Proteomics/QEXACTIVE_1/analytic_20240313/20240313_C34501_001_autoQC01.raw 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(): 0 nrow dataFiltered(): 455 using 'ggh4x' package ... p34570/Proteomics/QEXACTIVE_1/analytic_20240312/20240312_C34570_007_autoQC03dda.raw NA p34570/Proteomics/QEXACTIVE_1/analytic_20240312/20240312_C34570_007_autoQC03dda.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710399196185686000.json': No such file or directory 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 dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 09:21:39.294423 | timeMax: 2024-03-14 09:21:39.294989 | timeDiff: 5184000.00056577 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 08:21:39.294 | timeMax: 2024-03-14 08:21:39.295 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). vals$rawrr: TRUE vals$rawDiag: TRUE p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw NA p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_001_autoQC01.raw vals$rawDiag: FALSE vals$rawrr: FALSE NA p33997/Proteomics/EXPLORIS_1/analytic_20240207/20240207_C33997_001_autoQC01.raw NA nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 22 rows containing missing values (`geom_point()`). nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 33 rows containing missing values (`geom_point()`). nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 22 rows containing missing values (`geom_point()`). nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). p34263/Proteomics/EXPLORIS_1/analytic_20240215/20240215_C34263_001_autoQC01.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:17:44.556093 | timeMax: 2024-03-14 10:17:44.556717 | timeDiff: 5184000.0006237 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:17:44.556 | timeMax: 2024-03-14 09:17:44.557 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). 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(): 486 using 'ggh4x' package ... nrow dataFiltered(): 260 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710407861497150000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp vals$rawDiag: TRUE Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:26:01.580992 | timeMax: 2024-03-14 10:26:01.581566 | timeDiff: 5184000.00057316 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:26:01.581 | timeMax: 2024-03-14 09:26:01.582 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). vals$rawDiag: TRUE p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710404496024564000.json': No such file or directory 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 plotClick: fn has changed to /srv/www/htdocs//p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw plotChargeState Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-rawDiag-autoQC03-plot 1: runApp reading index for 20240312_011_autoQC01.raw... NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw Plotting chromatograms ... Read 22032 items p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_006_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_006_autoQC01.raw Reading raw file: /srv/www/htdocs//p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_006_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases reading index for 20240312_006_autoQC01.raw... NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:35:18.719141 | timeMax: 2024-03-14 10:35:18.719712 | timeDiff: 5184000.00057125 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:35:18.719 | timeMax: 2024-03-14 09:35:18.72 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). NA p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710408358524851000.json': No such file or directory 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 dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:35:49.421944 | timeMax: 2024-03-14 10:35:49.422524 | timeDiff: 5184000.00058007 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:35:49.422 | timeMax: 2024-03-14 09:35:49.423 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710408915420342000.json': No such file or directory 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 dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:36:50.533246 | timeMax: 2024-03-14 10:36:50.533825 | timeDiff: 5184000.00057912 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:36:50.533 | timeMax: 2024-03-14 09:36:50.534 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710408946340597000.json': No such file or directory 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 dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:38:48.678801 | timeMax: 2024-03-14 10:38:48.679385 | timeDiff: 5184000.00058389 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:38:48.679 | timeMax: 2024-03-14 09:38:48.679 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710409007451498000.json': No such file or directory 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 dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:39:17.826024 | timeMax: 2024-03-14 10:39:17.826618 | timeDiff: 5184000.00059366 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:39:17.826 | timeMax: 2024-03-14 09:39:17.827 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 800 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). NA p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_006_autoQC01.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710409125310539000.json': No such file or directory 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 p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw NA p3000/Proteomics/EXPLORIS_1/lkunz_20240304/20240304_001_autoQC01.raw p24073/Proteomics/EXPLORIS_1/wilkin_20240312_20240312_swBOOZE_TUBI/20240312_011_autoQC01.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-14 10:41:27.990718 | timeMax: 2024-03-14 10:41:27.991329 | timeDiff: 5184000.00061083 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 816 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-14 09:41:27.991 | timeMax: 2024-03-14 09:41:27.991 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 816 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). p30646/Proteomics/EXPLORIS_1/gnarduzzi_20240313/20240313_001_autoQC01.raw vals$rawrr: TRUE vals$rawDiag: TRUE plotClick: fn has changed to /srv/www/htdocs//p30646/Proteomics/EXPLORIS_1/gnarduzzi_20240313/20240313_001_autoQC01.raw plotChargeState Reading raw file: /srv/www/htdocs//p30646/Proteomics/EXPLORIS_1/gnarduzzi_20240313/20240313_001_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-rawDiag-autoQC03-plot 1: runApp reading index for 20240313_001_autoQC01.raw... p30646/Proteomics/EXPLORIS_1/gnarduzzi_20240313/20240313_001_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710409154717450000.json': No such file or directory 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 plotInjectionTime plotLockMassCorrection plotMassDistribution plotChargeState Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710409284842786000.json': No such file or directory 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 'logs-qc//shinylogs_fgczqcms-dashboard_1710399316254006000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Execution halted Warning messages: 1: agg could not write to the given file 2: agg could not write to the given file