Listening on http://127.0.0.1:34609 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-15 12:04:03.145492 | timeMax: 2024-03-15 12:04:03.146296 | timeDiff: 5184000.00080466 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1376 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... Warning: Removed 5 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-15 11:04:03.145 | timeMax: 2024-03-15 11:04:03.146 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 5 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 5 rows containing missing values (`geom_point()`). 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-15 16:02:05.330648 | timeMax: 2024-03-15 16:02:05.33122 | timeDiff: 5184000.00057173 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1280 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-15 15:02:05.331 | timeMax: 2024-03-15 15:02:05.331 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1280 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_001_autoQC01.raw NA p34551/Proteomics/EXPLORIS_2/analytic_20240313/20240313_C34551_026_autoQC01.raw p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_001_autoQC01.raw NA p34551/Proteomics/EXPLORIS_2/analytic_20240313/20240313_C34551_026_autoQC01.raw p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_001_autoQC01.raw NA p34574/Proteomics/EXPLORIS_2/analytic_20240313/20240313_C34574_001_autoQC01.raw NA 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(): 522 using 'ggh4x' package ... nrow dataFiltered(): 273 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_002_autoQC03dda.raw nrow dataFiltered(): 273 using 'ggh4x' package ... NA p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_002_autoQC03dda.raw NA NA nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 273 using 'ggh4x' package ... nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 273 using 'ggh4x' package ... nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 522 using 'ggh4x' package ... nrow dataFiltered(): 273 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/analytic_20240315/20240315_002_autoQC03dda.raw NA NA Warning in observe() : timeDiff is higher than timeRange nFacets: 5 nrow dataFiltered(): 1720 using 'ggh4x' package ... Warning: Removed 7 rows containing missing values (`geom_point()`). nFacets: 6 nrow dataFiltered(): 2064 using 'ggh4x' package ... Warning: Removed 8 rows containing missing values (`geom_point()`). nFacets: 7 nrow dataFiltered(): 2408 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). nFacets: 8 nrow dataFiltered(): 2752 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). nFacets: 9 nrow dataFiltered(): 3096 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 10 nrow dataFiltered(): 3440 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). nFacets: 11 nrow dataFiltered(): 3784 using 'ggh4x' package ... Warning: Removed 16 rows containing missing values (`geom_point()`). 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-15 17:45:53.89774 | timeMax: 2024-03-15 17:45:53.898474 | timeDiff: 5184000.00073457 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 5 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-15 16:45:53.898 | timeMax: 2024-03-15 16:45:53.898 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 5 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710500638511078000.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 nFacets: 5 nrow dataFiltered(): 1720 using 'ggh4x' package ... Warning: Removed 7 rows containing missing values (`geom_point()`). nFacets: 6 nrow dataFiltered(): 2064 using 'ggh4x' package ... Warning: Removed 8 rows containing missing values (`geom_point()`). nFacets: 7 nrow dataFiltered(): 2408 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). nFacets: 8 nrow dataFiltered(): 2752 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). nFacets: 9 nrow dataFiltered(): 3096 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 10 nrow dataFiltered(): 3440 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). nFacets: 11 nrow dataFiltered(): 3784 using 'ggh4x' package ... Warning: Removed 16 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710521150814354000.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 nFacets: 1 nrow dataFiltered(): 455 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 0 nrow dataFiltered(): 0 nrow dataFiltered(): 455 using 'ggh4x' package ... p34570/Proteomics/QEXACTIVE_1/analytic_20240312/20240312_C34570_007_autoQC03dda.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-16 16:15:46.550972 | timeMax: 2024-03-16 16:15:46.551553 | timeDiff: 5184000.00058103 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1936 using 'ggh4x' package ... Warning: Removed 43 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2024-01-16 15:15:46.551 | timeMax: 2024-03-16 15:15:46.552 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1936 using 'ggh4x' package ... Warning: Removed 43 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710514921975479000.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 p34572/Proteomics/QEXACTIVE_1/analytic_20240315/20240315_C34572_001_autoQC01.raw p34572/Proteomics/QEXACTIVE_1/analytic_20240315/20240315_C34572_004_autoQC01.raw p34572/Proteomics/QEXACTIVE_1/analytic_20240315/20240315_C34572_004_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(): 468 using 'ggh4x' package ... p34572/Proteomics/QEXACTIVE_1/analytic_20240315/20240315_C34572_005_autoQC03dda.raw p3000/Proteomics/QEXACTIVE_1/analytic_20240315/20240315_C3000_005_autoQC03dda.raw NA autoQC01 module APEX wide nrow: 263340 autoQC01 module APEX long nrow: 1452 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 68 rows containing missing values (`geom_point()`). Warning: Removed 3 rows containing missing values (`geom_line()`). 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-18 12:46:14.963454 | timeMax: 2024-03-18 12:46:14.964025 | timeDiff: 5184000.00057101 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp 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(): 522 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-01-18 11:46:14.96345 | timeMax: 2024-03-18 11:46:14.96402 | timeDiff: 5184000.00057006 nFacets: 1 nrow dataFiltered(): 247 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 522 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2024-01-18 11:46:14.963 | timeMax: 2024-03-18 11:46:14.964 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 247 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 522 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1248 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... NA nFacets: 4 nrow dataFiltered(): 780 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 162 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1248 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2024-01-18 14:34:48.114236 | timeMax: 2024-03-18 14:34:48.114809 | timeDiff: 5184000.00057268 nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1824 using 'ggh4x' package ... Warning: Removed 38 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2024-01-18 13:34:48.114 | timeMax: 2024-03-18 13:34:48.115 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1824 using 'ggh4x' package ... Warning: Removed 38 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710602143494383000.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_1710768884795255000.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_1710762371891566000.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