Listening on http://127.0.0.1:44939 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-17 17:38:18.5051 | timeMax: 2024-01-16 17:38:18.506017 | timeDiff: 5184000.00091672 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1248 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-17 16:38:18.505 | timeMax: 2024-01-16 16:38:18.506 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1248 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 976 using 'ggh4x' package ... Warning: Removed 19 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). NA p33961/Proteomics/QEXACTIVE_1/analytic_20240115/20240115_C33961_004_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33961/Proteomics/QEXACTIVE_1/analytic_20240115/20240115_C33961_004_autoQC01.raw NA nrow dataFiltered(): 976 using 'ggh4x' package ... Warning: Removed 38 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). nrow dataFiltered(): 976 using 'ggh4x' package ... Warning: Removed 19 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). p33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_008_autoQC01.raw NA p33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_001_autoQC01_rep.raw NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-17 19:56:54.41047 | timeMax: 2024-01-16 19:56:54.411053 | timeDiff: 5184000.00058293 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1248 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-17 18:56:54.41 | timeMax: 2024-01-16 18:56:54.411 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1248 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). 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) Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705431411160876000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:04:16.693155 | timeMax: 2024-01-17 08:04:16.693729 | timeDiff: 5184000.00057435 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 07:04:16.693 | timeMax: 2024-01-17 07:04:16.694 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:05:09.659407 | timeMax: 2024-01-17 08:05:09.659988 | timeDiff: 5184000.0005815 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 07:05:09.659 | timeMax: 2024-01-17 07:05:09.66 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). 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) Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705475053622345000.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_fgczmsqc-dashboard_1705475106649499000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:34:11.801151 | timeMax: 2024-01-17 08:34:11.801728 | timeDiff: 5184000.00057721 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:34:15.384462 | timeMax: 2024-01-17 08:34:15.385027 | timeDiff: 5184000.00056458 nFacets: 4 input timeRange: 7776000 | timeMin: 2023-11-18 07:34:11.801 | timeMax: 2024-01-17 07:34:11.802 | timeDiff: 5184000.00099993 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 07:34:15.384 | timeMax: 2024-01-17 07:34:15.385 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:34:20.252096 | timeMax: 2024-01-17 08:34:20.252712 | timeDiff: 5184000.0006156 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 07:34:20.252 | timeMax: 2024-01-17 07:34:20.253 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705476848529151000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705476852171679000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp p3026/Proteomics/LUMOS_1/naziegle_20201103_CLA_CWT-CKO-24h-rep4/20201103_072_autoQC01_40C.raw NA nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_001r_autoQC01_20240111193413.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_001r_autoQC01_20240111193413.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 08:48:13.54295 | timeMax: 2024-01-17 08:48:13.543529 | timeDiff: 5184000.00057817 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 07:48:13.543 | timeMax: 2024-01-17 07:48:13.544 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 09:21:30.580712 | timeMax: 2024-01-17 09:21:30.58128 | timeDiff: 5184000.00056863 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 08:21:30.581 | timeMax: 2024-01-17 08:21:30.581 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 09:21:38.290371 | timeMax: 2024-01-17 09:21:38.290949 | timeDiff: 5184000.00057721 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 08:21:38.29 | timeMax: 2024-01-17 08:21:38.291 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). 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) 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 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705479695226001000.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_fgczmsqc-dashboard_1705479687553044000.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_fgczmsqc-dashboard_1705477690461044000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 09:52:10.230061 | timeMax: 2024-01-17 09:52:10.230659 | timeDiff: 5184000.00059843 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 08:52:10.23 | timeMax: 2024-01-17 08:52:10.231 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). plotClick: fn has changed to /srv/www/htdocs//NA p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 09:54:19.1162 | timeMax: 2024-01-17 09:54:19.11677 | timeDiff: 5184000.00056911 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 08:54:19.116 | timeMax: 2024-01-17 08:54:19.117 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705481527124392000.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 p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 09:55:13.709663 | timeMax: 2024-01-17 09:55:13.710241 | timeDiff: 5184000.00057817 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 08:55:13.71 | timeMax: 2024-01-17 08:55:13.71 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705476857211485000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw Plotting chromatograms ... Read 22032 items NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw Plotting chromatograms ... Read 22032 items p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_020_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_020_autoQC01.raw Reading raw file: /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_020_autoQC01.raw Plotting chromatograms ... Read 22032 items p29369/Proteomics/LUMOS_1/moslu_20231205_231212_TTTS_samples/20231205_038_autoQC01.raw p29369/Proteomics/LUMOS_1/moslu_20231205_231212_TTTS_samples/20231205_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p29369/Proteomics/LUMOS_1/moslu_20231205_231212_TTTS_samples/20231205_008_autoQC01.raw Reading raw file: /srv/www/htdocs//p29369/Proteomics/LUMOS_1/moslu_20231205_231212_TTTS_samples/20231205_008_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw Reading raw file: /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw Plotting chromatograms ... Read 22032 items NA nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... NA vals$rawrr: TRUE NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... plotClick: nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Plotting chromatograms ... nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Read 22032 items Plotting chromatograms ... Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp nrow dataFiltered(): 624 using 'ggh4x' package ... vals$rawrr: TRUE nrow dataFiltered(): 624 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705423093465011000.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: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:11:51.801974 | timeMax: 2024-01-17 10:11:51.802552 | timeDiff: 5184000.00057769 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:11:51.802 | timeMax: 2024-01-17 09:11:51.803 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). 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(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... NA p33780/Proteomics/LUMOS_1/vismi_20231220/20231220_006_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33780/Proteomics/LUMOS_1/vismi_20231220/20231220_006_autoQC03dda.raw vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p33780/Proteomics/LUMOS_1/vismi_20231220/20231220_006_autoQC03dda.raw Plotting chromatograms ... Read 22032 items plotClick: NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705481710667873000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:16:39.967152 | timeMax: 2024-01-17 10:16:39.967761 | timeDiff: 5184000.00060916 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:16:39.967 | timeMax: 2024-01-17 09:16:39.968 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:17:19.141459 | timeMax: 2024-01-17 10:17:19.162882 | timeDiff: 5184000.02142334 nFacets: 4 Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:17:22.257289 | timeMax: 2024-01-17 10:17:22.257884 | timeDiff: 5184000.00059462 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705482996928511000.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$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:17:19.141 | timeMax: 2024-01-17 09:17:19.163 | timeDiff: 5184000.02200007 nFacets: 4 input timeRange: 7776000 | timeMin: 2023-11-18 09:17:22.257 | timeMax: 2024-01-17 09:17:22.258 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705483036110068000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:17:57.946344 | timeMax: 2024-01-17 10:17:57.946939 | timeDiff: 5184000.00059533 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:17:57.946 | timeMax: 2024-01-17 09:17:57.947 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705483039255720000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp NA p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_030_autoQC03dda.raw NA p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_030_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_030_autoQC03dda.raw NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: NA Plotting chromatograms ... p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Plotting chromatograms ... Plotting chromatograms ... NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Plotting chromatograms ... NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. 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$autoQC03-DIA-rawrr-autoQC03-plotTools 1: runApp p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw NA p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw Plotting chromatograms ... vals$rawrr: TRUE NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_09_autoQC03dia.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 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.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 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_03_autoQC03dia.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 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Plotting chromatograms ... Plotting chromatograms ... plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw Plotting chromatograms ... p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw NA Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... vals$rawDiag: TRUE Plotting chromatograms ... plotChargeState reading index for 20231212_005_autoQC03dia.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw Plotting chromatograms ... Plotting chromatograms ... plotCycleLoad `geom_smooth()` using formula = 'y ~ x' plotCycleTime plotInjectionTime p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Plotting chromatograms ... reading index for 20240104_10_autoQC03dia.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. plotChargeState Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_10_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Warning: Error in lm.wfit: 0 (non-NA) cases 176: stop 175: lm.wfit 174: lm 173: .fitChromatographicPeak 172: FUN 171: lapply 170: .fitPeak.rawrrChromatogram 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp Plotting chromatograms ... plotCycleLoad `geom_smooth()` using formula = 'y ~ x' plotPrecursorHeatmap plotMzDistribution plotLockMassCorrection plotInjectionTime plotTicBasepeak p33640/Proteomics/LUMOS_1/kretschmer_20240105/20240105_005_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33640/Proteomics/LUMOS_1/kretschmer_20240105/20240105_005_autoQC03dda.raw Reading raw file: /srv/www/htdocs//p33640/Proteomics/LUMOS_1/kretschmer_20240105/20240105_005_autoQC03dda.raw Plotting chromatograms ... Read 22032 items plotClick: fn has changed to /srv/www/htdocs//p33780/Proteomics/LUMOS_1/vismi_20231220/20231221_013_autoQC03dda.raw Reading raw file: /srv/www/htdocs//p33780/Proteomics/LUMOS_1/vismi_20231220/20231221_013_autoQC03dda.raw Plotting chromatograms ... Read 22032 items p33780/Proteomics/LUMOS_1/vismi_20231220/20231221_013_autoQC03dda.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_02_autoQC03dda.raw NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_02_autoQC03dda.raw p33640/Proteomics/LUMOS_1/kretschmer_20240105/20240105_005_autoQC03dda.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_030_autoQC03dda.raw NA NA NA input timeRange: 7776000 | timeMin: 2023-11-05 09:18:05.557 | timeMax: 2024-01-17 09:17:57.947 | timeDiff: 6307192.3900001 nFacets: 4 nrow dataFiltered(): 884 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 using 'ggh4x' package ... Plotting chromatograms ... input timeRange: 7776000 | timeMin: 2023-11-06 09:18:05.557 | timeMax: 2024-01-17 09:17:57.947 | timeDiff: 6220792.3900001 nFacets: 4 nrow dataFiltered(): 884 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 216 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:43:52.045452 | timeMax: 2024-01-17 10:43:52.046052 | timeDiff: 5184000.0006001 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:43:52.045 | timeMax: 2024-01-17 09:43:52.046 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705481656071757000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705483074932394000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp p23777/Proteomics/LUMOS_1/noheld_20231122/20231122_003_autoQC01_20231123152940.raw p33544/Proteomics/LUMOS_1/roschi_20231203_new_yeast_DDA_OT_IT/20231203_001_autoQC01.raw nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... NA p33595/Proteomics/LUMOS_1/eichenberger_20231208/20231208_048_autoQC03dda_autoQC4L.raw plotClick: fn has changed to /srv/www/htdocs//p33595/Proteomics/LUMOS_1/eichenberger_20231208/20231208_048_autoQC03dda_autoQC4L.raw vals$rawrr: TRUE p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_030_autoQC03dda.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:46:32.67102 | timeMax: 2024-01-17 10:46:32.671608 | timeDiff: 5184000.00058794 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 09:46:32.67102 | timeMax: 2024-01-17 09:46:32.67161 | timeDiff: 5184000.00059009 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 09:46:32.671 | timeMax: 2024-01-17 09:46:32.672 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... NA NA p3000/Proteomics/EXPLORIS_2/analytic_20231121/20231121_005_autoQC4L_K562.raw input timeRange: 7776000 | timeMin: 2023-10-26 09:46:36.309 | timeMax: 2024-01-17 09:46:32.672 | timeDiff: 7171196.36299992 nFacets: 1 nrow dataFiltered(): 299 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_023_autoQC03dia_2ul.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_023_autoQC03dia_2ul.raw nrow dataFiltered(): 299 using 'ggh4x' package ... nrow dataFiltered(): 299 using 'ggh4x' package ... nrow dataFiltered(): 299 using 'ggh4x' package ... NA nrow dataFiltered(): 252 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-10-26 09:46:36.309 | timeMax: 2024-01-17 10:48:25.204772 | timeDiff: 7171308.8957715 nFacets: 1 nrow dataFiltered(): 299 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 299 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-10-26 09:46:36.309 | timeMax: 2024-01-17 09:48:25.205 | timeDiff: 7171308.89599991 nFacets: 1 nrow dataFiltered(): 299 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... input timeRange: 31536000 | timeMin: 2023-02-06 09:48:26.645 | timeMax: 2024-01-17 09:48:25.205 | timeDiff: 29807998.5599999 nFacets: 1 nrow dataFiltered(): 1612 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... nrow dataFiltered(): 252 using 'ggh4x' package ... NA nFacets: 1 nrow dataFiltered(): 13 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(): 594 using 'ggh4x' package ... nrow dataFiltered(): 594 using 'ggh4x' package ... nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 78 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 36 using 'ggh4x' package ... nrow dataFiltered(): 78 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 1612 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... nrow dataFiltered(): 1612 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/analytic_20240104/20240104_003_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20240104/20240104_003_autoQC03dda.raw nFacets: 4 nrow dataFiltered(): 8672 using 'ggh4x' package ... Warning: Removed 45 rows containing missing values (`geom_point()`). NA p33648/Proteomics/EXPLORIS_2/analytic_20231208/20231208_C33648_007_autoQC01.raw NA vals$rawDiag: TRUE vals$rawrr: TRUE plotClick: fn has changed to /srv/www/htdocs//p33773/Proteomics/EXPLORIS_2/analytic_20231219/20231219_C33773_017_autoQC01.raw p33773/Proteomics/EXPLORIS_2/analytic_20231219/20231219_C33773_017_autoQC01.raw plotChargeState Reading raw file: /srv/www/htdocs//p33773/Proteomics/EXPLORIS_2/analytic_20231219/20231219_C33773_017_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-rawDiag-autoQC03-plot 1: runApp reading index for 20231219_C33773_017_autoQC01.raw... p3000/Proteomics/EXPLORIS_2/analytic_20231211/20231211_003_autoQC01.raw Reading raw file: /srv/www/htdocs//p33773/Proteomics/EXPLORIS_2/analytic_20231219/20231219_C33773_017_autoQC01.raw Plotting chromatograms ... Read 22032 items plotInjectionTime 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 10:53:14.351075 | timeMax: 2024-01-17 10:53:14.351838 | timeDiff: 5184000.00076222 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 09:53:14.351 | timeMax: 2024-01-17 09:53:14.352 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1488 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). NA nFacets: 5 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 540 using 'ggh4x' package ... nrow dataFiltered(): 1118 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 4 nrow dataFiltered(): 624 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... NA nFacets: 3 nrow dataFiltered(): 585 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nFacets: 5 nrow dataFiltered(): 1118 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 540 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705482708793177000.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 autoQC01 module APEX wide nrow: 257334 autoQC01 module APEX long nrow: 1248 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 48 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: 2023-11-18 11:08:59.174328 | timeMax: 2024-01-17 11:08:59.175126 | timeDiff: 5184000.00079751 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 10:08:59.174 | timeMax: 2024-01-17 10:08:59.175 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1664 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705484628971883000.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 p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw nFacets: 1 nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 594 using 'ggh4x' package ... nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 78 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 36 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_001r_autoQC01_20240111193413.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_010_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_001r_autoQC01.raw p33898/Proteomics/LUMOS_1/analytic_20240111/20240111_C33898_029_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 11:48:17.134992 | timeMax: 2024-01-17 11:48:17.135595 | timeDiff: 5184000.00060272 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 10:48:17.13499 | timeMax: 2024-01-17 10:48:17.13559 | timeDiff: 5184000.0006001 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 10:48:17.135 | timeMax: 2024-01-17 10:48:17.136 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 13 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 594 using 'ggh4x' package ... NA p32853/Proteomics/TIMSTOF_1/analytic_20231207/zip/20231207_001_autoQC03dda.d.zip plotClick: fn has changed to /srv/www/htdocs//p32853/Proteomics/TIMSTOF_1/analytic_20231207/zip/20231207_001_autoQC03dda.d.zip NA p32853/Proteomics/TIMSTOF_1/analytic_20231207/zip/20231207_001_autoQC03dda.d.zip Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 11:58:18.452578 | timeMax: 2024-01-17 11:58:18.453147 | timeDiff: 5184000.00056911 nFacets: 4 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 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 10:58:18.45258 | timeMax: 2024-01-17 10:58:18.45315 | timeDiff: 5184000.00056982 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-18 10:58:18.453 | timeMax: 2024-01-17 10:58:18.453 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 252 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 594 using 'ggh4x' package ... p3000/Proteomics/TIMSTOF_1/spfammatter_20240112_RFQuadchanged/zip/20240112_003_autoQC03dda.d.zip input timeRange: 7776000 | timeMin: 2023-10-21 10:58:21.127 | timeMax: 2024-01-17 10:58:18.453 | timeDiff: 7603197.32599998 nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 594 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705489095417477000.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_fgczmsqc-dashboard_1705484789583688000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 12:16:53.985104 | timeMax: 2024-01-17 12:16:53.985701 | timeDiff: 5184000.00059724 nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-18 11:16:53.9851 | timeMax: 2024-01-17 11:16:53.9857 | timeDiff: 5184000.00059986 Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705485191228432000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 13:14:11.929285 | timeMax: 2024-01-17 13:14:11.929874 | timeDiff: 5184000.00058961 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 12:14:11.929 | timeMax: 2024-01-17 12:14:11.93 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA vals$rawrr: TRUE p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705493648941393000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 13:19:37.070565 | timeMax: 2024-01-17 13:19:37.071559 | timeDiff: 5184000.00099373 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 12:19:37.071 | timeMax: 2024-01-17 12:19:37.072 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1312 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(): 252 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 594 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705486136089979000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 13:53:09.932912 | timeMax: 2024-01-17 13:53:09.933847 | timeDiff: 5184000.00093508 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 12:53:09.933 | timeMax: 2024-01-17 12:53:09.934 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 13:53:42.769436 | timeMax: 2024-01-17 13:53:42.770397 | timeDiff: 5184000.00096083 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 12:53:42.769 | timeMax: 2024-01-17 12:53:42.77 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705495986403141000.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 p29369/Proteomics/LUMOS_1/moslu_20231205_231212_TTTS_samples/20231205_036_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 13:59:51.718179 | timeMax: 2024-01-17 13:59:51.718996 | timeDiff: 5184000.00081754 nFacets: 4 Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705496388197238000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 14:38:27.887415 | timeMax: 2024-01-17 14:38:27.888346 | timeDiff: 5184000.00093079 nFacets: 4 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 13:38:27.887 | timeMax: 2024-01-17 13:38:27.888 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA nFacets: 5 nrow dataFiltered(): 2100 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nFacets: 6 nrow dataFiltered(): 2520 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 7 nrow dataFiltered(): 2940 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 8 nrow dataFiltered(): 3360 using 'ggh4x' package ... Warning: Removed 3 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 9 nrow dataFiltered(): 3780 using 'ggh4x' package ... Warning: Removed 3 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 10 nrow dataFiltered(): 4200 using 'ggh4x' package ... Warning: Removed 3 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 11 nrow dataFiltered(): 4620 using 'ggh4x' package ... Warning: Removed 27 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). 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(): 144 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... nrow dataFiltered(): 624 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705498702988157000.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 nrow dataFiltered(): 26 using 'ggh4x' package ... nrow dataFiltered(): 594 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705493972877068000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 15:11:52.769663 | timeMax: 2024-01-17 15:11:52.770499 | timeDiff: 5184000.00083613 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 14:11:52.77 | timeMax: 2024-01-17 14:11:52.771 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw plotClick: p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_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 NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705500708166254000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-18 15:48:40.525496 | timeMax: 2024-01-17 15:48:40.526112 | timeDiff: 5184000.00061631 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-18 14:48:40.526 | timeMax: 2024-01-17 14:48:40.526 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1680 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw vals$rawrr: TRUE NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw NA p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_002_autoQC01.raw p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_003_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczmsqc-dashboard_1705502917536179000.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