Listening on http://127.0.0.1:38469 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-24 11:03:57.309539 | timeMax: 2024-01-23 11:03:57.31058 | timeDiff: 5184000.00104046 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1264 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-24 10:03:57.31 | timeMax: 2024-01-23 10:03:57.311 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 4 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). NA nFacets: 4 nrow dataFiltered(): 1904 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1904 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). plotClick: fn has changed to /srv/www/htdocs//NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-25 12:10:05.352761 | timeMax: 2024-01-24 12:10:05.353336 | timeDiff: 5184000.0005753 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-25 11:10:05.353 | timeMax: 2024-01-24 11:10:05.353 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1952 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw vals$rawrr: TRUE NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_001_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 p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240122_026_autoQC01.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240122_025_autoQC01.raw nrow dataFiltered(): 1952 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_001_autoQC01.raw NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_014_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/LUMOS_1/roschi_20240117_autoQC/20240117_004_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$rawDiag: FALSE nrow dataFiltered(): 162 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_027_autoQC03dda.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_027_autoQC03dda.raw NA input timeRange: 7776000 | timeMin: 2023-11-12 11:13:34.491 | timeMax: 2024-01-24 11:10:05.353 | timeDiff: 6306990.86199999 nFacets: 4 nrow dataFiltered(): 988 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_027_autoQC03dda.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_027_autoQC03dda.raw NA vals$rawrr: TRUE p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw NA vals$rawrr: TRUE p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_028_autoQC03dia.raw NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_027_autoQC03dda.raw nrow dataFiltered(): 988 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw NA p33212/Proteomics/LUMOS_1/roschi_20231202_K562_DIA_autoQC/20231202_007_S580219_K562_incl_iRT_2_autoQC03dia.raw p3000/Proteomics/LUMOS_1/roschi_20231212_autoQC/20231212_005_autoQC03dia.raw NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-25 13:20:28.423205 | timeMax: 2024-01-24 13:20:28.424168 | timeDiff: 5184000.00096226 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: 2023-11-25 12:20:28.42321 | timeMax: 2024-01-24 12:20:28.42417 | timeDiff: 5184000.00096011 Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706098824938228000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706094601439410000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-25 14:53:04.378066 | timeMax: 2024-01-24 14:53:04.378763 | timeDiff: 5184000.00069785 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-25 13:53:04.378 | timeMax: 2024-01-24 13:53:04.379 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1968 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw vals$rawrr: TRUE 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(): 180 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706104380142218000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-25 15:27:45.358724 | timeMax: 2024-01-24 15:27:45.359295 | timeDiff: 5184000.00057054 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-25 14:27:45.359 | timeMax: 2024-01-24 14:27:45.359 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1968 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 180 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... NA NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw vals$rawrr: TRUE NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw Plotting chromatograms ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706106462370390000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-25 17:47:40.395474 | timeMax: 2024-01-24 17:47:40.39614 | timeDiff: 5184000.00066614 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-25 16:47:40.395 | timeMax: 2024-01-24 16:47:40.396 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706114857201511000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 07:50:25.634209 | timeMax: 2024-01-25 07:50:25.634779 | timeDiff: 5184000.00057054 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-26 06:50:25.634 | timeMax: 2024-01-25 06:50:25.635 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 4 nrow dataFiltered(): 1984 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_007_autoQC01.raw 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(): 180 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_028_autoQC03dia.raw NA p34029/Proteomics/LUMOS_1/analytic_20240123/20240123_C34029_007_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34029/Proteomics/LUMOS_1/analytic_20240123/20240123_C34029_007_autoQC01.raw NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p34029/Proteomics/LUMOS_1/analytic_20240123/20240123_C34029_007_autoQC01.raw Plotting chromatograms ... Read 22032 items p34029/Proteomics/LUMOS_1/analytic_20240123/20240123_C34029_007_autoQC01.raw plotClick: NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 09:12:44.340397 | timeMax: 2024-01-25 09:12:44.340962 | timeDiff: 5184000.00056505 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-26 08:12:44.34 | timeMax: 2024-01-25 08:12:44.341 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 10:01:36.727445 | timeMax: 2024-01-25 10:01:36.728019 | timeDiff: 5184000.00057387 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-26 09:01:36.727 | timeMax: 2024-01-25 09:01:36.728 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706165422607840000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706170360995908000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 10:54:20.150887 | timeMax: 2024-01-25 10:54:20.151465 | timeDiff: 5184000.00057721 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-26 09:54:20.151 | timeMax: 2024-01-25 09:54:20.151 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). vals$rawrr: TRUE NA nFacets: 4 nrow dataFiltered(): 2000 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 180 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706176457123500000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 12:47:09.503595 | timeMax: 2024-01-25 12:47:09.504166 | timeDiff: 5184000.00057054 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-11-26 11:47:09.504 | timeMax: 2024-01-25 11:47:09.504 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706173293665957000.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_2/lkunz_20240123/20240123_001_autoQC01.raw vals$rawrr: TRUE plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_011_autoQC01.raw NA p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_011_autoQC01.raw input timeRange: 7776000 | timeMin: 2024-01-16 11:47:10.431 | timeMax: 2024-01-25 11:47:09.504 | timeDiff: 777599.072999954 nFacets: 4 nrow dataFiltered(): 304 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw Plotting chromatograms ... Read 22032 items input timeRange: 7776000 | timeMin: 2024-01-20 11:51:30.656 | timeMax: 2024-01-25 11:47:09.504 | timeDiff: 431738.84800005 nFacets: 4 nrow dataFiltered(): 160 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw NA p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_001_autoQC01.raw p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... NA nrow dataFiltered(): 160 using 'ggh4x' package ... nFacets: 2 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$rawDiag: FALSE nrow dataFiltered(): 18 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nrow dataFiltered(): 52 using 'ggh4x' package ... p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw input timeRange: 7776000 | timeMin: 2024-01-11 11:55:10.794 | timeMax: 2024-01-25 11:47:09.504 | timeDiff: 1209118.71000004 nFacets: 2 nrow dataFiltered(): 104 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 72 using 'ggh4x' package ... NA p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw plotClick: vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... nrow dataFiltered(): 104 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-26 14:01:50.605197 | timeMax: 2024-01-25 14:01:50.605783 | timeDiff: 5184000.00058651 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-26 13:01:50.6052 | timeMax: 2024-01-25 13:01:50.60578 | timeDiff: 5184000.00058007 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-26 13:01:50.605 | timeMax: 2024-01-25 13:01:50.606 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1040 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 414 using 'ggh4x' package ... p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_002_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_002_autoQC03dia.raw plotClick: NA p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw nFacets: 4 nrow dataFiltered(): 936 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 180 using 'ggh4x' package ... NA p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240104_028_autoQC03dia.raw p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240123_YEAST_DIA/20240123_015_autoQC03dia.raw plotClick: Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706183226190289000.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: 2023-11-27 07:17:03.036187 | timeMax: 2024-01-26 07:17:03.036795 | timeDiff: 5184000.00060773 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1168 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-27 06:17:03.036 | timeMax: 2024-01-26 06:17:03.037 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). autoQC01 module APEX wide nrow: 258478 autoQC01 module APEX long nrow: 1236 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 44 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(): 180 using 'ggh4x' package ... nrow dataFiltered(): 936 using 'ggh4x' package ... NA p34029/Proteomics/LUMOS_1/analytic_20240123/20240123_C34029_014_autoQC03dda.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 07:22:04.217094 | timeMax: 2024-01-26 07:22:04.217676 | timeDiff: 5184000.00058246 nFacets: 4 Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706250121106226000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 11:20:50.918924 | timeMax: 2024-01-26 11:20:50.919616 | timeDiff: 5184000.00069141 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 11:20:54.621241 | timeMax: 2024-01-26 11:20:54.621816 | timeDiff: 5184000.00057554 nFacets: 4 input timeRange: 7776000 | timeMin: 2023-11-27 10:20:50.919 | timeMax: 2024-01-26 10:20:50.92 | timeDiff: 5184000.00100017 nFacets: 4 Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 11:20:57.986762 | timeMax: 2024-01-26 11:20:57.987333 | timeDiff: 5184000.00057125 nFacets: 4 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1648 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-27 10:20:57.987 | timeMax: 2024-01-26 10:20:57.987 | timeDiff: 5184000 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(): 180 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706264447785955000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706264451618118000.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 p33956/Proteomics/LUMOS_1/linares_20240125/20240125_016_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33956/Proteomics/LUMOS_1/linares_20240125/20240125_016_autoQC03dda.raw Reading raw file: /srv/www/htdocs//p33956/Proteomics/LUMOS_1/linares_20240125/20240125_016_autoQC03dda.raw Plotting chromatograms ... Read 22032 items NA Plotting chromatograms ... 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 Read 22032 items Reading raw file: /srv/www/htdocs//p33780/Proteomics/LUMOS_1/vismi_20231220/20231220_006_autoQC03dda.raw Plotting chromatograms ... NA Plotting chromatograms ... Plotting chromatograms ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... p25334/Proteomics/LUMOS_1/dlesli_20240119_DLP230/20240119_022_autoQC4L.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706249819979470000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706004232142468000.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: 2023-11-27 11:51:30.191423 | timeMax: 2024-01-26 11:51:30.192043 | timeDiff: 5184000.00061989 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1168 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-27 10:51:30.191 | timeMax: 2024-01-26 10:51:30.192 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1168 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 12:57:16.541355 | timeMax: 2024-01-26 12:57:16.542065 | timeDiff: 5184000.00070977 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-27 11:57:16.541 | timeMax: 2024-01-26 11:57:16.542 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1168 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706270233472316000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 16:14:38.996569 | timeMax: 2024-01-26 16:14:38.997163 | timeDiff: 5184000.0005939 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-27 15:14:38.997 | timeMax: 2024-01-26 15:14:38.997 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... 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(): 216 using 'ggh4x' package ... nrow dataFiltered(): 169 using 'ggh4x' package ... NA p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw NA p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw NA p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw nrow dataFiltered(): 169 using 'ggh4x' package ... NA nrow dataFiltered(): 169 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 169 using 'ggh4x' package ... nrow dataFiltered(): 169 using 'ggh4x' package ... p33922/Proteomics/EXPLORIS_2/analytic_20240116/20240116_C33922_006_autoQC03dda.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706282075917011000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-27 16:24:40.62579 | timeMax: 2024-01-26 16:24:40.62637 | timeDiff: 5184000.0005796 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1184 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-27 15:24:40.626 | timeMax: 2024-01-26 15:24:40.626 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1184 using 'ggh4x' package ... p33922/Proteomics/EXPLORIS_2/analytic_20240116/20240116_C33922_005_autoQC01.raw nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 169 using 'ggh4x' package ... NA NA p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 216 using 'ggh4x' package ... NA p3000/Proteomics/EXPLORIS_2/analytic_20240115/20240104_005_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw nrow dataFiltered(): 169 using 'ggh4x' package ... nrow dataFiltered(): 169 using 'ggh4x' package ... NA p33996/Proteomics/EXPLORIS_2/analytic_20240119/20240119_C33996_007_autoQC03dda.raw p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_033_autoQC03dda.raw input timeRange: 7776000 | timeMin: 2023-11-11 15:26:13.243 | timeMax: 2024-01-26 15:24:40.626 | timeDiff: 6566307.3829999 nFacets: 1 nrow dataFiltered(): 247 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... nrow dataFiltered(): 247 using 'ggh4x' package ... NA plotClick: fn has changed to /srv/www/htdocs//NA p33922/Proteomics/EXPLORIS_2/analytic_20240116/20240116_C33922_006_autoQC03dda.raw NA nrow dataFiltered(): 247 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706282677587442000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706266287161537000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706264454982952000.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: 2023-11-29 16:17:01.472602 | timeMax: 2024-01-28 16:17:01.473169 | timeDiff: 5184000.0005672 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-29 15:17:01.473 | timeMax: 2024-01-28 15:17:01.473 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706455018431260000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 06:21:00.622537 | timeMax: 2024-01-29 06:21:00.623113 | timeDiff: 5184000.00057578 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 05:21:00.623 | timeMax: 2024-01-29 05:21:00.623 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 0 input timeRange: 7776000 | timeMin: 2023-11-10 05:21:01.619 | timeMax: 2024-01-29 05:21:00.623 | timeDiff: 6911999.00399995 nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 2288 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706505657587836000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 08:48:01.319034 | timeMax: 2024-01-29 08:48:01.319613 | timeDiff: 5184000.00057912 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 07:48:01.319 | timeMax: 2024-01-29 07:48:01.32 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw NA p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw plotClick: NA p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw plotClick: p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw plotClick: p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw NA nFacets: 3 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 533 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw NA p34007/Proteomics/LUMOS_2/analytic_20240119/20240119_C34007_014_autoQC03dia.raw NA p34007/Proteomics/LUMOS_2/analytic_20240119/20240119_C34007_006_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_2/analytic_20240119/20240119_C34007_006_autoQC03dda.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 08:54:27.891813 | timeMax: 2024-01-29 08:54:27.892526 | timeDiff: 5184000.00071335 nFacets: 4 nFacets: 3 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 533 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? input timeRange: 7776000 | timeMin: 2023-11-30 07:54:27.89181 | timeMax: 2024-01-29 07:54:27.89253 | timeDiff: 5184000.00072002 nFacets: 3 nrow dataFiltered(): 533 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(): 216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 07:54:27.892 | timeMax: 2024-01-29 07:54:27.893 | timeDiff: 5184000.00099993 nFacets: 3 nrow dataFiltered(): 533 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(): 216 using 'ggh4x' package ... p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706514478303710000.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 p34007/Proteomics/LUMOS_2/analytic_20240119/20240119_C34007_014_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_2/analytic_20240119/20240119_C34007_014_autoQC03dia.raw NA p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240115/20240115_003_autoQC03dda.raw p3000/Proteomics/LUMOS_2/cfortes_20240115/20240115_003_autoQC03dda.raw p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw nrow dataFiltered(): 533 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? plotClick: p33642/Proteomics/LUMOS_2/analytic_20240122/20240122_C33642_012_autoQC03dda.raw Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:00:17.421611 | timeMax: 2024-01-29 09:00:17.422205 | timeDiff: 5184000.00059485 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 08:00:17.422 | timeMax: 2024-01-29 08:00:17.422 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706514864828750000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:00:43.81084 | timeMax: 2024-01-29 09:00:43.811467 | timeDiff: 5184000.00062704 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 08:00:43.811 | timeMax: 2024-01-29 08:00:43.811 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:04:23.168295 | timeMax: 2024-01-29 09:04:23.168872 | timeDiff: 5184000.00057673 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 08:04:23.168 | timeMax: 2024-01-29 08:04:23.169 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706515214404646000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:32:37.539376 | timeMax: 2024-01-29 09:32:37.539954 | timeDiff: 5184000.0005784 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 08:32:37.539 | timeMax: 2024-01-29 08:32:37.54 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). NA nFacets: 3 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 533 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706515460177936000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:35:57.65247 | timeMax: 2024-01-29 09:35:57.653072 | timeDiff: 5184000.00060201 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 08:35:57.652 | timeMax: 2024-01-29 08:35:57.653 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706517154528359000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 09:41:50.166817 | timeMax: 2024-01-29 09:41:50.16741 | timeDiff: 5184000.00059319 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 08:41:50.167 | timeMax: 2024-01-29 08:41:50.167 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1520 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). NA vals$rawrr: TRUE p34029/Proteomics/LUMOS_1/analytic_20240126/20240126_C34029_007_autoQC01.raw p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_020_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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 10:01:35.969295 | timeMax: 2024-01-29 10:01:35.969922 | timeDiff: 5184000.00062752 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 09:01:35.969 | timeMax: 2024-01-29 09:01:35.97 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). nFacets: 3 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 216 using 'ggh4x' package ... nrow dataFiltered(): 559 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? NA p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706517354637788000.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 p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw NA nrow dataFiltered(): 559 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? p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw plotClick: NA nrow dataFiltered(): 559 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nrow dataFiltered(): 559 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? p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw plotClick: Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706518892843476000.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: 2023-11-30 10:03:17.858746 | timeMax: 2024-01-29 10:03:17.859317 | timeDiff: 5184000.00057125 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 09:03:17.859 | timeMax: 2024-01-29 09:03:17.859 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... vals$rawrr: TRUE NA nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... vals$rawDiag: TRUE nFacets: 3 nrow dataFiltered(): 559 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(): 216 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw plotChargeState Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-rawDiag-autoQC03-plot 1: runApp plotClick: reading index for 20240126_001_autoQC03dda.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. NA plotCycleLoad `geom_smooth()` using formula = 'y ~ x' vals$rawrr: TRUE plotChargeState Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_001_autoQC03dda.raw Plotting chromatograms ... Read 22032 items vals$rawDiag: FALSE Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706517707125770000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706515240786201000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 12:17:29.36686 | timeMax: 2024-01-29 12:17:29.367432 | timeDiff: 5184000.00057149 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 11:17:29.367 | timeMax: 2024-01-29 11:17:29.367 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706518994872391000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 12:32:14.512205 | timeMax: 2024-01-29 12:32:14.512789 | timeDiff: 5184000.00058436 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 11:32:14.512 | timeMax: 2024-01-29 11:32:14.513 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 832 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 180 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706187707537545000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp NA nFacets: 0 nrow dataFiltered(): 0 nFacets: 1 nrow dataFiltered(): 0 Warning: Error in graphics::plot.new: figure margins too large 104: graphics::plot.new 101: startPNG 100: plotPNG 99: resizeSavedPlot 97: func 95: f 94: Reduce 85: do 84: hybrid_chain 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp Warning: Error in graphics::plot.new: figure margins too large 104: graphics::plot.new 101: startPNG 100: plotPNG 99: resizeSavedPlot 97: func 95: f 94: Reduce 85: do 84: hybrid_chain 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 4 Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 396 using 'ggh4x' package ... nrow dataFiltered(): 832 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1344 using 'ggh4x' package ... Warning: Removed 8 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 12:46:49.590041 | timeMax: 2024-01-29 12:46:49.590685 | timeDiff: 5184000.00064325 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-30 11:46:49.59 | timeMax: 2024-01-29 11:46:49.591 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706527046329511000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 13:33:45.568057 | timeMax: 2024-01-29 13:33:45.568699 | timeDiff: 5184000.00064206 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 12:33:45.568 | timeMax: 2024-01-29 12:33:45.569 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1488 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). p34029/Proteomics/LUMOS_1/analytic_20240126/20240126_C34029_007_autoQC01.raw NA p34029/Proteomics/LUMOS_1/analytic_20240126/20240126_C34029_007_autoQC01.raw NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706531622544080000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 16:37:25.01713 | timeMax: 2024-01-29 16:37:25.017739 | timeDiff: 5184000.00060892 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 15:37:25.01713 | timeMax: 2024-01-29 15:37:25.01774 | timeDiff: 5184000.00061011 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 15:37:25.017 | timeMax: 2024-01-29 15:37:25.018 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706542641943673000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 16:44:23.129107 | timeMax: 2024-01-29 16:44:23.129685 | timeDiff: 5184000.0005784 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 15:44:23.129 | timeMax: 2024-01-29 15:44:23.13 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... 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(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... NA nrow dataFiltered(): 234 using 'ggh4x' package ... NA p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw vals$rawrr: TRUE nrow dataFiltered(): 234 using 'ggh4x' package ... Reading raw file: /srv/www/htdocs//p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 17:01:30.942918 | timeMax: 2024-01-29 17:01:30.943491 | timeDiff: 5184000.00057316 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(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 16:01:30.94292 | timeMax: 2024-01-29 16:01:30.94349 | timeDiff: 5184000.00057006 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 16:01:30.943 | timeMax: 2024-01-29 16:01:30.943 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 156 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_2/analytic_20240115/20240104_005_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p3000/Proteomics/EXPLORIS_2/analytic_20240104/20240104_009_autoQC03dia.raw NA p3000/Proteomics/EXPLORIS_2/analytic_20240104/20240104_009_autoQC03dia.raw p3000/Proteomics/EXPLORIS_2/analytic_20240115/20240104_005_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw p3000/Proteomics/EXPLORIS_2/analytic_20240115/20240104_005_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA p34034/Proteomics/EXPLORIS_2/shigup_20240126/20240126_012_autoQC03dia.raw p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_040_autoQC03dia.raw NA nrow dataFiltered(): 234 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706544087483614000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706543060052675000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 17:21:31.921653 | timeMax: 2024-01-29 17:21:31.922243 | timeDiff: 5184000.00058961 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 16:21:31.922 | timeMax: 2024-01-29 16:21:31.922 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1504 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). p3000/Proteomics/LUMOS_1/pgehrig_20231211_autoQC/20240129_42_autoQC01.raw p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw Plotting chromatograms ... Read 22032 items p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw p3000/Proteomics/LUMOS_1/pgehrig_20231211_autoQC/20240129_42_autoQC01.raw NA plotClick: p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw NA p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/LUMOS_1/pgehrig_20231211_autoQC/20240129_42_autoQC01.raw p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240129_029_autoQC01.raw plotClick: Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706545288910182000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 17:57:10.232469 | timeMax: 2024-01-29 17:57:10.233049 | timeDiff: 5184000.00057936 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-30 16:57:10.232 | timeMax: 2024-01-29 16:57:10.233 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706547427207445000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-30 22:28:58.902527 | timeMax: 2024-01-29 22:28:58.903134 | timeDiff: 5184000.00060678 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-30 21:28:58.903 | timeMax: 2024-01-29 21:28:58.903 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706563735650281000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 08:17:48.56168 | timeMax: 2024-01-30 08:17:48.562249 | timeDiff: 5184000.00056887 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-01 07:17:48.562 | timeMax: 2024-01-30 07:17:48.562 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1472 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). vals$rawrr: TRUE NA p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_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 p25334/Proteomics/LUMOS_1/dlesli_20240119_DLP230/20240119_021_autoQC01.raw p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Plotting chromatograms ... Read 22032 items nFacets: 4 nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 11 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_autoQC01.raw Reading raw file: /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_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 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases NA p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_autoQC01.raw p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/lkunz_20240123/20240123_002_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240126/20240126_003_autoQC01.raw Plotting chromatograms ... Read 22032 items NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. 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$__autoQC01__-rawrr-autoQC03-plotTools 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 08:22:41.51421 | timeMax: 2024-01-30 08:22:41.5148 | timeDiff: 5184000.0005908 nFacets: 4 p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw plotClick: NA plotClick: Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706599358475667000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp vals$rawDiag: TRUE Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. vals$rawrr: FALSE p34007/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_FASP/20240129_000_autoQC01.raw p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw plotChargeState reading index for 20240129_001_autoQC01.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. reading index for 20240129_001_autoQC01.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. NA plotTicBasepeak p34007/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_FASP/20240129_000_autoQC01.raw p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw NA vals$rawDiag: FALSE vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_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 p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw plotClick: plotClick: NA input timeRange: 7776000 | timeMin: 2024-01-25 07:17:49.526 | timeMax: 2024-01-30 07:17:48.562 | timeDiff: 431999.036000013 nFacets: 4 nrow dataFiltered(): 64 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_autoQC01.raw Reading raw file: /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_sp3_beads_3_species/20240129_008_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 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases NA p34007/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_FASP/20240129_000_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_FASP/20240129_000_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_FASP/20240129_000_autoQC01.raw Plotting chromatograms ... Read 22032 items NA plotClick: fn has changed to /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34004/Proteomics/LUMOS_2/roschi_20240129_yeast_DIA_sp3_beads/20240129_001_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 nFacets: 4 nrow dataFiltered(): 128 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-07 07:26:07.142 | timeMax: 2024-01-30 07:17:48.562 | timeDiff: 4665101.42000008 nFacets: 4 nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 2 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1200 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw NA input timeRange: 7776000 | timeMin: 2024-01-20 07:28:22.4 | timeMax: 2024-01-30 07:17:48.562 | timeDiff: 863366.161999941 nFacets: 4 nrow dataFiltered(): 304 using 'ggh4x' package ... nrow dataFiltered(): 304 using 'ggh4x' package ... nrow dataFiltered(): 304 using 'ggh4x' package ... p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw NA vals$rawDiag: TRUE nrow dataFiltered(): 304 using 'ggh4x' package ... plotChargeState reading index for 20240129_001_autoQC01.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. p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_001_autoQC01.raw Plotting chromatograms ... Read 22032 items reading index for 20240129_001_autoQC01.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. NA p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw Reading raw file: /srv/www/htdocs//p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_007_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases reading index for 20240129_007_autoQC01.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. 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: 2023-12-01 09:38:39.485881 | timeMax: 2024-01-30 09:38:39.486449 | timeDiff: 5184000.00056863 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-01 08:38:39.486 | timeMax: 2024-01-30 08:38:39.486 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). vals$rawrr: TRUE NA plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. plotClick: Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706603916503678000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706528806275567000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 12:46:19.992571 | timeMax: 2024-01-30 12:46:19.993147 | timeDiff: 5184000.0005765 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 12:46:23.393579 | timeMax: 2024-01-30 12:46:23.394164 | timeDiff: 5184000.00058508 nFacets: 4 input timeRange: 7776000 | timeMin: 2023-12-01 11:46:19.993 | timeMax: 2024-01-30 11:46:19.993 | timeDiff: 5184000 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-01 11:46:23.394 | timeMax: 2024-01-30 11:46:23.394 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... NA nFacets: 4 nrow dataFiltered(): 1520 using 'ggh4x' package ... Warning: Removed 1 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706615176964826000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 198 using 'ggh4x' package ... nrow dataFiltered(): 884 using 'ggh4x' package ... NA p34007/Proteomics/LUMOS_1/roschi_20240129_YEAST_DIA_insol/20240129_015_autoQC03dia.raw Warning: Error in basename: a character vector argument expected 63: basename 62: use_tracking 1: runApp Warning: Error in basename: a character vector argument expected 63: basename 62: use_tracking 1: runApp