Listening on http://127.0.0.1:44351 Attaching package: 'shinydashboard' The following object is masked from 'package:graphics': box Loading required package: readr Loading required package: reshape2 Loading required package: lattice Loading required package: rawDiag Loading required package: rawrr Loading required package: ggnewscale fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-21 14:01:16.9133 | timeMax: 2024-02-19 14:01:16.91389 | timeDiff: 5184000.00059056 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 848 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-21 13:01:16.913 | timeMax: 2024-02-19 13:01:16.914 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 848 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 1248 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA p34284/Proteomics/FUSION_2/adelizliang_20240215/20240215_004_autoQC01.raw nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 1040 using 'ggh4x' package ... fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-21 16:50:13.543381 | timeMax: 2024-02-19 16:50:13.543977 | timeDiff: 5184000.00059581 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 848 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-21 15:50:13.543 | timeMax: 2024-02-19 15:50:13.544 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 848 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_001_autoQC01.raw p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_001_autoQC01.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708357810396060000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-21 20:56:17.721323 | timeMax: 2024-02-19 20:56:17.721899 | timeDiff: 5184000.00057578 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 864 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-21 19:56:17.721 | timeMax: 2024-02-19 19:56:17.722 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 864 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw Plotting chromatograms ... Read 22032 items plotClick: NA p34255/Proteomics/FUSION_2/fabiac_20240214/20240214_001_autoQC01.raw p3000/Proteomics/FUSION_2/analytic_20240214/20240214_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/analytic_20240214/20240214_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/FUSION_2/analytic_20240214/20240214_001_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_005_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_005_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_005_autoQC01.raw Plotting chromatograms ... Read 22032 items NA nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). p34284/Proteomics/FUSION_2/adelizliang_20240215/20240214_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34284/Proteomics/FUSION_2/adelizliang_20240215/20240214_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34284/Proteomics/FUSION_2/adelizliang_20240215/20240214_001_autoQC01.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_005_autoQC01.raw p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_004_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_004_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_004_autoQC01.raw Plotting chromatograms ... Read 22032 items p34176/Proteomics/FUSION_2/chiawei_20240207/20240207_017_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34176/Proteomics/FUSION_2/chiawei_20240207/20240207_017_autoQC01.raw Reading raw file: /srv/www/htdocs//p34176/Proteomics/FUSION_2/chiawei_20240207/20240207_017_autoQC01.raw Plotting chromatograms ... Read 22032 items NA 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: 4 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 988 using 'ggh4x' package ... p34284/Proteomics/FUSION_2/adelizliang_20240215/20240215_005_autoQC03dda.raw NA vals$rawrr: TRUE nrow dataFiltered(): 252 using 'ggh4x' package ... nrow dataFiltered(): 988 using 'ggh4x' package ... autoQC01 module APEX wide nrow: 260898 autoQC01 module APEX long nrow: 948 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 26 rows containing missing values (`geom_point()`). NA nrow dataFiltered(): 1264 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708372574653458000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-22 09:57:58.885665 | timeMax: 2024-02-20 09:57:58.886307 | timeDiff: 5184000.00064182 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 848 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-22 08:57:58.886 | timeMax: 2024-02-20 08:57:58.886 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 848 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1456 using 'ggh4x' package ... vals$rawrr: TRUE NA p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_061_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_061_autoQC01.raw Reading raw file: /srv/www/htdocs//p34192/Proteomics/LUMOS_1/analytic_20240219/20240219_C34192_061_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708419475822609000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-22 11:45:49.686146 | timeMax: 2024-02-20 11:45:49.686721 | timeDiff: 5184000.00057411 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 44 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-22 10:45:49.686 | timeMax: 2024-02-20 10:45:49.687 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 44 rows containing missing values (`geom_point()`). input timeRange: 15552000 | timeMin: 2023-12-22 10:45:49.686 | timeMax: 2024-02-20 11:46:03.831046 | timeDiff: 5184014.145046 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 44 rows containing missing values (`geom_point()`). input timeRange: 15552000 | timeMin: 2023-12-22 10:45:49.686 | timeMax: 2024-02-20 10:46:03.831 | timeDiff: 5184014.14499998 nFacets: 4 nrow dataFiltered(): 1232 using 'ggh4x' package ... Warning: Removed 44 rows containing missing values (`geom_point()`). input timeRange: 15552000 | timeMin: 2023-11-01 10:46:05.135 | timeMax: 2024-02-20 10:46:03.831 | timeDiff: 9590398.6960001 nFacets: 4 nrow dataFiltered(): 2560 using 'ggh4x' package ... Warning: Removed 76 rows containing missing values (`geom_point()`). 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(): 0 nrow dataFiltered(): 689 using 'ggh4x' package ... Warning in observe() : timeDiff is higher than timeRange nrow dataFiltered(): 689 using 'ggh4x' package ... nrow dataFiltered(): 689 using 'ggh4x' package ... p34189/Proteomics/QEXACTIVE_1/analytic_20240219/20240219_C34189_011_autoQC03dda.raw NA p34189/Proteomics/QEXACTIVE_1/analytic_20240219/20240219_C34189_011_autoQC03dda.raw vals$rawrr: TRUE nrow dataFiltered(): 689 using 'ggh4x' package ... p34189/Proteomics/QEXACTIVE_1/analytic_20240219/20240219_C34189_011_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p34189/Proteomics/QEXACTIVE_1/analytic_20240219/20240219_C34189_011_autoQC03dda.raw Reading raw file: /srv/www/htdocs//p34189/Proteomics/QEXACTIVE_1/analytic_20240219/20240219_C34189_011_autoQC03dda.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... Plotting chromatograms ... Plotting chromatograms ... NA nrow dataFiltered(): 689 using 'ggh4x' package ... nrow dataFiltered(): 689 using 'ggh4x' package ... nrow dataFiltered(): 689 using 'ggh4x' package ... nrow dataFiltered(): 689 using 'ggh4x' package ... Plotting chromatograms ... plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. Read 22032 items Warning: Error in hist.default: 'x' must be numeric 171: stop 170: hist.default 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-rawrr-autoQC03-plotTools 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708425946576483000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-22 16:34:23.180933 | timeMax: 2024-02-20 16:34:23.18173 | timeDiff: 5184000.00079703 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1280 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-22 15:34:23.181 | timeMax: 2024-02-20 15:34:23.182 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1280 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708347673186743000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp NA p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_002_autoQC01.raw p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_001_autoQC01.raw p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_002_autoQC01.raw NA p33801/Proteomics/FUSION_2/wuethrich_20240117/20240117_001_autoQC01.raw NA input timeRange: 7776000 | timeMin: 2023-12-12 15:34:24.324 | timeMax: 2024-02-20 15:34:23.182 | timeDiff: 6047998.85800004 nFacets: 4 nrow dataFiltered(): 1520 using 'ggh4x' package ... Warning: Removed 12 rows containing missing values (`geom_point()`). p34255/Proteomics/FUSION_2/fabiac_20240214/20240214_002_autoQC01_rep.raw NA p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_001_autoQC01.raw NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p33277/Proteomics/FUSION_2/roschi_20240220_one/20240220_001_autoQC01.raw Plotting chromatograms ... Read 22032 items 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-22 16:55:00.251717 | timeMax: 2024-02-20 16:55:00.252477 | timeDiff: 5184000.00075984 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-12-22 15:55:00.252 | timeMax: 2024-02-20 15:55:00.252 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1280 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708443259030469000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp input timeRange: 7776000 | timeMin: 2023-11-28 15:55:00.961 | timeMax: 2024-02-20 15:55:00.252 | timeDiff: 7257599.29100013 nFacets: 4 nrow dataFiltered(): 2000 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). NA fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-23 15:34:02.684332 | timeMax: 2024-02-21 15:34:02.684906 | timeDiff: 5184000.00057387 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(): 342 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-23 14:34:02.68433 | timeMax: 2024-02-21 14:34:02.68491 | timeDiff: 5184000.00057983 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-23 14:34:02.684 | timeMax: 2024-02-21 14:34:02.685 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 342 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 260 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 162 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-27 14:34:04.668 | timeMax: 2024-02-21 14:34:02.685 | timeDiff: 7430398.01699996 nFacets: 1 nrow dataFiltered(): 377 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 198 using 'ggh4x' package ... nrow dataFiltered(): 377 using 'ggh4x' package ... nrow dataFiltered(): 377 using 'ggh4x' package ... p3000/Proteomics/EXPLORIS_1/antdit_20240219/20240219_002_autoQC03dda.raw p3000/Proteomics/EXPLORIS_1/antdit_20240219/20240219_003_autoQC03dia.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708526039617589000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-23 15:41:10.334549 | timeMax: 2024-02-21 15:41:10.335132 | timeDiff: 5184000.00058293 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 896 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-23 14:41:10.335 | timeMax: 2024-02-21 14:41:10.335 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 896 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708526467251997000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-23 23:25:45.699325 | timeMax: 2024-02-21 23:25:45.700036 | timeDiff: 5184000.00071049 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-23 22:25:45.699 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). p34006/Proteomics/FUSION_2/limingqin_20240119/20240119_001_autoQC01.raw NA input timeRange: 7776000 | timeMin: 2023-11-23 22:25:46.80128 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775998.89872003 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:18.028039 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775967.67196131 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:18.028 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775967.67199993 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:20.260173 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775965.43982744 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:20.26 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775965.44000006 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:22.429418 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775963.27058172 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:22.429 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775963.27100015 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:24.584928 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775961.11507177 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:24.585 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775961.11500001 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:26.776433 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775958.92356753 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:26.776 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775958.92400002 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:28.995485 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775956.70451546 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:28.995 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775956.70500016 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:31.176593 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775954.52340722 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:31.177 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775954.523 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:33.365641 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775952.33435917 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:33.366 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775952.33400011 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:35.63952 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775950.06047988 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:35.64 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775950.05999994 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:37.990895 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775947.70910501 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:37.991 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775947.70900011 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:40.135057 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775945.5649426 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:40.135 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775945.56500006 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:42.256181 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775943.44381857 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:42.256 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775943.44400001 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:44.398742 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775941.30125833 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:44.399 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775941.30100012 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:46.554363 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775939.14563704 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:46.554 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775939.14600015 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:48.771276 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775936.92872381 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:48.771 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775936.92900014 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:51.097879 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775934.60212135 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:51.098 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775934.602 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:53.236858 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775932.46314216 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:53.237 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775932.46300006 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:55.423422 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775930.27657795 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:55.423 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775930.27699995 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:57.646878 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775928.05312181 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 22:26:57.647 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775928.05299997 nFacets: 4 nrow dataFiltered(): 2144 using 'ggh4x' package ... Warning: Removed 14 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 23:26:59.812768 | timeMax: 2024-02-21 22:25:45.7 | timeDiff: 7775925.88723207 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-23 23:27:02.952098 | timeMax: 2024-02-21 23:27:02.952674 | timeDiff: 5184000.00057578 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-23 22:27:02.952 | timeMax: 2024-02-21 22:27:02.953 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-02 22:27:03.945 | timeMax: 2024-02-21 22:27:02.953 | timeDiff: 6998399.00800014 nFacets: 4 nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708554342652375000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw Plotting chromatograms ... Read 22032 items NA vals$rawDiag: TRUE plotChargeState reading index for 20240220_008_autoQC01.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. plotTicBasepeak plotLockMassCorrection plotInjectionTime plotScanTime Warning: Error in dplyr::mutate: ℹ In argument: `transient = dplyr::case_when(...)`. Caused by error in `dplyr::case_when()`: ! Failed to evaluate the left-hand side of formula 1. Caused by error: ! object 'FTResolution' not found 202: 201: signalCondition 200: signal_abort 199: abort 198: 197: signalCondition 196: signal_abort 195: abort 194: h 193: .handleSimpleError 192: eval_tidy 190: case_formula_evaluate 189: dplyr::case_when 188: eval 187: mask$eval_all_mutate 186: mutate_col 184: mutate_cols 183: mutate.data.frame 181: .calcTransient 170: plotScanTime 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$__autoQC01__-rawDiag-autoQC03-plot 1: runApp plotCycleLoad `geom_smooth()` using formula = 'y ~ x' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-23 23:32:04.202151 | timeMax: 2024-02-21 23:32:04.202733 | timeDiff: 5184000.00058198 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-23 22:32:04.202 | timeMax: 2024-02-21 22:32:04.203 | timeDiff: 5184000.00100017 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). vals$rawrr: TRUE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 20 rows containing missing values (`geom_point()`). NA p3000/Proteomics/FUSION_2/chiawei_20240103/20240103_004_autoQC01.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708554419938312000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp input timeRange: 7776000 | timeMin: 2023-12-10 22:32:05.169 | timeMax: 2024-02-21 22:32:04.203 | timeDiff: 6307199.03400016 nFacets: 4 nrow dataFiltered(): 1600 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1600 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1600 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). NA p1000/Proteomics/FUSION_2/lkunz_20180827_autoQC/20180925_02_autoQC01.raw NA p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_001_autoQC01.raw p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_001_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p3000/Proteomics/FUSION_2/roschi_20240219_before_course/20240219_005_autoQC01.raw NA p34009/Proteomics/FUSION_2/unay_20240124/20240124_006_autoQC01.raw NA p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw Reading raw file: /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw Plotting chromatograms ... Read 22032 items p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_autoQC01.raw Reading raw file: /srv/www/htdocs//p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_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 nrow dataFiltered(): 1600 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1600 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-02 22:32:21.087 | timeMax: 2024-02-21 22:32:04.203 | timeDiff: 6998383.11600018 nFacets: 4 nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw NA p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw Reading raw file: /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw Plotting chromatograms ... Read 22032 items NA p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw plotClick: NA p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_008_autoQC01.raw p34176/Proteomics/FUSION_2/chiawei_20240207/20240207_017_autoQC01.raw NA nrow dataFiltered(): 1696 using 'ggh4x' package ... Warning: Removed 26 rows containing missing values (`geom_point()`). p34255/Proteomics/FUSION_2/fabiac_20240214/20240214_001_autoQC01.raw NA p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_001_autoQC01.raw p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_autoQC01.raw p33731/Proteomics/FUSION_2/analytic_20231213/20231213_C33731_010_autoQC01.raw p33591/Proteomics/FUSION_2/hasanali_20231208/20231208_010_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33591/Proteomics/FUSION_2/hasanali_20231208/20231208_010_autoQC01.raw Reading raw file: /srv/www/htdocs//p33591/Proteomics/FUSION_2/hasanali_20231208/20231208_010_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 p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_autoQC01.raw Reading raw file: /srv/www/htdocs//p33665/Proteomics/FUSION_2/aeberle_20231211/20231211_005_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 Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708554721177040000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA 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: 2023-12-24 09:20:59.290794 | timeMax: 2024-02-22 09:20:59.291375 | timeDiff: 5184000.00058031 nFacets: 4 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1408 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-24 08:20:59.291 | timeMax: 2024-02-22 08:20:59.291 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1408 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_001_autoQC01.raw NA plotClick: p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p34041/Proteomics/LUMOS_2/analytic_20240216/20240219_C34041_012_autoQC01.raw p34041/Proteomics/LUMOS_2/analytic_20240216/20240219_C34041_012_autoQC01.raw NA 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(): 234 using 'ggh4x' package ... nrow dataFiltered(): 546 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_002_autoQC03dda.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_002_autoQC03dda.raw NA nrow dataFiltered(): 546 using 'ggh4x' package ... NA p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_002_autoQC03dda.raw plotClick: NA p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_002_autoQC03dda.raw NA p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_002_autoQC03dda.raw nrow dataFiltered(): 234 using 'ggh4x' package ... p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_003_autoQC03dia.raw vals$rawDiag: TRUE nrow dataFiltered(): 234 using 'ggh4x' package ... plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_003_autoQC03dia.raw p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_003_autoQC03dia.raw plotChargeState Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawDiag-autoQC03-plot 1: runApp reading index for 20240221_003_autoQC03dia.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. vals$rawDiag: FALSE vals$rawrr: TRUE NA vals$rawrr: FALSE vals$rawrr: TRUE vals$rawrr: FALSE vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/cfortes_20240221/20240221_003_autoQC03dia.raw Plotting chromatograms ... Read 22032 items vals$rawrr: FALSE vals$rawrr: TRUE vals$rawrr: FALSE vals$rawrr: TRUE vals$rawrr: FALSE vals$rawrr: TRUE vals$rawrr: FALSE vals$rawrr: FALSE 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 10:00:37.631162 | timeMax: 2024-02-22 10:00:37.632135 | timeDiff: 5184000.00097251 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-24 09:00:37.631 | timeMax: 2024-02-22 09:00:37.632 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). NA p3000/Proteomics/EXPLORIS_2/analytic_20240212/20240212_002_autoQC01.raw NA p34241/Proteomics/EXPLORIS_2/analytic_20240215/20240215_C34241_001_autoQC01.raw NA fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 10:01:16.714456 | timeMax: 2024-02-22 10:01:16.715626 | timeDiff: 5184000.00117016 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-24 09:01:16.714 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 5184000.00200009 nFacets: 4 nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). p33914/Proteomics/EXPLORIS_2/analytic_20240117/20240117_C33914_039_autoQC01.raw p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_001_autoQC01.raw p33989/Proteomics/EXPLORIS_2/analytic_20240119/20240119_C33989_001_autoQC01.raw NA nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 360 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... NA NA plotClick: fn has changed to /srv/www/htdocs//p34114/Proteomics/EXPLORIS_2/analytic_20240202/20240202_C34114_001_autoQC01.raw p34114/Proteomics/EXPLORIS_2/analytic_20240202/20240202_C34114_001_autoQC01.raw plotClick: NA p34114/Proteomics/EXPLORIS_2/analytic_20240202/20240202_C34114_001_autoQC01.raw NA autoQC01 module APEX wide nrow: 261162 autoQC01 module APEX long nrow: 684 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 20 rows containing missing values (`geom_point()`). p34114/Proteomics/EXPLORIS_2/analytic_20240202/20240202_C34114_001_autoQC01.raw NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20240130/20240130_002_autoQC01.raw p3000/Proteomics/EXPLORIS_2/analytic_20240130/20240130_002_autoQC01.raw p3000/Proteomics/EXPLORIS_2/analytic_20240201/20240201_001_autoQC01.raw NA Warning: Removed 20 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20240130/20240130_002_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 p33801/Proteomics/FUSION_2/wuethrich_20240117/20240117_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p33801/Proteomics/FUSION_2/wuethrich_20240117/20240117_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p33801/Proteomics/FUSION_2/wuethrich_20240117/20240117_001_autoQC01.raw Plotting chromatograms ... Read 22032 items plotClick: plotClick: NA nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). p3000/Proteomics/FUSION_2/chiawei_20240205/20240205_003_autoQC01.raw p3000/Proteomics/FUSION_2/chiawei_20240205/20240205_003_autoQC01.raw NA plotClick: p33801/Proteomics/FUSION_2/wuethrich_20240117/20240117_001_autoQC01.raw nFacets: 4 nrow dataFiltered(): 0 NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw plotClick: NA input timeRange: 7776000 | timeMin: 2023-12-20 09:01:18.525 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 5529598.19099998 nFacets: 4 nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 12 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). input timeRange: 7776000 | timeMin: 2023-12-11 09:00:40.139 | timeMax: 2024-02-22 09:00:37.632 | timeDiff: 6307197.49300003 nFacets: 4 nrow dataFiltered(): 0 p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_004_autoQC01.raw p34009/Proteomics/FUSION_2/unay_20240124/20240124_006_autoQC01.raw input timeRange: 7776000 | timeMin: 2023-12-05 09:00:40.139 | timeMax: 2024-02-22 09:00:37.632 | timeDiff: 6825597.49300003 nFacets: 4 nrow dataFiltered(): 0 input timeRange: 7776000 | timeMin: 2023-12-03 09:03:48.612 | timeMax: 2024-02-22 09:00:37.632 | timeDiff: 6998209.01999998 nFacets: 4 nrow dataFiltered(): 0 input timeRange: 7776000 | timeMin: 2023-12-03 09:03:43.69 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 6998253.02600002 nFacets: 4 nrow dataFiltered(): 1712 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). vals$rawrr: TRUE NA plotClick: p3000/Proteomics/FUSION_2/chiawei_20240115/20240115_001_autoQC01.raw NA p3000/Proteomics/FUSION_2/chiawei_20240123/20240123_C34012_001_autoQC01.raw p3000/Proteomics/FUSION_2/chiawei_20240123/20240123_C34012_001_autoQC01.raw NA nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 0 p34068/Proteomics/FUSION_2/aeberle_20240201/20240201_001_autoQC01.raw nFacets: 4 nrow dataFiltered(): 1712 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). NA p34068/Proteomics/FUSION_2/aeberle_20240201/20240201_001_autoQC01.raw NA vals$rawDiag: TRUE input timeRange: 7776000 | timeMin: 2023-12-09 09:03:53.194 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 6479843.52200007 nFacets: 4 nrow dataFiltered(): 1664 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-10 09:05:57.135 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 6393319.58100009 nFacets: 4 nrow dataFiltered(): 1632 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-10 09:06:03.088 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 6393313.62800002 nFacets: 4 nrow dataFiltered(): 1632 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-11 09:06:24.799 | timeMax: 2024-02-22 09:01:16.716 | timeDiff: 6306891.91700006 nFacets: 4 nrow dataFiltered(): 1616 using 'ggh4x' package ... Warning: Removed 13 rows containing missing values (`geom_point()`). vals$rawrr: FALSE vals$rawrr: TRUE vals$rawDiag: FALSE p3000/Proteomics/FUSION_2/chiawei_20240103/20240103_003_autoQC01.raw p3000/Proteomics/FUSION_2/chiawei_20240103/20240103_001a_autoQC01.raw nrow dataFiltered(): 546 using 'ggh4x' package ... nrow dataFiltered(): 234 using 'ggh4x' package ... 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 10:21:16.713198 | timeMax: 2024-02-22 10:21:16.713856 | timeDiff: 5184000.00065827 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-24 09:21:16.713 | timeMax: 2024-02-22 09:21:16.714 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). nFacets: 4 nrow dataFiltered(): 0 nFacets: 0 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 0 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 10:21:52.787791 | timeMax: 2024-02-22 10:21:52.788634 | timeDiff: 5184000.00084376 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 0 input timeRange: 7776000 | timeMin: 2023-12-24 09:21:52.788 | timeMax: 2024-02-22 09:21:52.789 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 0 nFacets: 4 nrow dataFiltered(): 1328 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708593672847609000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_016_autoQC01.raw nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 936 using 'ggh4x' package ... NA p34284/Proteomics/FUSION_2/adelizliang_20240215/20240215_005_autoQC03dda.raw NA plotClick: fn has changed to /srv/www/htdocs//NA plotClick: fn has changed to /srv/www/htdocs//p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_017_autoQC03dia.raw p34343/Proteomics/FUSION_2/giostrazza_20240220_omics_course/20240220_017_autoQC03dia.raw Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708593708307349000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708444496725602000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 10:52:43.237766 | timeMax: 2024-02-22 10:52:43.238446 | timeDiff: 5184000.00068021 nFacets: 4 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1472 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-24 09:52:43.238 | timeMax: 2024-02-22 09:52:43.238 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1472 using 'ggh4x' package ... NA vals$rawrr: TRUE p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240221_034_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240221_034_autoQC01.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_1/pgehrig_20240104_autoQC/20240221_034_autoQC01.raw Plotting chromatograms ... Read 22032 items Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708595559923999000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708592433231300000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708592473244936000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-24 16:13:38.699716 | timeMax: 2024-02-22 16:13:38.700299 | timeDiff: 5184000.00058246 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-12-24 15:13:38.7 | timeMax: 2024-02-22 15:13:38.7 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 912 using 'ggh4x' package ... Warning: Removed 10 rows containing missing values (`geom_point()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708614815220415000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1708590055575525000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Execution halted Warning messages: 1: agg could not write to the given file 2: agg could not write to the given file