Listening on http://127.0.0.1:40009 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 14:59:28.201414 | timeMax: 2024-01-22 14:59:28.202356 | timeDiff: 5184000.00094223 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 nFacets: 1 nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 612 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... nrow dataFiltered(): 26 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-23 13:59:28.20141 | timeMax: 2024-01-22 13:59:28.20236 | timeDiff: 5184000.00095034 nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 612 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-23 13:59:28.201 | timeMax: 2024-01-22 13:59:28.202 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 612 using 'ggh4x' package ... NA p33939/Proteomics/TIMSTOF_1/jagall_20240119_/zip/20240119_007_autoQC03dia.d.zip plotClick: fn has changed to /srv/www/htdocs//p33939/Proteomics/TIMSTOF_1/jagall_20240119_/zip/20240119_007_autoQC03dia.d.zip p33868/Proteomics/TIMSTOF_1/galliserena_20240117_/zip/20240117_001_autoQC03dia.d.zip plotClick: fn has changed to /srv/www/htdocs//p33868/Proteomics/TIMSTOF_1/galliserena_20240117_/zip/20240117_001_autoQC03dia.d.zip NA p33939/Proteomics/TIMSTOF_1/jagall_20240119_/zip/20240119_007_autoQC03dia.d.zip plotClick: fn has changed to /srv/www/htdocs//p33939/Proteomics/TIMSTOF_1/jagall_20240119_/zip/20240119_007_autoQC03dia.d.zip Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 15:41:21.209031 | timeMax: 2024-01-22 15:41:21.210486 | timeDiff: 5184000.00145459 nFacets: 4 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-23 14:41:21.209 | timeMax: 2024-01-22 14:41:21.21 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1344 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). autoQC01 module APEX wide nrow: 257994 autoQC01 module APEX long nrow: 1008 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 34 rows containing missing values (`geom_point()`). Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 15:41:40.966543 | timeMax: 2024-01-22 15:41:40.967981 | timeDiff: 5184000.00143766 nFacets: 4 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) vals$rawrr: FALSE vals$rawDiag: FALSE input timeRange: 7776000 | timeMin: 2023-11-23 14:41:40.96654 | timeMax: 2024-01-22 14:41:40.96798 | timeDiff: 5184000.00143981 NA NA p33642/Proteomics/LUMOS_2/analytic_20240104/20240104_C33642_001_autoQC01.raw NA p33642/Proteomics/LUMOS_2/analytic_20240104/20240104_C33642_001_autoQC01.raw NA nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 6 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 14:41:40.967 | timeMax: 2024-01-22 14:41:40.968 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1296 using 'ggh4x' package ... Warning: Removed 6 rows containing missing values (`geom_point()`). NA reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 15:44:28.941791 | timeMax: 2024-01-22 15:44:28.942472 | timeDiff: 5184000.00068092 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: 2023-11-23 14:44:28.94179 | timeMax: 2024-01-22 14:44:28.94247 | timeDiff: 5184000.00067997 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-23 14:44:28.942 | timeMax: 2024-01-22 14:44:28.942 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 486 using 'ggh4x' package ... NA NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1705934665664146000.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_1705934474139298000.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_1705931963601516000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 17:38:29.092178 | timeMax: 2024-01-22 17:38:29.093053 | timeDiff: 5184000.00087523 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 6 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-11-23 16:38:29.092 | timeMax: 2024-01-22 16:38:29.093 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1312 using 'ggh4x' package ... Warning: Removed 6 rows containing missing values (`geom_point()`). NA plotClick: fn has changed to /srv/www/htdocs//NA p33969/Proteomics/EXPLORIS_2/analytic_20240122/20240122_C33969_001_autoQC01.raw NA nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1376 using 'ggh4x' package ... Warning: Removed 9 rows containing missing values (`geom_point()`). p33862/Proteomics/LUMOS_2/analytic_20240108/20240108_C33862_001_autoQC01.raw NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1705941505615616000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-23 20:31:11.101431 | timeMax: 2024-01-22 20:31:11.102006 | timeDiff: 5184000.0005753 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: 2023-11-23 19:31:11.10143 | timeMax: 2024-01-22 19:31:11.10201 | timeDiff: 5184000.00058007 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-23 19:31:11.101 | timeMax: 2024-01-22 19:31:11.102 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 612 using 'ggh4x' package ... NA Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1705934494452060000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-24 10:06:17.144212 | timeMax: 2024-01-23 10:06:17.144801 | timeDiff: 5184000.00058842 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 270 using 'ggh4x' package ... nrow dataFiltered(): 195 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-24 09:06:17.14421 | timeMax: 2024-01-23 09:06:17.1448 | timeDiff: 5184000.00059009 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-24 09:06:17.144 | timeMax: 2024-01-23 09:06:17.145 | timeDiff: 5184000.00099993 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... nFacets: 4 nrow dataFiltered(): 1092 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 486 using 'ggh4x' package ... NA p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: plotClick: plotClick: plotClick: NA p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: plotClick: NA p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw plotClick: NA p34014/Proteomics/FUSION_2/analytic_20240119/20240119_C34014_005_autoQC03dia.raw NA Warning in dir.create(path) : cannot create dir 'logs-qc', reason 'Permission denied' fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-24 14:16:38.854627 | timeMax: 2024-01-23 14:16:38.855191 | timeDiff: 5184000.00056362 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: 2023-11-24 13:16:38.85463 | timeMax: 2024-01-23 13:16:38.85519 | timeDiff: 5184000.00056005 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-24 13:16:38.855 | timeMax: 2024-01-23 13:16:38.855 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 270 using 'ggh4x' package ... 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$autoQC03-DDA-plot 1: runApp nFacets: 1 Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp nFacets: 1 nrow dataFiltered(): 0 nrow dataFiltered(): 286 using 'ggh4x' package ... nrow dataFiltered(): 286 using 'ggh4x' package ... NA input timeRange: 7776000 | timeMin: 2023-10-26 13:16:40.892 | timeMax: 2024-01-23 13:16:38.855 | timeDiff: 7689597.96300006 nFacets: 1 nrow dataFiltered(): 494 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 0 nrow dataFiltered(): 494 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1706015795843688000.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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-24 17:31:57.160902 | timeMax: 2024-01-23 17:31:57.161471 | timeDiff: 5184000.00056911 nFacets: 4 nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: The following named parsers don't match the column names: Time, Size, Precursors.Identified, Proteins.Identified Warning: Error in : id variables not found in data: Md5, File.Name, time 179: stop 178: melt_check 177: melt.data.frame 175: readFUN 174: 158: data 151: 135: dataFiltered 131: 115: nFacets 97: renderUI 96: func 83: renderFunc 82: output$autoQC03-DIA-ui 1: runApp nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 26 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-24 16:31:57.1609 | timeMax: 2024-01-23 16:31:57.16147 | timeDiff: 5184000.00057006 nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-24 16:31:57.161 | timeMax: 2024-01-23 16:31:57.161 | timeDiff: 5184000 nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... NA nFacets: 1 nrow dataFiltered(): 78 using 'ggh4x' package ... p3000/Proteomics/TIMSTOFFLEX_1/antdit_20240108/zip/20240108_003_autoQC03dda_25ng.d.zip plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/TIMSTOFFLEX_1/antdit_20240108/zip/20240108_003_autoQC03dda_25ng.d.zip NA nFacets: 1 nrow dataFiltered(): 26 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 195 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1705951866922169000.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_1706027513935342000.json': No such file or directory Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp Execution halted Warning messages: 1: agg could not write to the given file 2: agg could not write to the given file