Listening on http://127.0.0.1:41801 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 15:34:40.812922 | timeMax: 2024-01-30 15:34:40.813506 | timeDiff: 5184000.00058317 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-01 15:34:50.862831 | timeMax: 2024-01-30 15:34:50.863405 | timeDiff: 5184000.00057435 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-01 14:34:50.863 | timeMax: 2024-01-30 14:34:50.863 | timeDiff: 5184000 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1706625277061066000.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 nFacets: 4 nrow dataFiltered(): 0 NA 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$autoQC03-DDA-plot 1: runApp nrow dataFiltered(): 702 using 'ggh4x' package ... NA p34002/Proteomics/TIMSTOF_1/spfammatter_20240126/zip/20240126_013_autoQC03dia.d.zip NA vals$rawrr: TRUE vals$rawrr: FALSE p33915/Proteomics/TIMSTOF_1/cfortes_20240129_/zip/20240129_007_autoQC03dia.d.zip p33915/Proteomics/TIMSTOF_1/cfortes_20240129_/zip/20240129_012_autoQC03dia.d.zip p34002/Proteomics/TIMSTOF_1/spfammatter_20240126/zip/20240126_013_autoQC03dia.d.zip plotClick: fn has changed to /srv/www/htdocs//p34002/Proteomics/TIMSTOF_1/spfammatter_20240126/zip/20240126_013_autoQC03dia.d.zip NA p34002/Proteomics/TIMSTOF_1/spfammatter_20240126/zip/20240126_013_autoQC03dia.d.zip plotClick: NA p33868/Proteomics/TIMSTOF_1/galliserena_20240117_/zip/20240117_001_autoQC03dia.d.zip NA input timeRange: 7776000 | timeMin: 2023-11-01 14:35:21.73349 | timeMax: 2024-01-30 14:34:50.863 | timeDiff: 7775969.12950993 nFacets: 0 nFacets: 1 nrow dataFiltered(): 774 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-01 16:38:03.499155 | timeMax: 2024-01-30 14:34:50.863 | timeDiff: 7772207.36384463 nFacets: 0 nFacets: 1 nrow dataFiltered(): 774 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-11-01 15:38:03.499 | timeMax: 2024-01-30 14:34:50.863 | timeDiff: 7772207.36399984 nFacets: 0 nFacets: 1 nrow dataFiltered(): 774 using 'ggh4x' package ... Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-plot 1: runApp 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-12-02 09:39:31.046206 | timeMax: 2024-01-31 09:39:31.046778 | timeDiff: 5184000.00057125 nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 1216 using 'ggh4x' package ... input timeRange: 7776000 | timeMin: 2023-12-02 08:39:31.046 | timeMax: 2024-01-31 08:39:31.047 | timeDiff: 5184000.00099993 nFacets: 4 nrow dataFiltered(): 1216 using 'ggh4x' package ... nFacets: 1 reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt Warning: One or more parsing issues, call `problems()` on your data frame for details, e.g.: dat <- vroom(...) problems(dat) nFacets: 1 vals$rawrr: FALSE vals$rawDiag: FALSE vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 234 using 'ggh4x' package ... nrow dataFiltered(): 156 using 'ggh4x' package ... NA input timeRange: 7776000 | timeMin: 2023-11-07 08:39:58.854 | timeMax: 2024-01-31 08:39:31.047 | timeDiff: 7343972.19299984 nrow dataFiltered(): 286 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 288 using 'ggh4x' package ... nFacets: 1 input timeRange: 283824000 | timeMin: 2023-11-07 08:39:58.854 | timeMax: 2024-01-31 09:40:27.404409 | timeDiff: 7344028.5504086 nrow dataFiltered(): 286 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 288 using 'ggh4x' package ... nFacets: 1 input timeRange: 283824000 | timeMin: 2023-11-07 08:39:58.854 | timeMax: 2024-01-31 08:40:27.404 | timeDiff: 7344028.54999995 nrow dataFiltered(): 286 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 288 using 'ggh4x' package ... nFacets: 1 input timeRange: 283824000 | timeMin: 2015-11-21 08:40:28.668 | timeMax: 2024-01-31 08:40:27.404 | timeDiff: 258595198.736 nrow dataFiltered(): 3042 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 288 using 'ggh4x' package ... nFacets: 1 nFacets: 4 nrow dataFiltered(): 15696 using 'ggh4x' package ... Warning: Removed 83 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). Warning in file(con, "w") : cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1706625287477454000.json': Permission denied Warning: Error in file: cannot open the connection 34: file 33: writeLines 32: jsonlite::write_json 31: write_logs_json 30: write_logs 29: callback 1: runApp vals$rawDiag: TRUE plotClick: fn has changed to /srv/www/htdocs//p31999/Proteomics/EXPLORIS_2/analytic_20230622/20230622_C31999_010a_autoQC01.raw p31999/Proteomics/EXPLORIS_2/analytic_20230622/20230622_C31999_010a_autoQC01.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$__autoQC01__-rawDiag-autoQC03-plot 1: runApp reading index for 20230622_C31999_010a_autoQC01.raw... NA vals$rawrr: TRUE Reading raw file: /srv/www/htdocs//p31999/Proteomics/EXPLORIS_2/analytic_20230622/20230622_C31999_010a_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 p33922/Proteomics/EXPLORIS_2/analytic_20240116/20240116_C33922_001_autoQC01.raw p3000/Proteomics/EXPLORIS_2/lkunz_20221209/20221209_001_autoQC01.raw p32778/Proteomics/EXPLORIS_2/analytic_20230907/20230907_C32778_004_autoQC01_PepSep.raw NA p33164/Proteomics/EXPLORIS_2/analytic_20231026/20231026_C33164_001c_autoQC01.raw p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_001_autoQC01.raw nrow dataFiltered(): 15696 using 'ggh4x' package ... Warning: Removed 166 rows containing missing values (`geom_point()`). Warning: Removed 1 row containing missing values (`geom_line()`). NA p30103/Proteomics/EXPLORIS_2/analytic_20221130/20221129_C30103_008_autoQC01.raw p31749/Proteomics/EXPLORIS_2/analytic_20230613/20230613_C31749_071_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_1706690367992225000.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 3: agg could not write to the given file