Listening on http://127.0.0.1:45741

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
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Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ...
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: 2024-08-19 16:51:08.367233 | timeMax: 2024-10-18 16:51:08.36788 | timeDiff: 5184000.00064754
Loading required package: bfabricShiny

Attaching package: 'bfabricShiny'

The following object is masked from 'package:base':

    save

nFacets: 4
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$__autoQC01__-ui
   1: runApp
Reading /scratch/DIAQC/qc/dump/comet.RData ...
nFacets: 0
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$autoQC03-DDA-ui
   1: runApp
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
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$autoQC03-DIA-ui
   1: runApp
nFacets: 1
nFacets: 1
vals$rawrr: FALSE
vals$rawDiag: FALSE
vals$rawrr: FALSE
vals$rawDiag: FALSE
nrow dataFiltered(): 195
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DDA-plot
    1: runApp
nrow dataFiltered(): 324
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DIA-plot
    1: runApp
input timeRange: 7776000 | timeMin: 2024-08-19 14:51:08.36723 | timeMax: 2024-10-18 14:51:08.36788 | timeDiff: 5184000.00064993
nFacets: 1
nrow dataFiltered(): 195
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DDA-plot
    1: runApp
nFacets: 1
nrow dataFiltered(): 324
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DIA-plot
    1: runApp
nrow dataFiltered(): 324
Loading required package: ggh4x
Loading required package: ggplot2

Attaching package: 'ggh4x'

The following object is masked from 'package:ggplot2':

    guide_axis_logticks

using 'ggh4x' package ...
nrow dataFiltered(): 195
using 'ggh4x' package ...
input timeRange: 7776000 | timeMin: 2024-08-19 14:51:08.367 | timeMax: 2024-10-18 14:51:08.368 | timeDiff: 5184000.00099993
nFacets: 1
nrow dataFiltered(): 195
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 324
using 'ggh4x' package ...
fn has changed to NA
fn has changed to NA
fn has changed to NA
fn has changed to NA
Reading /scratch/DIAQC/qc/dump/autoQC01-fit-apex-auc-fwhm.txt ...
nFacets: 4
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$__autoQC01__-ui
   1: runApp
input timeRange: 7776000 | timeMin: 2024-08-19 16:55:29.756195 | timeMax: 2024-10-18 16:55:29.756787 | timeDiff: 5184000.00059223
nFacets: 4
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$__autoQC01__-ui
   1: runApp
Reading /scratch/DIAQC/qc/dump/comet.RData ...
nFacets: 0
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$autoQC03-DDA-ui
   1: runApp
reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt
Warning: One or more parsing issues, call `problems()` on your data frame for
details, e.g.:
  dat <- vroom(...)
  problems(dat)
nFacets: 1
Warning: Error in if: argument is of length zero
  97: renderUI
  96: func
  83: renderFunc
  82: output$autoQC03-DIA-ui
   1: runApp
nFacets: 1
nFacets: 1
vals$rawrr: FALSE
vals$rawDiag: FALSE
vals$rawrr: FALSE
vals$rawDiag: FALSE
nrow dataFiltered(): 195
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DDA-plot
    1: runApp
nrow dataFiltered(): 324
Warning: Error in .ggplot: !is.null(variables) is not TRUE
  173: <Anonymous>
  172: stop
  171: stopifnot
  170: .ggplot
  169: ggplot2FUN
  168: renderPlot
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$autoQC03-DIA-plot
    1: runApp
nrow dataFiltered(): 324
using 'ggh4x' package ...
nrow dataFiltered(): 195
using 'ggh4x' package ...
input timeRange: 7776000 | timeMin: 2024-08-19 14:55:29.7562 | timeMax: 2024-10-18 14:55:29.75679 | timeDiff: 5184000.00059009
nFacets: 1
nrow dataFiltered(): 195
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 324
using 'ggh4x' package ...
input timeRange: 7776000 | timeMin: 2024-08-19 14:55:29.756 | timeMax: 2024-10-18 14:55:29.757 | timeDiff: 5184000.00099993
nFacets: 1
nrow dataFiltered(): 195
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 324
using 'ggh4x' package ...
NA
plotClick: 
fn has changed to /srv/www/htdocs//NA
plotClick: 
plotClick: 
plotClick: 
NA
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
NA
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
NA
p3000/Proteomics/EXPLORIS_2/lkunz_20241014/20241014_002_autoQC03dda.raw
p3000/Proteomics/EXPLORIS_2/lkunz_20241007/20241007_002_autoQC03dda.raw
NA
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
Warning in file(con, "w") :
  cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1729263325713487000.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
nrow dataFiltered(): 195
using 'ggh4x' package ...
NA
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
p36355/Proteomics/EXPLORIS_2/analytic_20241016/20241016_C36355_005_autoQC03dia.raw
p36635/Proteomics/EXPLORIS_2/analytic_20241018/20241018_C36635_002_autoQC03dda.raw
NA
p3000/Proteomics/EXPLORIS_2/lkunz_20241014/20241014_002_autoQC03dda.raw
NA
p36073/Proteomics/EXPLORIS_2/analytic_20240829/20240828_C36073_013_autoQC03dda.raw
nFacets: 4
nrow dataFiltered(): 988
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 288
using 'ggh4x' package ...
NA
nrow dataFiltered(): 988
using 'ggh4x' package ...
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
p3127/Proteomics/LUMOS_2/mesche_20241008/20241008_021_autoQC03dda_old.raw
p36467/Proteomics/LUMOS_2/domingo_20241004/20241004_017_autoQC03dda.raw
p3000/Proteomics/LUMOS_2/pgehrig_20240930_Nic_Dimet/20240930_15_autoQC03dda.raw
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
NA
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
NA
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
NA
nrow dataFiltered(): 988
using 'ggh4x' package ...
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
Warning: One or more parsing issues, call `problems()` on your data frame for
details, e.g.:
  dat <- vroom(...)
  problems(dat)
autoQC01 module APEX wide nrow: 281215
autoQC01 module APEX long nrow: 0
LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK
APEXAUC.lg2
autoQC01 module APEX long nrow: 948
LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK
APEXAUC.lg2
Warning: Removed 4 rows containing missing values or values outside the scale
range (`geom_point()`).
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_line()`).
p3000/Proteomics/LUMOS_2/pgehrig_20240930_Nic_Dimet/20240930_15_autoQC03dda.raw
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
NA
p3000/Proteomics/LUMOS_2/pgehrig_20241009_autoQC/20241011_003_autoQC03dda_old.raw
NA
Warning in file(con, "w") :
  cannot open file '/usr/local/lib/R/site-library/fgczqcms/shiny/fgczqcms-dashboard/logs-qc/shinylogs_fgczqcms-dashboard_1729263064051787000.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