Listening on http://127.0.0.1:44211

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: 2024-01-15 11:17:05.876905 | timeMax: 2024-03-15 11:17:05.878277 | timeDiff: 5184000.00137234
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$__autoQC01__-ui
   1: runApp
nFacets: 4
vals$rawrr: FALSE
vals$rawDiag: FALSE
nrow dataFiltered(): 1312
Loading required package: ggh4x
Loading required package: ggplot2
using 'ggh4x' package ...
Warning: Removed 10 rows containing missing values (`geom_point()`).
input timeRange: 7776000 | timeMin: 2024-01-15 10:17:05.877 | timeMax: 2024-03-15 10:17:05.878 | timeDiff: 5184000.00099993
nFacets: 4
nrow dataFiltered(): 1312
using 'ggh4x' package ...
Warning: Removed 10 rows containing missing values (`geom_point()`).
reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt
Warning: One or more parsing issues, call `problems()` on your data frame for
details, e.g.:
  dat <- vroom(...)
  problems(dat)
nFacets: 1
nFacets: 1
vals$rawrr: FALSE
vals$rawDiag: FALSE
vals$rawrr: FALSE
vals$rawDiag: FALSE
nrow dataFiltered(): 504
using 'ggh4x' package ...
nrow dataFiltered(): 260
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 338
using 'ggh4x' package ...
nFacets: 1
nrow dataFiltered(): 144
using 'ggh4x' package ...
autoQC01 module APEX wide nrow: 263208
autoQC01 module APEX long nrow: 636
LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK
APEXAUC.lg2
Warning: Removed 32 rows containing missing values (`geom_point()`).
input timeRange: 315360000 | timeMin: 2024-01-15 10:17:05.877 | timeMax: 2024-03-15 11:25:33.087813 | timeDiff: 5184507.21081281
autoQC01 module APEX long nrow: 636
LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK
APEXAUC.lg2
Warning: Removed 32 rows containing missing values (`geom_point()`).
nFacets: 4
nrow dataFiltered(): 848
using 'ggh4x' package ...
Warning: Removed 11 rows containing missing values (`geom_point()`).
input timeRange: 315360000 | timeMin: 2024-01-15 10:17:05.877 | timeMax: 2024-03-15 10:25:33.088 | timeDiff: 5184507.21099997
nFacets: 4
nrow dataFiltered(): 848
using 'ggh4x' package ...
Warning: Removed 11 rows containing missing values (`geom_point()`).
input timeRange: 315360000 | timeMin: 2015-11-15 10:25:46.873 | timeMax: 2024-03-15 10:25:33.088 | timeDiff: 262915186.215
nFacets: 4
nrow dataFiltered(): 29312
using 'ggh4x' package ...
Warning: Removed 242 rows containing missing values (`geom_point()`).
p24795/Proteomics/EXPLORIS_1/antdit_20210610/20210614_001_autoQC01.raw
nFacets: 4
nrow dataFiltered(): 36528
using 'ggh4x' package ...
Warning: Removed 658 rows containing missing values (`geom_point()`).
NA
nFacets: 4
nrow dataFiltered(): 25632
using 'ggh4x' package ...
Warning: Removed 339 rows containing missing values (`geom_point()`).
vals$rawDiag: TRUE
p2883/Proteomics/QEXACTIVEHFX_1/lkunz_20180913_OID4796_DIA/20180913_002c_autoQC01.raw
plotClick: 
fn has changed to /srv/www/htdocs//p2883/Proteomics/QEXACTIVEHFX_1/lkunz_20180913_OID4796_DIA/20180913_002c_autoQC01.raw
plotChargeState
Warning: Error in graphics::plot.new: figure margins too large
  130: graphics::plot.new
  127: startPNG
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$__autoQC01__-rawDiag-autoQC03-plot
    1: runApp
reading index for 20180913_002c_autoQC01.raw...
NA
p1000/Proteomics/QEXACTIVEHFX_1/tobiasko_20181108/20181108_17_autoQC01.raw
plotCycleLoad
`geom_smooth()` using formula = 'y ~ x'
plotCycleTime
plotInjectionTime
plotMassDistribution
plotPrecursorHeatmap
plotTicBasepeak
vals$rawrr: TRUE
plotChargeState
Reading raw file: /srv/www/htdocs//p2883/Proteomics/QEXACTIVEHFX_1/lkunz_20180913_OID4796_DIA/20180913_002c_autoQC01.raw
Plotting chromatograms ...
Read 22032 items
Warning in file(con, "w") :
  cannot open file 'logs-qc//shinylogs_fgczqcms-dashboard_1710497817773641000.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 message:
agg could not write to the given file