Listening on http://127.0.0.1:35555 Loading required package: shinydashboard 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: rawrr fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-09 13:54:59.578385 | timeMax: 2023-11-30 13:54:59.579036 | timeDiff: 1814400.00065112 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save input timeRange: 7776000 | timeMin: 2023-11-09 12:54:59.578 | timeMax: 2023-11-30 12:54:59.579 | timeDiff: 1814400.00099993 nrow dataFiltered(): 1496 Warning: Removed 30 rows containing missing values (`geom_point()`). fn has changed to NA fn has changed to NA fn has changed to NA fn has changed to NA Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-09 14:03:13.616122 | timeMax: 2023-11-30 14:03:13.616745 | timeDiff: 1814400.00062275 input timeRange: 7776000 | timeMin: 2023-11-09 13:03:13.616 | timeMax: 2023-11-30 13:03:13.617 | timeDiff: 1814400.00100017 nrow dataFiltered(): 1496 Warning: Removed 30 rows containing missing values (`geom_point()`). autoQC01 module APEX wide nrow: 253374 autoQC01 module APEX long nrow: 408 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 20 rows containing missing values (`geom_point()`). reading /scratch/DIAQC/qc/dump/autoQC03-diann.txt nrow dataFiltered(): 54 nrow dataFiltered(): 117 nrow dataFiltered(): 0 nrow dataFiltered(): 72 input timeRange: 7776000 | timeMin: 2023-10-14 13:03:22.98 | timeMax: 2023-11-30 13:03:13.617 | timeDiff: 4060790.63700008 nrow dataFiltered(): 0 nrow dataFiltered(): 72 NA p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_002_autoQC03diaPASEF.d.zip plotClick: fn has changed to /srv/www/htdocs//p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_002_autoQC03diaPASEF.d.zip NA plotClick: fn has changed to /srv/www/htdocs//p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_001_autoQC03diaPASEF.d.zip p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_001_autoQC03diaPASEF.d.zip plotClick: fn has changed to /srv/www/htdocs//p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_002_autoQC03diaPASEF.d.zip p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_002_autoQC03diaPASEF.d.zip NA nrow dataFiltered(): 299 nrow dataFiltered(): 54 Reading raw file: /srv/www/htdocs//p33383/Proteomics/TIMSTOF_1/spfammatter_20231128_/zip/20231128_002_autoQC03diaPASEF.d.zip Warning: Error in .rawrrSystem2Source: Rcode file to parse does not exist. '/var/www/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason. Please check the debug files: /tmp/Rtmp4IRnPh/file3a22a569d5f328.stderr /tmp/Rtmp4IRnPh/file3a22a57a9fb5.stdout and the System Requirements 194: stop 193: .rawrrSystem2Source 192: rawrr::readChromatogram 191: 189: .func 186: contextFunc 185: env$runWith 178: ctx$run 177: self$.updateValue 175: peptideProfile 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotChromatograms 1: runApp Read 22032 items Warning: Error in .rawrrSystem2Source: Rcode file to parse does not exist. '/var/www/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason. Please check the debug files: /tmp/Rtmp4IRnPh/file3a22a569d5f328.stderr /tmp/Rtmp4IRnPh/file3a22a57a9fb5.stdout and the System Requirements 174: 173: stop 172: peptideProfile 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotTools 1: runApp Warning: Error in .rawrrSystem2Source: Rcode file to parse does not exist. '/var/www/.cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason. Please check the debug files: /tmp/Rtmp4IRnPh/file3a22a569d5f328.stderr /tmp/Rtmp4IRnPh/file3a22a57a9fb5.stdout and the System Requirements 171: 170: stop 169: peptideProfile 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DIA-rawrr-autoQC03-plotProfiles 1: runApp plotClick: fn has changed to /srv/www/htdocs//NA Warning in renderUI() : raw file /srv/www/htdocs//NA does not exist. NA autoQC01 module APEX long nrow: 996 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 34 rows containing missing values (`geom_point()`). nrow dataFiltered(): 3652 Warning: Removed 37 rows containing missing values (`geom_point()`). NA p32865/Proteomics/EXPLORIS_2/analytic_20231018/20231019_C32865_001_autoQC01.raw plotClick: fn has changed to /srv/www/htdocs//p32865/Proteomics/EXPLORIS_2/analytic_20231018/20231019_C32865_001_autoQC01.raw Reading raw file: /srv/www/htdocs//p32865/Proteomics/EXPLORIS_2/analytic_20231018/20231019_C32865_001_autoQC01.raw Plotting chromatograms ... Read 22032 items Plotting chromatograms ... Plotting chromatograms ... p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_010_autoQC01.raw plotClick: 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$__autoQC01__-rawrr-autoQC03-plotTools 1: runApp NA plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_024_autoQC03dia_2ul.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_024_autoQC03dia_2ul.raw Plotting chromatograms ... Read 22032 items p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_024_autoQC03dia_2ul.raw p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_024_autoQC03dia_2ul.raw plotClick: input timeRange: 7776000 | timeMin: 2023-09-24 13:03:38.208 | timeMax: 2023-11-30 13:03:13.617 | timeDiff: 5788775.40900016 nrow dataFiltered(): 351 nrow dataFiltered(): 54 p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_025_autoQC03dia_2ul.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_025_autoQC03dia_2ul.raw Reading raw file: /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C3000_025_autoQC03dia_2ul.raw Plotting chromatograms ... Read 22032 items nrow dataFiltered(): 351 Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. nrow dataFiltered(): 54 nrow dataFiltered(): 728 nrow dataFiltered(): 144 nrow dataFiltered(): 2158 nrow dataFiltered(): 162 input timeRange: 7776000 | timeMin: 2023-09-07 13:05:37.799 | timeMax: 2023-11-30 13:03:13.617 | timeDiff: 7257455.81800008 nrow dataFiltered(): 2678 nrow dataFiltered(): 162 nrow dataFiltered(): 520 nrow dataFiltered(): 0 nrow dataFiltered(): 1508 nrow dataFiltered(): 72 nrow dataFiltered(): 2678 nrow dataFiltered(): 162 input timeRange: 7776000 | timeMin: 2023-10-31 13:07:38.429 | timeMax: 2023-11-30 13:03:13.617 | timeDiff: 2591735.1880002 nrow dataFiltered(): 1170 nrow dataFiltered(): 162 Execution halted