Listening on http://127.0.0.1:40593 Attaching package: 'shinydashboard' The following object is masked from 'package:graphics': box Loading required package: readr Loading required package: reshape2 Warning: The select input "file" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. Warning: The select input "file" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. Loading required package: lattice 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$cometPlot 1: runApp calling iRTprofileRawDIA() ... Warning: Error in seq.default: 'to' must be of length 1 191: stop 190: seq.default 187: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#111] 185: .func 182: contextFunc 181: env$runWith 174: ctx$run 173: self$.updateValue 171: iRTprofileRawDIA 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#351] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDIAiRTprofiles 1: runApp calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... /srv/www/htdocs//p33212/Proteomics/LUMOS_2/tobiasko_20231020/20231020_002_S580219_K562_incl_iRT_Group_1.raw Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cometPlot 1: runApp /srv/www/htdocs//p33212/Proteomics/LUMOS_2/tobiasko_20231020/20231020_002_S580219_K562_incl_iRT_Group_1.raw 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$cometPlot 1: runApp Warning: The select input "file" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cometPlot 1: runApp 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$cometPlot 1: runApp /srv/www/htdocs//p33212/Proteomics/LUMOS_2/tobiasko_20231020/20231020_002_S580219_K562_incl_iRT_Group_1.raw /srv/www/htdocs//p33212/Proteomics/LUMOS_2/tobiasko_20231020/20231020_004_S580219_K562_incl_iRT_Group_1.raw calling iRTprofileRawDIA() ... Warning: Error in seq.default: 'to' must be of length 1 191: stop 190: seq.default 187: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#111] 185: .func 182: contextFunc 181: env$runWith 174: ctx$run 173: self$.updateValue 171: iRTprofileRawDIA 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#351] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDIAiRTprofiles 1: runApp calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cometPlot 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/RtmpyEAeLD/file10789353f4d55c.stderr /tmp/RtmpyEAeLD/file107893344d2459.stdout and the System Requirements 189: stop 188: .rawrrSystem2Source 187: rawrr::readChromatogram 186: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#89] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: iRTprofileRawDDA 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#339] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotiRTDDAChromatograms 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/RtmpyEAeLD/file10789353f4d55c.stderr /tmp/RtmpyEAeLD/file107893344d2459.stdout and the System Requirements 193: 192: stop 191: iRTprofileRawDDA 186: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#139] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#362] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTprofiles 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/RtmpyEAeLD/file10789353f4d55c.stderr /tmp/RtmpyEAeLD/file107893344d2459.stdout and the System Requirements 173: 172: stop 171: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#375] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTfits 1: runApp Warning: Error in if: argument is of length zero 192: .extractMaximumPeak 191: FUN 190: lapply 189: rawrr:::pickPeak.rawrrChromatogram 186: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#139] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#362] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTprofiles 1: runApp Warning: Error in if: argument is of length zero 173: 172: stop 171: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#375] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTfits 1: runApp Warning: Error in if: argument is of length zero 192: .extractMaximumPeak 191: FUN 190: lapply 189: rawrr:::pickPeak.rawrrChromatogram 186: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#139] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#362] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTprofiles 1: runApp Warning: Error in if: argument is of length zero 173: 172: stop 171: rtFittedAPEX 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#375] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDDAiRTfits 1: runApp /srv/www/htdocs//p33212/Proteomics/LUMOS_2/tobiasko_20231020/20231020_002_S580219_K562_incl_iRT_Group_1.raw Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cometPlot 1: runApp 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$cometPlot 1: runApp calling iRTprofileRawDIA() ... Warning: Error in seq.default: 'to' must be of length 1 191: stop 190: seq.default 187: [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#111] 185: .func 182: contextFunc 181: env$runWith 174: ctx$run 173: self$.updateValue 171: iRTprofileRawDIA 168: renderPlot [/export/data01/scratch/DIAQC/qc/inst/shiny/fgczmsqc-dashboard/server.R#351] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plotDIAiRTprofiles 1: runApp calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... calling iRTprofileRawDIA() ... Warning: Error in graphics::plot.new: figure margins too large 130: graphics::plot.new 127: startPNG 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cometPlot 1: runApp Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases 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$cometPlot 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 4: agg could not write to the given file 5: agg could not write to the given file 6: agg could not write to the given file 7: agg could not write to the given file 8: agg could not write to the given file 9: agg could not write to the given file 10: agg could not write to the given file