Listening on http://127.0.0.1:42485 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: rawDiag Loading required package: rawrr 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$__autoQC01__-ui 1: runApp input timeRange: 7776000 | timeMin: 2023-11-28 13:46:40.590007 | timeMax: 2023-12-19 13:46:40.591792 | timeDiff: 1814400.0017848 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save nFacets: 4 Warning: Error in if: argument is of length zero 97: renderUI 96: func 83: renderFunc 82: output$__autoQC01__-ui 1: runApp nFacets: 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 input timeRange: 7776000 | timeMin: 2023-11-28 12:46:40.59001 | timeMax: 2023-12-19 12:46:40.59179 | timeDiff: 1814400.00178003 nFacets: 1 nFacets: 1 input timeRange: 7776000 | timeMin: 2023-11-28 12:46:40.59 | timeMax: 2023-12-19 12:46:40.592 | timeDiff: 1814400.00200009 nFacets: 1 nFacets: 1 nrow dataFiltered(): 90 Loading required package: ggh4x Loading required package: ggplot2 using 'ggh4x' package ... nrow dataFiltered(): 78 using 'ggh4x' package ... nFacets: 3 nrow dataFiltered(): 221 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nFacets: 1 nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 221 using 'ggh4x' package ... Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nrow dataFiltered(): 144 using 'ggh4x' package ... nrow dataFiltered(): 221 using 'ggh4x' package ... `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? `geom_line()`: Each group consists of only one observation. ℹ Do you need to adjust the group aesthetic? nrow dataFiltered(): 144 using 'ggh4x' package ... vals$rawDiag: TRUE vals$rawrr: TRUE p3000/Proteomics/LUMOS_2/analytics_20231206/20231214_C3000_004_autoQC03dda1_autoQC4L.raw plotClick: fn has changed to /srv/www/htdocs//p3000/Proteomics/LUMOS_2/analytics_20231206/20231214_C3000_004_autoQC03dda1_autoQC4L.raw plotChargeState Reading raw file: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/analytics_20231206/20231214_C3000_004_autoQC03dda1_autoQC4L.raw Plotting chromatograms ... Read 22032 items 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$autoQC03-DDA-rawDiag-autoQC03-plot 1: runApp reading index for 20231214_C3000_004_autoQC03dda1_autoQC4L.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. plotLockMassCorrection plotScanTime Warning: Error in dplyr::mutate: ℹ In argument: `transient = dplyr::case_when(...)`. Caused by error in `dplyr::case_when()`: ! Failed to evaluate the left-hand side of formula 1. Caused by error: ! object 'FTResolution' not found 202: 201: signalCondition 200: signal_abort 199: abort 198: 197: signalCondition 196: signal_abort 195: abort 194: h 193: .handleSimpleError 192: eval_tidy 190: case_formula_evaluate 189: dplyr::case_when 188: eval 187: mask$eval_all_mutate 186: mutate_col 184: mutate_cols 183: mutate.data.frame 181: .calcTransient 170: plotScanTime 168: renderPlot 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$autoQC03-DDA-rawDiag-autoQC03-plot 1: runApp plotPrecursorHeatmap plotMzDistribution plotLockMassCorrection plotInjectionTime plotCycleTime plotCycleLoad `geom_smooth()` using formula = 'y ~ x' plotCycleTime plotChargeState plotMassDistribution NA input timeRange: 7776000 | timeMin: 2023-09-27 12:46:45.098 | timeMax: 2023-12-19 12:46:40.592 | timeDiff: 7171195.49399996 nFacets: 3 nrow dataFiltered(): 897 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... plotChargeState input timeRange: 94608000 | timeMin: 2023-09-27 12:46:45.098 | timeMax: 2023-12-19 13:54:09.161649 | timeDiff: 7171644.06364918 nFacets: 3 nrow dataFiltered(): 897 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... input timeRange: 94608000 | timeMin: 2023-09-27 12:46:45.098 | timeMax: 2023-12-19 12:54:09.162 | timeDiff: 7171644.06399989 nFacets: 3 nrow dataFiltered(): 897 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... input timeRange: 94608000 | timeMin: 2021-04-20 12:54:12.778 | timeMax: 2023-12-19 12:54:09.162 | timeDiff: 84067196.3839998 nFacets: 3 nrow dataFiltered(): 8125 using 'ggh4x' package ... nFacets: 1 nrow dataFiltered(): 234 using 'ggh4x' package ... nFacets: 4 vals$rawrr: FALSE vals$rawDiag: FALSE nrow dataFiltered(): 21120 using 'ggh4x' package ... Warning: Removed 139 rows containing missing values (`geom_point()`). NA vals$rawDiag: TRUE p33212/Proteomics/LUMOS_2/cfortes_20231206/20231206_001_S580219_K562_incl_iRT_autoQC03dia.raw plotClick: fn has changed to /srv/www/htdocs//p33212/Proteomics/LUMOS_2/cfortes_20231206/20231206_001_S580219_K562_incl_iRT_autoQC03dia.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$autoQC03-DIA-rawDiag-autoQC03-plot 1: runApp reading index for 20231206_001_S580219_K562_incl_iRT_autoQC03dia.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. NA plotCycleTime plotPrecursorHeatmap Execution halted Warning messages: 1: agg could not write to the given file 2: agg could not write to the given file