Listening on http://127.0.0.1:41159 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 input timeRange: 7776000 | timeMin: 2023-11-02 21:56:05.87153 | timeMax: 2023-11-23 21:56:05.872154 | timeDiff: 1814400.00062394 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save input timeRange: 7776000 | timeMin: 2023-11-02 20:56:05.872 | timeMax: 2023-11-23 20:56:05.872 | timeDiff: 1814400 nrow dataFiltered(): 0 nrow dataFiltered(): 91 autoQC01 module APEX wide nrow: 252263 autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). plot_click: p33402/Proteomics/EXPLORIS_2/analytic_20231122/20231122_C33402_012_autoQC01.raw plot_click: p33402/Proteomics/EXPLORIS_2/analytic_20231122/20231122_C33402_012_autoQC01.raw fn has changed to /srv/www/htdocs//p33402/Proteomics/EXPLORIS_2/analytic_20231122/20231122_C33402_012_autoQC01.raw Reading raw file: /srv/www/htdocs//p33402/Proteomics/EXPLORIS_2/analytic_20231122/20231122_C33402_012_autoQC01.raw length = 3 Plotting chromatograms ... Read 22032 items plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw fn has changed to /srv/www/htdocs//p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw Reading raw file: /srv/www/htdocs//p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw length = 3 Plotting chromatograms ... Read 22032 items autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw | plot_click: p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_039_autoQC01.raw autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 444 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 6 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 1332 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 26 rows containing missing values (`geom_point()`). Reading raw file: /srv/www/htdocs//p33281/Proteomics/EXPLORIS_2/analytic_20231117_m3_m4/20231117_C33281_077_autoQC01.raw length = 9 Plotting chromatograms ... Read 22032 items Plotting chromatograms ... input timeRange: 7776000 | timeMin: 2023-09-18 20:56:07.998 | timeMax: 2023-11-23 20:56:05.872 | timeDiff: 5702397.87400007 autoQC01 module APEX long nrow: 4320 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 60 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 3816 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 36 rows containing missing values (`geom_point()`). plot_click: p32981/Proteomics/LUMOS_2/analytic_20231031/20231031_C32981_058_autoQC01.raw plot_click: p32981/Proteomics/LUMOS_2/analytic_20231031/20231031_C32981_058_autoQC01.raw fn has changed to /srv/www/htdocs//p32981/Proteomics/LUMOS_2/analytic_20231031/20231031_C32981_058_autoQC01.raw Read 22032 items Reading raw file: /srv/www/htdocs//p32981/Proteomics/LUMOS_2/analytic_20231031/20231031_C32981_058_autoQC01.raw length = 9 Warning in predict.lm(fit, data.frame(xc = xx)) : prediction from rank-deficient fit; attr(*, "non-estim") has doubtful cases Plotting chromatograms ... Plotting chromatograms ... Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. Warning: Removed 36 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-09-18 20:57:47.749 | timeMax: 2023-11-23 20:56:05.872 | timeDiff: 5702298.12299991 autoQC01 module APEX long nrow: 3816 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 36 rows containing missing values (`geom_point()`). input timeRange: 7776000 | timeMin: 2023-09-02 20:57:47.749 | timeMax: 2023-11-23 20:56:05.872 | timeDiff: 7084698.12299991 autoQC01 module APEX long nrow: 4608 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 40 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 4788 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 108 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). Warning: Removed 108 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw | plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_001_autoQC01.raw | plot_click: p3000/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw | plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_001_autoQC01.raw | plot_click: p3000/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw fn has changed to /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 9 Plotting chromatograms ... input timeRange: 189216000 | timeMin: 2023-09-02 20:57:47.749 | timeMax: 2023-11-23 22:00:13.389477 | timeDiff: 7084945.64047647 autoQC01 module APEX long nrow: 4788 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 108 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw | plot_click: p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_001_autoQC01.raw | plot_click: p3000/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_001_autoQC01.raw | plot_click: p33206/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33206_010_autoQC01.raw input timeRange: 189216000 | timeMin: 2023-09-02 20:57:47.749 | timeMax: 2023-11-23 21:00:13.389 | timeDiff: 7084945.63999987 autoQC01 module APEX long nrow: 4788 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 108 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). input timeRange: 189216000 | timeMin: 2018-07-06 21:00:14.973 | timeMax: 2023-11-23 21:00:13.389 | timeDiff: 169862398.416 autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, GTFIIDPGGVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, GTFIIDPAAVIR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, GAGSSEPVTGLDAK, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, VEATFGVDESNAK, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, LFLQFGAQGSPFLK, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 76176 LGGNEQVTR, TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 636 rows containing missing values (`geom_point()`). Warning: Removed 2 rows containing missing values (`geom_line()`). autoQC01 module APEX long nrow: 33856 LGGNEQVTR, TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 166 rows containing missing values (`geom_point()`). Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 4 Plotting chromatograms ... autoQC01 module APEX long nrow: 33856 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 166 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 25392 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 56 rows containing missing values (`geom_point()`). Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 3 Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 3 Plotting chromatograms ... input timeRange: 189216000 | timeMin: 2018-07-06 21:00:14.973 | timeMax: 2019-04-25 21:00:21.503 | timeDiff: 25315206.53 autoQC01 module APEX long nrow: 36 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 input timeRange: 189216000 | timeMin: 2018-11-09 21:01:22.345 | timeMax: 2019-08-29 21:01:28.875 | timeDiff: 25315206.53 autoQC01 module APEX long nrow: 36 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 autoQC01 module APEX long nrow: 4884 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK APEXAUC.lg2 Warning: Removed 44 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 4884 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK AUC.lg2 Warning: Removed 22 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 4884 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK, GAGSSEPVTGLDAK AUC.lg2 Warning: Removed 22 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 6512 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK, GAGSSEPVTGLDAK AUC.lg2 Warning: Removed 28 rows containing missing values (`geom_point()`). Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 4 Plotting chromatograms ... autoQC01 module APEX long nrow: 6512 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK, GAGSSEPVTGLDAK, DGLDAASYYAPVR AUC.lg2 Warning: Removed 28 rows containing missing values (`geom_point()`). autoQC01 module APEX long nrow: 8140 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK, GAGSSEPVTGLDAK, DGLDAASYYAPVR AUC.lg2 Warning: Removed 34 rows containing missing values (`geom_point()`). Read 22032 items Reading raw file: /srv/www/htdocs//p33199/Proteomics/QEXACTIVE_1/analytic_20231020/20231020_C33199_001_autoQC01.raw length = 5 Plotting chromatograms ... plot_click: p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_040_autoQC01.raw | plot_click: p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_039_autoQC01.raw plot_click: p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_040_autoQC01.raw | plot_click: p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_039_autoQC01.raw fn has changed to /srv/www/htdocs//p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_040_autoQC01.raw Read 22032 items Reading raw file: /srv/www/htdocs//p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_040_autoQC01.raw length = 5 Plotting chromatograms ... Read 22032 items Reading raw file: /srv/www/htdocs//p3026/Proteomics/LUMOS_1/sgeisen_20190618_p3026_HCEC_SPE/20190618_040_autoQC01.raw length = 5 Plotting chromatograms ... input timeRange: 189216000 | timeMin: 2020-01-23 21:01:27.209 | timeMax: 2020-11-14 21:01:33.739 | timeDiff: 25574406.53 autoQC01 module APEX long nrow: 8980 TPVISGGPYEYR, TPVITGAPYEYR, YILAGVENSK, GAGSSEPVTGLDAK, DGLDAASYYAPVR AUC.lg2 Warning: Removed 26 rows containing missing values (`geom_point()`). plot_click: plot_click: p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw | plot_click: p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw plot_click: p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw | plot_click: p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw fn has changed to /srv/www/htdocs//p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw Read 22032 items Reading raw file: /srv/www/htdocs//p2933/Proteomics/LUMOS_1/tdtaylor_20200629_DDApools/20200629_007_autoQC01.raw length = 5 Plotting chromatograms ... Execution halted