Listening on http://127.0.0.1:43213 Loading required package: rawDiag Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save plotTicBasepeak output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE saving 'login and webservicepassword' ... output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... resourcesSelected: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw vals$rawfile: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw reading index for 20231113_002_S193756_K-562_N_A_tMS2org.raw... Warning in validate_read.raw(rawrrIndex) : Missing column FTResolution. Warning in validate_read.raw(rawrrIndex) : Missing column LMCorrection. Warning in validate_read.raw(rawrrIndex) : Missing column PrescanMode. resourcesSelected: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_004_S193756_K-562_N_A_DIA30k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_008_S193756_K-562_N_A_tMS2new.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_007_S193756_K-562_N_A_DIA30k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_003_S193756_K-562_N_A_DIA15k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_005_S193756_K-562_N_A_tMS2new.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_010_S193756_K-562_N_AtMS2org.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_009_S193756_K-562_N_A_DIA15k.raw vals$rawfile: /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_004_S193756_K-562_N_A_DIA30k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_008_S193756_K-562_N_A_tMS2new.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_007_S193756_K-562_N_A_DIA30k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_003_S193756_K-562_N_A_DIA15k.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_005_S193756_K-562_N_A_tMS2new.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_010_S193756_K-562_N_AtMS2org.raw, /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_009_S193756_K-562_N_A_DIA15k.raw reading index for 20231113_002_S193756_K-562_N_A_tMS2org.raw... reading index for 20231113_004_S193756_K-562_N_A_DIA30k.raw... reading index for 20231113_008_S193756_K-562_N_A_tMS2new.raw... reading index for 20231113_007_S193756_K-562_N_A_DIA30k.raw... reading index for 20231113_003_S193756_K-562_N_A_DIA15k.raw... reading index for 20231113_005_S193756_K-562_N_A_tMS2new.raw... reading index for 20231113_010_S193756_K-562_N_AtMS2org.raw... reading index for 20231113_009_S193756_K-562_N_A_DIA15k.raw... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... determining ElapsedScanTimesec ... reading trailer AGC ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... determining ElapsedScanTimesec ... reading trailer AGC ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading TIC ... reading TIC ... reading TIC ... reading TIC ... reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... reading BasePeakIntensity ... reading BasePeakIntensity ... reading BasePeakIntensity ... reading BasePeakIntensity ... 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. 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. 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. 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. reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... 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. 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. reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... 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. 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. plotChargeState output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE saving 'login and webservicepassword' ... output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... resourcesSelected: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw vals$rawfile: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw reading index for 20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw... reading index for 20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... reading trailer AGC ... reading trailer AGC ... reading trailer AGC PS Mode ... reading trailer AGC PS Mode ... reading trailer FT Resolution ... reading trailer FT Resolution ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... plotTicBasepeak resourcesSelected: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw vals$rawfile: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231218-160546_plotTicBasepeak.pdf Warning: Error in +: non-numeric argument to binary operator 1: runApp plotTicBasepeak output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE saving 'login and webservicepassword' ... output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... resourcesSelected: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw vals$rawfile: /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw, /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw reading index for 20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw... reading index for 20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_rep.raw... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... reading trailer AGC ... reading trailer AGC ... reading trailer AGC PS Mode ... reading trailer AGC PS Mode ... reading trailer FT Resolution ... reading trailer FT Resolution ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... plotLockMassCorrection plotTicBasepeak ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231218-160854_plotTicBasepeak.pdf saving 'login and webservicepassword' ... The current plot is available as workunit 297952. Rendering actionButton to link workunit 297952 in B-Fabric. saving 'login and webservicepassword' ... plotLockMassCorrection ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231218-160922_plotLockMassCorrection.pdf The current plot is available as workunit 297953. Rendering actionButton to link workunit 297953 in B-Fabric. plotInjectionTime ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231218-160939_plotInjectionTime.pdf The current plot is available as workunit 297954. Rendering actionButton to link workunit 297954 in B-Fabric. plotPrecursorHeatmap ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231218-161009_plotPrecursorHeatmap.pdf The current plot is available as workunit 297955. Rendering actionButton to link workunit 297955 in B-Fabric. plotTicBasepeak plotChargeState output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE saving 'login and webservicepassword' ... output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... resourcesSelected: /srv/www/htdocs//p32312/Proteomics/EXPLORIS_2/analytic_20230725_dia/20230725_C32312_008_autoQC4L.raw vals$rawfile: /srv/www/htdocs//p32312/Proteomics/EXPLORIS_2/analytic_20230725_dia/20230725_C32312_008_autoQC4L.raw reading index for 20230725_C32312_008_autoQC4L.raw... plotLockMassCorrection ggplot2::ggsave to file /tmp/RtmpxrYPTu/rawDiag_20231219-084950_plotLockMassCorrection.pdf saving 'login and webservicepassword' ... The current plot is available as workunit 297972. Rendering actionButton to link workunit 297972 in B-Fabric. saving 'login and webservicepassword' ... resourcesSelected: /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_004_S408771_Kuppfer_KF_200_enriched_DDA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_005_S408772_Kuppfer_KF_50_enriched_DDA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_021_S408766_Kuppfer_Bravo_50_ft_DIA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_015_S408768_Kuppfer_Bravo_50_enriched_DIA.raw vals$rawfile: /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_004_S408771_Kuppfer_KF_200_enriched_DDA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_005_S408772_Kuppfer_KF_50_enriched_DDA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_021_S408766_Kuppfer_Bravo_50_ft_DIA.raw, /srv/www/htdocs//p3000/Proteomics/EXPLORIS_2/lkunz_20220819/20220819_015_S408768_Kuppfer_Bravo_50_enriched_DIA.raw reading index for 20220819_004_S408771_Kuppfer_KF_200_enriched_DDA.raw... reading index for 20220819_005_S408772_Kuppfer_KF_50_enriched_DDA.raw... reading index for 20220819_021_S408766_Kuppfer_Bravo_50_ft_DIA.raw... reading index for 20220819_015_S408768_Kuppfer_Bravo_50_enriched_DIA.raw... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... reading trailer AGC ... reading trailer AGC ... reading trailer AGC PS Mode ... reading trailer AGC PS Mode ... reading trailer FT Resolution ... reading trailer FT Resolution ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... determining ElapsedScanTimesec ... reading trailer LM m/z-Correction (ppm) ... reading trailer AGC ... reading trailer AGC ... reading trailer AGC PS Mode ... reading trailer AGC PS Mode ... reading trailer FT Resolution ... reading trailer FT Resolution ... reading trailer Ion Injection Time (ms) ... reading trailer Ion Injection Time (ms) ... reading TIC ... reading TIC ... reading BasePeakIntensity ... reading BasePeakIntensity ... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3)