Listening on http://127.0.0.1:41279 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 358982 output$tic.basepeak <- renderPlot({ #rows are 358982 output$download 2... saving 'login and webservicepassword' ... Warning: Removed 52571 rows containing non-finite values (`stat_smooth()`). 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) 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) 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) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. 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) Warning: Removed 7 rows containing missing values (`geom_line()`). #rows are 358982 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 358982 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 358982 output$download 2... DEBUG renderPlot plotQCs #rows are 358982 output$download 2... #rows are 358982 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 358982 output$download 2... DEBUG renderPlot plotQCs #rows are 358982 output$download 2... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 358982 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 358982 output$download 2...