Listening on http://127.0.0.1:44111 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 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 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//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_023_S504968_20230505_CY_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_004_S504969_20230505_CY_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_009_S504978_20230505_CY_11.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_022_S504979_20230505_CY_12.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 #rows are 314617 output$tic.basepeak <- renderPlot({ #rows are 314617 output$download 2... saving 'login and webservicepassword' ... `geom_smooth()` using formula = 'y ~ x' #rows are 314617 output$download 2... #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... #rows are 314617 output$download 2... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are 314617 output$download 2... #rows are 314617 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 314617 output$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") #rows are 314617 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 314617 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 314617 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 314617 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 314617 output$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") #rows are 314617 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 314617 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_031_S489062_KIF21AROS1_3_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_025_S489057_CLIP1ROS1_1_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_030_S489061_KIF21AROS1_2_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_027_S489059_CLIP1ROS1_3_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_018_S489053_ROS1_EV3_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_022_S489056_GOPCROS1_3_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_021_S489055_GOPCROS1_2_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_026_S489058_CLIP1ROS1_2_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_017_S489052_ROS1_EV2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_016_S489051_ROS1_EV1_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_020_S489054_GOPCROS1_1_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 missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 #rows are 287809 `geom_smooth()` using formula = 'y ~ x' #rows are 314617 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 314617 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 287809 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_010_S504970_20230505_CY_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_018_S504971_20230505_CY_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_011_S504981_20230505_CY_14.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_003_S504980_20230505_CY_13.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode output$tic.basepeak <- renderPlot({ #rows are 313585 output$download 2... saving 'login and webservicepassword' ... `geom_smooth()` using formula = 'y ~ x' #rows are 313585 output$download 2... #rows are 313585 output$download 2... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c167720e9b6.pdf generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c167720e9b6.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288731 #rows are 287809 output$download 1... saving 'login and webservicepassword' ... `geom_smooth()` using formula = 'y ~ x' #rows are 313585 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 287809 output$download 2... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c166ec241b5.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c166ec241b5.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288732 #rows are 287809 output$download 1... Warning: Removed 36 rows containing non-finite values (`stat_smooth()`). #rows are 287809 output$download 2... #rows are 287809 output$download 2... #rows are 287809 output$download 2... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c16589f3ebd.pdf generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c16589f3ebd.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288733 #rows are 287809 output$download 1... #rows are 313585 output$download 2... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 313585 output$download 2... #rows are 313585 output$download 2... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot 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 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot 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 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... DEBUG renderPlot Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 287809 output$download 1... 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") plotQCs #rows are 287809 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 287809 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 287809 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 287809 output$download 2... #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5002/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$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//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_007_S489067_CCDC88AALK_2_Group_6.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_008_S489068_CCDC88AALK_3_Group_6.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_003_S489064_ALK_EV2_Group_5.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_006_S489066_CCDC88AALK_1_Group_6.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_012_S489071_PPP1CBALK_3_Group_7.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_011_S489070_PPP1CBALK_2_Group_7.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_004_S489065_ALK_EV3_Group_5.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_002_S489063_ALK_EV1_Group_5.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31306/Proteomics/EXPLORIS_2/analytic_20230426/20230426_C31306_010_S489069_PPP1CBALK_1_Group_7.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 missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 #rows are 265481 output$tic.basepeak <- renderPlot({ #rows are 265481 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c167ebf4647.pdf generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c167ebf4647.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288734 #rows are 265481 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 265481 output$download 2... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c1639efa488.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c1639efa488.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288735 #rows are 265481 output$download 1... Warning: Removed 44 rows containing non-finite values (`stat_smooth()`). #rows are 265481 output$download 2... #rows are 265481 output$download 2... ggsave to file /tmp/RtmpwEFmfp/rawDiag-3e1c162aee6806.pdf generated pdf /tmp/RtmpwEFmfp/rawDiag-3e1c162aee6806.pdf bfabricShiny::uploadResource ... Warning in resources$relativepath == input$relativepath : longer object length is not a multiple of shorter object length The current plot is available as workunit 288736 #rows are 265481 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 265481 output$download 1... DEBUG renderPlot plotQCs #rows are 265481 output$download 1... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_013_S504982_20230505_CY_15.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_025_S504972_20230505_CY_5.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_021_S504973_20230505_CY_6.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_017_S504983_20230505_CY_16.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 313068 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 313068 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 313068 output$download 2... #rows are 313068 output$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") #rows are 313068 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 313068 output$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") #rows are 313068 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 313068 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_005_S504986_20230505_CY_19.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_019_S504977_20230505_CY_10.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_012_S504987_20230505_CY_20.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3189/Proteomics/EXPLORIS_1/kbende_20230505/20230505_016_S504976_20230505_CY_9.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode output$tic.basepeak <- renderPlot({ #rows are 291754 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 291754 output$download 2... #rows are 291754 output$download 2...