Listening on http://127.0.0.1:38655 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/ Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. 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({ 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//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_013_S489201_Nuc_ctrl_2_Group_2_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_016_S489202_Cyto_ctrl_1_Group_3_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_003_S489198_Total_ctrl_1_Group_1_DDA2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_006_S489199_Total_ctrl_2_Group_1_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_010_S489200_Nuc_ctrl_1_Group_2_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_019_S489203_Cyto_ctrl_2_Group_3_DDA.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 307334 output$tic.basepeak <- renderPlot({ #rows are 307334 output$download 2... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 307334 output$download 2... ggsave to file /tmp/RtmpNSOolk/rawDiag-21b4971dd2af0b.pdf generated pdf /tmp/RtmpNSOolk/rawDiag-21b4971dd2af0b.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288027 #rows are 307334 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 307334 output$download 2... ggsave to file /tmp/RtmpNSOolk/rawDiag-21b497769f19b1.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpNSOolk/rawDiag-21b497769f19b1.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288028 #rows are 307334 output$download 1... #rows are 307334 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation ideoms with `aes()` Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 307334 output$download 2... DEBUG renderPlot plotQCs #rows are 307334 output$download 2... DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp DEBUG renderPlot Warning: 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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_014_S489201_Nuc_ctrl_2_Group_2_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_020_S489203_Cyto_ctrl_2_Group_3_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_004_S489198_Total_ctrl_1_Group_1_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_007_S489199_Total_ctrl_2_Group_1_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_017_S489202_Cyto_ctrl_1_Group_3_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230412/20230412_C31310_011_S489200_Nuc_ctrl_1_Group_2_DIA.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 807783 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 807783 output$download 2... ggsave to file /tmp/RtmpNSOolk/rawDiag-21b4976357b924.pdf generated pdf /tmp/RtmpNSOolk/rawDiag-21b4976357b924.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 288029 #rows are 807783 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 807783 output$download 2... #rows are 807783 output$download 2... #rows are 807783 output$download 2... Execution halted