Listening on http://127.0.0.1:38163 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$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_020_S510476_C42BIgG-repeat3_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_006_S510468_C42BIgG-repeat1_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_017_S510474_LNCaPIgG-repeat3_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_013_S510472_C42BIgG-repeat2_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_010_S510470_LNCaPIgG-repeat2_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_003_S510466_LNCaPIgG-repeat1_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.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 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 745092 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_013_S510472_C42BIgG-repeat2_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_003_S510466_LNCaPIgG-repeat1_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_006_S510468_C42BIgG-repeat1_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_010_S510470_LNCaPIgG-repeat2_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_020_S510476_C42BIgG-repeat3_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_017_S510474_LNCaPIgG-repeat3_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.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 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 output$tic.basepeak <- renderPlot({ #rows are 745092 output$download 2... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. output$tic.basepeak <- renderPlot({ executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.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 391098 output$download 2... ggsave to file /tmp/RtmpUcYkeV/rawDiag-2dc5dd746509ad.pdf generated pdf /tmp/RtmpUcYkeV/rawDiag-2dc5dd746509ad.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 289792, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:34:07", createdby = "antdit", deletable = "true", description = "input files:\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.21.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2303263), list(`_classname` = "resource", `_id` = 2303262), list(`_classname` = "resource", `_id` = 2303261)), modified = "2023-06-07 11:34:07", modifiedby = "antdit", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2306469, container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:34:08", createdby = "antdit", deletable = "true", filechecksum = "d1bf201d7438a9c72cabc569fc2e7150", junk = "false", modified = "2023-06-07 11:34:08", modifiedby = "antdit", name = "WU289792-20230607-1134-rawDiag.pdf", relativepath = "container_31788/workunit_289792/WU289792-20230607-1134-rawDiag.pdf", size = "249390", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31788/workunit_289792/WU289792-20230607-1134-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31788/workunit_289792/WU289792-20230607-1134-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289792))) The current plot is available as workunit 289792 #rows are 391098 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. #rows are 391098 output$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 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 391098 output$download 2... #rows are 391098 output$download 2... #rows are 391098 output$download 2... #rows are 391098 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_013_S510472_C42BIgG-repeat2_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_006_S510468_C42BIgG-repeat1_C42B_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_020_S510476_C42BIgG-repeat3_C42B_control_IgG.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 347532 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 347532 output$download 2... ggsave to file /tmp/RtmpUcYkeV/rawDiag-2dc5dd1ca848e8.pdf generated pdf /tmp/RtmpUcYkeV/rawDiag-2dc5dd1ca848e8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 289793, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:47:40", createdby = "antdit", deletable = "true", description = "input files:\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_012_S510471_C42BFl2Ab-repeat2_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_005_S510467_C42BFl2Ab-repeat1_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_019_S510475_C42BFl2Ab-repeat3_C42B_cells.raw \np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_013_S510472_C42BIgG-repeat2_C42B_control_IgG.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_006_S510468_C42BIgG-repeat1_C42B_control_IgG.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_020_S510476_C42BIgG-repeat3_C42B_control_IgG.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.21.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", modified = "2023-06-07 11:47:40", modifiedby = "antdit", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2306470, container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:47:42", createdby = "antdit", deletable = "true", filechecksum = "f11dde739e5a9e30dea3448bf029f87b", junk = "false", modified = "2023-06-07 11:47:42", modifiedby = "antdit", name = "WU289793-20230607-1147-rawDiag.pdf", relativepath = "container_31788/workunit_289793/WU289793-20230607-1147-rawDiag.pdf", size = "257449", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31788/workunit_289793/WU289793-20230607-1147-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31788/workunit_289793/WU289793-20230607-1147-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289793))) The current plot is available as workunit 289793 #rows are 347532 output$download 1... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_010_S510470_LNCaPIgG-repeat2_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_017_S510474_LNCaPIgG-repeat3_LNCaP_control_IgG.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_003_S510466_LNCaPIgG-repeat1_LNCaP_control_IgG.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 output$tic.basepeak <- renderPlot({ #rows are 397560 output$download 2... ggsave to file /tmp/RtmpUcYkeV/rawDiag-2dc5dd726ab755.pdf generated pdf /tmp/RtmpUcYkeV/rawDiag-2dc5dd726ab755.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 289794, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:48:28", createdby = "antdit", deletable = "true", description = "input files:\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_003_S510466_LNCaPIgG-repeat1_LNCaP_control_IgG.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_010_S510470_LNCaPIgG-repeat2_LNCaP_control_IgG.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_017_S510474_LNCaPIgG-repeat3_LNCaP_control_IgG.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_016_S510473_LNCaPFl2Ab-repeat3_LNCaP_cell_line.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_009_S510469_LNCaPFl2Ab-repeat2_LNCaP_cell_line.raw\np31788/Proteomics/LUMOS_2/analytic_20230526/20230526_C31788_002_S510465_LNCaPFl2Ab-repeat1_LNCaP_cell_line.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.21.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2303264), list(`_classname` = "resource", `_id` = 2303263), list(`_classname` = "resource", `_id` = 2303262), list(`_classname` = "resource", `_id` = 2303261)), modified = "2023-06-07 11:48:28", modifiedby = "antdit", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2306471, container = list(`_classname` = "order", `_id` = 31788), created = "2023-06-07 11:48:29", createdby = "antdit", deletable = "true", filechecksum = "bf81212c16e3e8cc99eaf5fb181b443a", junk = "false", modified = "2023-06-07 11:48:29", modifiedby = "antdit", name = "WU289794-20230607-1148-rawDiag.pdf", relativepath = "container_31788/workunit_289794/WU289794-20230607-1148-rawDiag.pdf", size = "251703", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31788/workunit_289794/WU289794-20230607-1148-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31788/workunit_289794/WU289794-20230607-1148-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289794))) The current plot is available as workunit 289794 #rows are 397560 output$download 1... Execution halted