Listening on http://127.0.0.1:41213
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//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_008_S516045_HSV1_early_proteome.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_006_S516046_HSv1_late_TiIMAC.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_009_S516046_HSv1_late_proteome.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_003_S516045_HSV1_early_TiIMAC.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
#rows are 463120
output$tic.basepeak <- renderPlot({
#rows are 463120
output$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$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_009_S516046_HSv1_late_proteome.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_008_S516045_HSV1_early_proteome.raw qc ...
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
output$tic.basepeak <- renderPlot({
#rows are 267486
output$download 2...
ggsave to file /tmp/Rtmp04XSam/rawDiag-2ce85157cdd59c.pdf
generated pdf
/tmp/Rtmp04XSam/rawDiag-2ce85157cdd59c.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 291055, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31893), created = "2023-07-07 12:46:56", createdby = "antdit", deletable = "true", description = "input files:\np31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_009_S516046_HSv1_late_proteome.raw \np31893/Proteomics/LUMOS_2/analytic_20230705/20230705_C31893_008_S516045_HSV1_early_proteome.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2325938), list(`_classname` = "resource", `_id` = 2325937)), modified = "2023-07-07 12:46:56", modifiedby = "antdit", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2326427, container = list(`_classname` = "order", `_id` = 31893), created = "2023-07-07 12:46:58", createdby = "antdit", deletable = "true", filechecksum = "389907e9ea740eef5933db22588d40de", junk = "false", modified = "2023-07-07 12:46:58", modifiedby = "antdit", name = "WU291055-20230707-1246-rawDiag.pdf", relativepath = "container_31893/workunit_291055/WU291055-20230707-1246-rawDiag.pdf", size = "96342", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31893/workunit_291055/WU291055-20230707-1246-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31893/workunit_291055/WU291055-20230707-1246-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291055)))
The current plot is available as workunit 291055
#rows are 267486
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.


Execution halted