Listening on http://127.0.0.1:37107
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



#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//p33712/Proteomics/QEXACTIVE_1/analytic_20231214/20231214_C33712_004_S607913_LRRC8A.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33712/Proteomics/QEXACTIVE_1/analytic_20231214/20231214_C33712_002_S607912_TTYH2.raw qc ...
missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
MasterScanNumber calculated
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
MasterScanNumber calculated
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
#rows are 40586
output$tic.basepeak <- renderPlot({
#rows are 40586
output$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({
#rows are 40586
output$download 2...
ggsave to file /tmp/RtmpvM0Hwg/rawDiag-f612168fff6cf.pdf
generated pdf
/tmp/RtmpvM0Hwg/rawDiag-f612168fff6cf.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 297805, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33712), created = "2023-12-15 08:52:56", createdby = "spfammatter", description = "input files:\np33712/Proteomics/QEXACTIVE_1/analytic_20231214/20231214_C33712_002_S607912_TTYH2.raw \np33712/Proteomics/QEXACTIVE_1/analytic_20231214/20231214_C33712_004_S607913_LRRC8A.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2414364), list(`_classname` = "resource", `_id` = 2414363)), modified = "2023-12-15 08:52:56", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2414368, container = list(`_classname` = "order", `_id` = 33712), created = "2023-12-15 08:52:57", createdby = "spfammatter", filechecksum = "12ceb6201026358a63e5e30f209ba620", junk = "false", modified = "2023-12-15 08:52:57", modifiedby = "spfammatter", name = "WU297805-20231215-0852-rawDiag.pdf", relativepath = "container_33712/workunit_297805/WU297805-20231215-0852-rawDiag.pdf", size = "85701", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33712/workunit_297805/WU297805-20231215-0852-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33712/workunit_297805/WU297805-20231215-0852-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297805)))
The current plot is available as workunit 297805
#rows are 40586
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