Listening on http://127.0.0.1:39885
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({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$employee <- renderUI({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
Warning in shinyStore::updateStore(session, "login", isolate(input$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.
saving 'login and webservicepassword' ...
output$employee <- renderUI({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$employee <- renderUI({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE


#rows are 0
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({
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
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$project),  :
  Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user.
output$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//p33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_002_S588931_SMB440-1_Control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_003_S588944_SMB440-4_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_005_S588942_SMB440-2_Control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_004_S588943_SMB440-3_Group_1.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
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 76021
#rows are 76021
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$tic.basepeak <- renderPlot({
#rows are 76021
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 76021
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 76021
output$download 2...
ggsave to file /tmp/Rtmp47MqqQ/rawDiag-12765d5dc620d0.pdf
generated pdf
/tmp/Rtmp47MqqQ/rawDiag-12765d5dc620d0.pdf
bfabricShiny::uploadResource ...
list(list(`_classname` = "workunit", `_id` = 296154, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33399), created = "2023-11-16 08:38:08", createdby = "spfammatter", description = "input files:\np33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_002_S588931_SMB440-1_Control.raw\np33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_005_S588942_SMB440-2_Control.raw\np33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_004_S588943_SMB440-3_Group_1.raw\np33399/Proteomics/QEXACTIVE_1/analytic_20231115/20231115_C33399_003_S588944_SMB440-4_Group_1.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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 = "2023-11-16 08:38:08", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2395069, container = list(`_classname` = "order", `_id` = 33399), created = "2023-11-16 08:38:09", createdby = "spfammatter", filechecksum = "fe7e2f04efbaac764c644a471eb55089", junk = "false", modified = "2023-11-16 08:38:09", modifiedby = "spfammatter", name = "WU296154-20231116-0838-rawDiag.pdf", relativepath = "container_33399/workunit_296154/WU296154-20231116-0838-rawDiag.pdf", size = "176638", status = "available", storage = list(`_classname` = "storage", 
    `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33399/workunit_296154/WU296154-20231116-0838-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33399/workunit_296154/WU296154-20231116-0838-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296154)))
The current plot is available as workunit 296154
#rows are 76021
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.
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 76021
output$download 2...


Execution halted