Listening on http://127.0.0.1:44819
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
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//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_005_S512746_BioID-TDP-43_WT_B_Control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_002_S512748_BioID-TDP-43_6M_A_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_004_S512750_BioID-TDP-43_6M_C_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_009_S512745_BioID-TDP-43_WT_A_Control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_008_S512747_BioID-TDP-43_WT_C_Control.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31835/Proteomics/EXPLORIS_2/analytic_20230526/20230526_C31835_003_S512749_BioID-TDP-43_6M_B_Group_1.raw qc ...
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMmZCorrectionppm to LMCorrection
renamed AGCPSMode to PrescanMode
#rows are 182489
output$tic.basepeak <- renderPlot({
#rows are 182489
output$download 2...
saving 'login and webservicepassword' ...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e22165ec8e7f2.pdf
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e22165ec8e7f2.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289510
#rows are 182489
output$download 1...
saving 'login and webservicepassword' ...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 182489
output$download 2...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e22162cfa89a6.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e22162cfa89a6.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289511
#rows are 182489
output$download 1...
`geom_smooth()` using formula = 'y ~ x'
#rows are 182489
output$download 2...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e22161b387709.pdf
`geom_smooth()` using formula = 'y ~ x'
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e22161b387709.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289512
#rows are 182489
output$download 1...
Warning: Removed 60 rows containing non-finite values (`stat_smooth()`).
Warning: Removed 10 rows containing missing values (`geom_line()`).
#rows are 182489
output$download 2...
#rows are 182489
output$download 2...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e22166a23ab02.pdf
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e22166a23ab02.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289513
#rows are 182489
output$download 1...
#rows are 182489
output$download 2...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e22164237ee87.pdf
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e22164237ee87.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289514
#rows are 182489
output$download 1...
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
#rows are 182489
output$download 2...
ggsave to file /tmp/Rtmpi7frfz/rawDiag-3e2216b16137f.pdf
generated pdf
/tmp/Rtmpi7frfz/rawDiag-3e2216b16137f.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 289515
#rows are 182489
output$download 1...
DEBUG renderPlot
plotQCs
#rows are 182489
output$download 1...


Execution halted