Listening on http://127.0.0.1:38747
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$employee <- renderUI({
read bfabricposturl https://fgcz-c-072.uzh.ch:5000/.
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$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//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.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 293226
output$tic.basepeak <- renderPlot({
#rows are 293226
output$download 2...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_2_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_1_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_3_autoQC03dia.raw qc ...
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
#rows are 206181
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 206181
output$download 2...



#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.
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//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_004_S580219_K562_incl_iRT_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_003_S580219_K562_incl_iRT_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_005_S580219_K562_incl_iRT_autoQC03dia.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
#rows are 220239
output$tic.basepeak <- renderPlot({
#rows are 220239
output$download 2...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
#rows are 220239
output$download 2...
output$tic.basepeak <- renderPlot({
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_2_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_1_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/FUSION_2/chiawei_20231121/20231121_002_S580219_K562_incl_iRT_3_autoQC03dia.raw qc ...
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
#rows are 206181
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 206181
output$download 2...
Warning: Error in <Anonymous>: 'data' must be 2-dimensional (e.g. data frame or matrix)
  107: stop
  106: <Anonymous>
  104: processWidget
  103: widgetFunc
  102: ::
htmlwidgets
shinyRenderWidget
  101: func
   88: renderFunc
   87: renderFunc
   83: renderFunc
   82: output$tableInfo
    1: runApp
saving 'login and webservicepassword' ...
#rows are 206181
output$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: `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 206181
output$download 2...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 206181
output$download 2...
output$scan.frequency <- renderPlot
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_004_S580219_K562_incl_iRT_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_003_S580219_K562_incl_iRT_autoQC03dia.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_2/leonardoschwarz_20231116/20231116_005_S580219_K562_incl_iRT_autoQC03dia.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
#rows are 220239
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 220239
output$download 2...
#rows are 220239
output$download 2...
#rows are 220239
output$download 2...
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
#rows are 220239
output$download 2...
DEBUG renderPlot
plotQCs
#rows are 220239
output$download 2...