Listening on http://127.0.0.1:33871
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({
bfabricConnectionWorking TRUE
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//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_012_S534405_20230712_SC_RPS4B0526_flg22_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_018_S534400_20230712_SC_ADR1L20526_flg22_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_004_S534401_20230712_SC_ADR1L20526_DV_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_008_S534404_20230712_SC_RPS4B0526_mock_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_010_S534403_20230712_SC_RPS4B0504_flg22_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_003_S534399_20230712_SC_ADR1L20526_mock_TiElu.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_015_S534402_20230712_SC_RPS4B0504_mock_TiElu.raw qc ...
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
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 128164
output$tic.basepeak <- renderPlot({
#rows are 128164
output$download 2...
saving 'login and webservicepassword' ...
`geom_smooth()` using formula = 'y ~ x'
#rows are 128164
output$download 2...
#rows are 128164
output$download 2...
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
#rows are 128164
output$download 2...
#rows are 128164
output$download 2...
output$tic.basepeak <- renderPlot({
#rows are 128164
output$download 2...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_013_S534406_20230712_SC_ADR1L20526_mock_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_014_S534408_20230712_SC_ADR1L20526_DV_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_005_S534407_20230712_SC_ADR1L20526_flg22_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_002_S534412_20230712_SC_RPS4B0526_flg22_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_017_S534409_20230712_SC_RPS4B0504_mock_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_009_S534410_20230712_SC_RPS4B0504_flg22_TiFT.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p29260/Proteomics/EXPLORIS_1/kbende_20230712/20230712_007_S534411_20230712_SC_RPS4B0526_mock_TiFT.raw qc ...
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
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
output$tic.basepeak <- renderPlot({
#rows are 150077
output$download 2...
`geom_smooth()` using formula = 'y ~ x'
#rows are 150077
output$download 2...
#rows are 150077
output$download 2...
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
#rows are 150077
output$download 2...


Execution halted