Listening on http://127.0.0.1:41925
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/
Warning in value[[3L]](cond) :
  Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered.
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//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_010_S489200_Nuc_ctrl_1_Group_2_DDA.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_014_S489201_Nuc_ctrl_2_Group_2_DDA.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_017_S489202_Cyto_ctrl_1_Group_3_DDA.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_007_S489199_Total_ctrl_2_Group_1_DDA.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_004_S489198_Total_ctrl_1_Group_1_DDA.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31310/Proteomics/LUMOS_2/analytic_20230403/20230403_C31310_020_S489203_Cyto_ctrl_2_Group_3_DDA.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
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 483649
output$tic.basepeak <- renderPlot({
#rows are 483649
output$download 2...
saving 'login and webservicepassword' ...
ggsave to file /tmp/Rtmpm8ujED/rawDiag-e14913c662c94.pdf
generated pdf
/tmp/Rtmpm8ujED/rawDiag-e14913c662c94.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287813
#rows are 483649
output$download 1...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
#rows are 483649
output$download 2...
ggsave to file /tmp/Rtmpm8ujED/rawDiag-e14913b6b1ed.pdf
generated pdf
/tmp/Rtmpm8ujED/rawDiag-e14913b6b1ed.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287814
#rows are 483649
output$download 1...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 483649
output$download 2...
ggsave to file /tmp/Rtmpm8ujED/rawDiag-e149173f58183.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmpm8ujED/rawDiag-e149173f58183.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287815
#rows are 483649
output$download 1...
`geom_smooth()` using formula = 'y ~ x'
#rows are 483649
output$download 2...
#rows are 483649
output$download 2...
#rows are 483649
output$download 2...
ggsave to file /tmp/Rtmpm8ujED/rawDiag-e14915bd3a349.pdf
generated pdf
/tmp/Rtmpm8ujED/rawDiag-e14915bd3a349.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287816
#rows are 483649
output$download 1...
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
#rows are 483649
output$download 2...
DEBUG renderPlot
plotQCs
#rows are 483649
output$download 2...


Execution halted