Listening on http://127.0.0.1:40499
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
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//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_011_S487649_S10_C7_1_spike_Group_10_rep.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_003_S487641_S02_Negative_spike_Group_2.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_013_S487643_S04_C7_1_spike_Group_4.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_004_S487640_S01_Negative_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_008_S487644_S05_C7_2_Group_5_rep.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_010_S487648_S09_C7_1_Group_9_rep.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_014_S487645_S06_C7_2_spike_Group_6.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_005_S487647_S08_Negative_spike_Group_8.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_016_S487650_S11_C7_2_Group_15.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_015_S487651_S12_C7_2_spike_Group_20.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_002_S487646_S07_Negative_Group_7.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31265/Proteomics/FUSION_2/analytic_20230405/20230405_C31265_009_S487642_S03_C7_1_Group_3_rep.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 
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
renamed LMCorrectionppm to LMCorrection
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
copied AGC to AGCMode
calculated PrescanMode values
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode
NA values replaced in MasterScanNumber 
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
renamed LMCorrectionppm to LMCorrection
copied AGC to AGCMode
calculated PrescanMode values
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 
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
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 280415
output$tic.basepeak <- renderPlot({
#rows are 280415
output$download 2...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
#rows are 280415
output$download 2...
ggsave to file /tmp/RtmpUwfWuj/rawDiag-37b046af80f61.pdf
generated pdf
/tmp/RtmpUwfWuj/rawDiag-37b046af80f61.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287954
#rows are 280415
output$download 1...
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 280415
output$download 2...
saving 'login and webservicepassword' ...
ggsave to file /tmp/RtmpUwfWuj/rawDiag-37b0464ea54bda.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/RtmpUwfWuj/rawDiag-37b0464ea54bda.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 287956
#rows are 280415
output$download 1...
#rows are 280415
output$download 2...
#rows are 280415
output$download 2...
DEBUG renderPlot
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: '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")
plotQCs
#rows are 280415
output$download 2...
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
#rows are 280415
output$download 2...
saving 'login and webservicepassword' ...


Execution halted