Listening on http://127.0.0.1:34759
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$employee <- renderUI({
read bfabricposturl https://fgcz-c-072.uzh.ch:5002/.
Warning in .read(login = login, webservicepassword = webservicepassword,  :
  query failed.
bfabricConnectionWorking FALSE
output$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//p31696/Proteomics/EXPLORIS_1/analytic_20230512/20230512_C31696_004_S506525_Lct_3UTR_Group_2.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31696/Proteomics/EXPLORIS_1/analytic_20230512/20230512_C31696_002_S506524_Apob_3UTR_Group_1.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31696/Proteomics/EXPLORIS_1/analytic_20230512/20230512_C31696_008_S506527_Net1_motifs_Group_4.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31696/Proteomics/EXPLORIS_1/analytic_20230512/20230512_C31696_006_S506526_Net1_3UTR_Group_3.raw qc ...
executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31696/Proteomics/EXPLORIS_1/analytic_20230512/20230512_C31696_011_S506528_FLuc_CDS_Control.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 
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
#rows are 143444
output$tic.basepeak <- renderPlot({
#rows are 143444
output$download 2...
saving 'login and webservicepassword' ...
output$tic.basepeak <- renderPlot({
#rows are 143444
output$download 2...
ggsave to file /tmp/Rtmp1SC9sZ/rawDiag-2fcb14114f8c07.pdf
generated pdf
/tmp/Rtmp1SC9sZ/rawDiag-2fcb14114f8c07.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 
output$scan.frequency <- renderPlot
Warning: Removed 29 rows containing missing values (`geom_line()`).
#rows are 143444
output$download 2...
ggsave to file /tmp/Rtmp1SC9sZ/rawDiag-2fcb14e70ce84.pdf
Warning: Removed 29 rows containing missing values (`geom_line()`).
generated pdf
/tmp/Rtmp1SC9sZ/rawDiag-2fcb14e70ce84.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 
#rows are 143444
output$download 2...
#rows are 143444
output$download 2...
ggsave to file /tmp/Rtmp1SC9sZ/rawDiag-2fcb14542934de.pdf
generated pdf
/tmp/Rtmp1SC9sZ/rawDiag-2fcb14542934de.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 
#rows are 143444
output$download 2...
ggsave to file /tmp/Rtmp1SC9sZ/rawDiag-2fcb14436eadca.pdf
generated pdf
/tmp/Rtmp1SC9sZ/rawDiag-2fcb14436eadca.pdf
bfabricShiny::uploadResource ...
The current plot is available as workunit 
DEBUG renderPlot
DEBUG queryMass
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
Warning: 'readXICs' is deprecated.
Use 'rawrr::readChromatogram' instead.
See help("Deprecated")
plotQCs
#rows are 143444
output$download 2...
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 143444
output$download 2...
DEBUG renderPlot
plotQCs
#rows are 143444
output$download 2...
ggsave to file /tmp/Rtmp1SC9sZ/rawDiag-2fcb14415e40e1.pdf
Warning: Error in +: non-numeric argument to binary operator
  1: runApp


#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' ...


Execution halted