Listening on http://127.0.0.1:46131 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//p31679/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31679_004_S506147_S3_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31679/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31679_005_S506146_S2_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31679/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31679_002_S506149_C5_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31679/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31679_003_S506148_C4_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 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 121507 output$tic.basepeak <- renderPlot({ #rows are 121507 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223145b3ea90d.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-223145b3ea90d.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289284 #rows are 121507 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223144c3d07c1.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpUc7xgi/rawDiag-223144c3d07c1.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289285 #rows are 121507 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223142278fb15.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpUc7xgi/rawDiag-223142278fb15.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289286 #rows are 121507 output$download 1... Warning: Removed 36 rows containing non-finite values (`stat_smooth()`). #rows are 121507 output$download 2... #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223147e06ee.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-223147e06ee.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289287 #rows are 121507 output$download 1... #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-2231466f4228b.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-2231466f4228b.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289288 #rows are 121507 output$download 1... #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-2231460f325e1.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-2231460f325e1.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289289 #rows are 121507 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 121507 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223141c8d8c7c.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-223141c8d8c7c.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289290 #rows are 121507 output$download 1... DEBUG renderPlot plotQCs #rows are 121507 output$download 1... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 121507 output$download 2... #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' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31769/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31769_003_S509571_FoxoUb_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31769/Proteomics/EXPLORIS_2/analytic_20230517/20230517_C31769_002_S509572_FoxoCtrl_Group_2.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 #rows are 58417 output$tic.basepeak <- renderPlot({ #rows are 58417 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpUc7xgi/rawDiag-2231475f957fb.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-2231475f957fb.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289292 #rows are 58417 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-22314d2d0e95.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpUc7xgi/rawDiag-22314d2d0e95.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289293 #rows are 58417 output$download 1... #rows are 58417 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-2231456db7519.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpUc7xgi/rawDiag-2231456db7519.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289294 #rows are 58417 output$download 1... Warning: Removed 8 rows containing non-finite values (`stat_smooth()`). #rows are 58417 output$download 2... #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-22314657abdf2.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-22314657abdf2.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289295 #rows are 58417 output$download 1... #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-2231465f8c4e1.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-2231465f8c4e1.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289296 #rows are 58417 output$download 1... #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223144cece76c.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-223144cece76c.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289298 #rows are 58417 output$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") #rows are 58417 output$download 2... ggsave to file /tmp/RtmpUc7xgi/rawDiag-223142de00d4d.pdf generated pdf /tmp/RtmpUc7xgi/rawDiag-223142de00d4d.pdf bfabricShiny::uploadResource ... The current plot is available as workunit 289299 #rows are 58417 output$download 1... DEBUG renderPlot plotQCs #rows are 58417 output$download 1... DEBUG renderPlot plotQCs #rows are 58417 output$download 1... Execution halted