Listening on http://127.0.0.1:36387 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({ 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//p32864/Proteomics/LUMOS_2/analytic_20230928/20230928_C32864_002_S562094_4_2ul_StageTip.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 #rows are 72845 output$tic.basepeak <- renderPlot({ #rows are 72845 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/Rtmpnauai6/rawDiag-386ab451770860.pdf generated pdf /tmp/Rtmpnauai6/rawDiag-386ab451770860.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295560, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32864), created = "2023-11-01 14:45:13", createdby = "jonas", description = "input files:\np32864/Proteomics/LUMOS_2/analytic_20230928/20230928_C32864_002_S562094_4_2ul_StageTip.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2362530)), modified = "2023-11-01 14:45:13", modifiedby = "jonas", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382211, container = list(`_classname` = "order", `_id` = 32864), created = "2023-11-01 14:45:14", createdby = "jonas", filechecksum = "88a052080d96297184f11c2b921e64a1", junk = "false", modified = "2023-11-01 14:45:14", modifiedby = "jonas", name = "WU295560-20231101-1445-rawDiag.pdf", relativepath = "container_32864/workunit_295560/WU295560-20231101-1445-rawDiag.pdf", size = "18375", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32864/workunit_295560/WU295560-20231101-1445-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32864/workunit_295560/WU295560-20231101-1445-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295560))) The current plot is available as workunit 295560 #rows are 72845 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 72845 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 72845 output$download 2... #rows are 72845 output$download 2... #rows are 72845 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 72845 output$download 2... ggsave to file /tmp/Rtmpnauai6/rawDiag-386ab431d4b065.pdf generated pdf /tmp/Rtmpnauai6/rawDiag-386ab431d4b065.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295561, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32864), created = "2023-11-01 14:46:12", createdby = "jonas", description = "input files:\np32864/Proteomics/LUMOS_2/analytic_20230928/20230928_C32864_002_S562094_4_2ul_StageTip.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2362530)), modified = "2023-11-01 14:46:12", modifiedby = "jonas", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382212, container = list(`_classname` = "order", `_id` = 32864), created = "2023-11-01 14:46:13", createdby = "jonas", filechecksum = "8a1b8a5d7e591a3786aab9bd1168a953", junk = "false", modified = "2023-11-01 14:46:13", modifiedby = "jonas", name = "WU295561-20231101-1446-rawDiag.pdf", relativepath = "container_32864/workunit_295561/WU295561-20231101-1446-rawDiag.pdf", size = "10786", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32864/workunit_295561/WU295561-20231101-1446-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32864/workunit_295561/WU295561-20231101-1446-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295561))) The current plot is available as workunit 295561 #rows are 72845 output$download 1... DEBUG renderPlot plotQCs #rows are 72845 output$download 1... #rows are 72845 output$download 2... #rows are 72845 output$download 2... Execution halted