Listening on http://127.0.0.1:42319 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//p33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_009_S572519_4_TEDC1GD_lowconc.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_011_S572520_5_TEDC1GD_allfracconc.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_006_S572518_3_391-395.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_002_S572516_1_hTEDC1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_004_S572517_2_hTEDC1.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 104838 output$tic.basepeak <- renderPlot({ #rows are 104838 output$download 2... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 104838 output$download 2... ggsave to file /tmp/RtmpesQHe5/rawDiag-3c00cc3c4e8c3a.pdf generated pdf /tmp/RtmpesQHe5/rawDiag-3c00cc3c4e8c3a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294593, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33067), created = "2023-10-11 11:14:58", createdby = "spfammatter", deletable = "true", description = "input files:\np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_002_S572516_1_hTEDC1.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_006_S572518_3_391-395.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_011_S572520_5_TEDC1GD_allfracconc.raw\np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_004_S572517_2_hTEDC1.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_009_S572519_4_TEDC1GD_lowconc.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2367545), list(`_classname` = "resource", `_id` = 2367544), list(`_classname` = "resource", `_id` = 2367543), list(`_classname` = "resource", `_id` = 2367542), list(`_classname` = "resource", `_id` = 2367541)), modified = "2023-10-11 11:14:58", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2368910, container = list(`_classname` = "order", `_id` = 33067), created = "2023-10-11 11:14:59", createdby = "spfammatter", deletable = "true", filechecksum = "1c5ab23334b3ab218f7576fe6b7b19d1", junk = "false", modified = "2023-10-11 11:14:59", modifiedby = "spfammatter", name = "WU294593-20231011-1114-rawDiag.pdf", relativepath = "container_33067/workunit_294593/WU294593-20231011-1114-rawDiag.pdf", size = "167467", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33067/workunit_294593/WU294593-20231011-1114-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33067/workunit_294593/WU294593-20231011-1114-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294593))) The current plot is available as workunit 294593 #rows are 104838 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 104838 output$download 2... #rows are 104838 output$download 2... #rows are 104838 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 104838 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 104838 output$download 2... ggsave to file /tmp/RtmpesQHe5/rawDiag-3c00cc5b4c1060.pdf generated pdf /tmp/RtmpesQHe5/rawDiag-3c00cc5b4c1060.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294595, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33067), created = "2023-10-11 11:16:13", createdby = "spfammatter", deletable = "true", description = "input files:\np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_002_S572516_1_hTEDC1.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_006_S572518_3_391-395.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_011_S572520_5_TEDC1GD_allfracconc.raw\np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_004_S572517_2_hTEDC1.raw \np33067/Proteomics/QEXACTIVE_1/analytic_20231006/20231006_C33067_009_S572519_4_TEDC1GD_lowconc.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\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` = 2367545), list(`_classname` = "resource", `_id` = 2367544), list(`_classname` = "resource", `_id` = 2367543), list(`_classname` = "resource", `_id` = 2367542), list(`_classname` = "resource", `_id` = 2367541)), modified = "2023-10-11 11:16:13", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2368912, container = list(`_classname` = "order", `_id` = 33067), created = "2023-10-11 11:16:15", createdby = "spfammatter", deletable = "true", filechecksum = "51f5e5922e0611c9e14f0c9cd016e21d", junk = "false", modified = "2023-10-11 11:16:15", modifiedby = "spfammatter", name = "WU294595-20231011-1116-rawDiag.pdf", relativepath = "container_33067/workunit_294595/WU294595-20231011-1116-rawDiag.pdf", size = "170862", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33067/workunit_294595/WU294595-20231011-1116-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33067/workunit_294595/WU294595-20231011-1116-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294595))) The current plot is available as workunit 294595 #rows are 104838 output$download 1... Execution halted