Listening on http://127.0.0.1:45031 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 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({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 52340 output$tic.basepeak <- renderPlot({ #rows are 52340 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/Rtmpd26HJi/rawDiag-2942fb1efed498.pdf generated pdf /tmp/Rtmpd26HJi/rawDiag-2942fb1efed498.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290707, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:03", createdby = "tobiasko", deletable = "true", description = "input files:\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.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` = 2323665), list(`_classname` = "resource", `_id` = 2323664)), modified = "2023-06-30 09:24:03", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2323680, container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:04", createdby = "tobiasko", deletable = "true", filechecksum = "94819917b903cdb1ae6ccb3db400f673", junk = "false", modified = "2023-06-30 09:24:04", modifiedby = "tobiasko", name = "WU290707-20230630-0924-rawDiag.pdf", relativepath = "container_32149/workunit_290707/WU290707-20230630-0924-rawDiag.pdf", size = "83326", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32149/workunit_290707/WU290707-20230630-0924-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32149/workunit_290707/WU290707-20230630-0924-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290707))) The current plot is available as workunit 290707 #rows are 52340 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 52340 output$download 2... ggsave to file /tmp/Rtmpd26HJi/rawDiag-2942fb75981d75.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/Rtmpd26HJi/rawDiag-2942fb75981d75.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290708, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:22", createdby = "tobiasko", deletable = "true", description = "input files:\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.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` = 2323665), list(`_classname` = "resource", `_id` = 2323664)), modified = "2023-06-30 09:24:22", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2323681, container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:23", createdby = "tobiasko", deletable = "true", filechecksum = "f56eba9fc3cbd9ce68e1b6f12d6c15ee", junk = "false", modified = "2023-06-30 09:24:23", modifiedby = "tobiasko", name = "WU290708-20230630-0924-rawDiag.pdf", relativepath = "container_32149/workunit_290708/WU290708-20230630-0924-rawDiag.pdf", size = "66511", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32149/workunit_290708/WU290708-20230630-0924-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32149/workunit_290708/WU290708-20230630-0924-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290708))) The current plot is available as workunit 290708 #rows are 52340 output$download 1... #rows are 52340 output$download 2... ggsave to file /tmp/Rtmpd26HJi/rawDiag-2942fb4198296a.pdf generated pdf /tmp/Rtmpd26HJi/rawDiag-2942fb4198296a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290709, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:38", createdby = "tobiasko", deletable = "true", description = "input files:\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.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` = 2323665), list(`_classname` = "resource", `_id` = 2323664)), modified = "2023-06-30 09:24:38", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2323682, container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:39", createdby = "tobiasko", deletable = "true", filechecksum = "ceb954f4fe2f40b5b669a73fcd398f73", junk = "false", modified = "2023-06-30 09:24:39", modifiedby = "tobiasko", name = "WU290709-20230630-0924-rawDiag.pdf", relativepath = "container_32149/workunit_290709/WU290709-20230630-0924-rawDiag.pdf", size = "42205", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32149/workunit_290709/WU290709-20230630-0924-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32149/workunit_290709/WU290709-20230630-0924-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290709))) The current plot is available as workunit 290709 #rows are 52340 output$download 1... #rows are 52340 output$download 2... ggsave to file /tmp/Rtmpd26HJi/rawDiag-2942fb3e851b1d.pdf generated pdf /tmp/Rtmpd26HJi/rawDiag-2942fb3e851b1d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290710, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.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` = 2323665), list(`_classname` = "resource", `_id` = 2323664)), modified = "2023-06-30 09:24:58", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2323683, container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:24:59", createdby = "tobiasko", deletable = "true", filechecksum = "f2307f1585f8a39fd235905d4cba9dd5", junk = "false", modified = "2023-06-30 09:24:59", modifiedby = "tobiasko", name = "WU290710-20230630-0924-rawDiag.pdf", relativepath = "container_32149/workunit_290710/WU290710-20230630-0924-rawDiag.pdf", size = "217705", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32149/workunit_290710/WU290710-20230630-0924-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32149/workunit_290710/WU290710-20230630-0924-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290710))) The current plot is available as workunit 290710 #rows are 52340 output$download 1... #rows are 52340 output$download 2... ggsave to file /tmp/Rtmpd26HJi/rawDiag-2942fb2287f12a.pdf generated pdf /tmp/Rtmpd26HJi/rawDiag-2942fb2287f12a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290711, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:25:13", createdby = "tobiasko", deletable = "true", description = "input files:\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_003_S528143_SFM_withH2O2___H2O2.raw\np32149/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32149_002_S528142_CTR_noH2O2_Control.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` = 2323665), list(`_classname` = "resource", `_id` = 2323664)), modified = "2023-06-30 09:25:13", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2323684, container = list(`_classname` = "order", `_id` = 32149), created = "2023-06-30 09:25:14", createdby = "tobiasko", deletable = "true", filechecksum = "c994d50f78e11165f1408eba82124800", junk = "false", modified = "2023-06-30 09:25:14", modifiedby = "tobiasko", name = "WU290711-20230630-0925-rawDiag.pdf", relativepath = "container_32149/workunit_290711/WU290711-20230630-0925-rawDiag.pdf", size = "6417", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32149/workunit_290711/WU290711-20230630-0925-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32149/workunit_290711/WU290711-20230630-0925-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290711))) The current plot is available as workunit 290711 #rows are 52340 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 52340 output$download 1... Execution halted