Listening on http://127.0.0.1:33287 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$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$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//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_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 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 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 renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 532074 output$tic.basepeak <- renderPlot({ #rows are 532074 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee2090cc73.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee2090cc73.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290797, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:21:08", createdby = "tobiasko", deletable = "true", description = "input files:\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_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` = 2324465), list(`_classname` = "resource", `_id` = 2324464), list(`_classname` = "resource", `_id` = 2324463), list(`_classname` = "resource", `_id` = 2324462), list(`_classname` = "resource", `_id` = 2324461)), modified = "2023-07-03 09:21:08", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324475, container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:21:10", createdby = "tobiasko", deletable = "true", filechecksum = "8c72907e422f9559fae58087f95681fe", junk = "false", modified = "2023-07-03 09:21:10", modifiedby = "tobiasko", name = "WU290797-20230703-0921-rawDiag.pdf", relativepath = "container_32141/workunit_290797/WU290797-20230703-0921-rawDiag.pdf", size = "362868", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32141/workunit_290797/WU290797-20230703-0921-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32141/workunit_290797/WU290797-20230703-0921-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290797))) The current plot is available as workunit 290797 #rows are 532074 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 532074 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee14a62a07.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee14a62a07.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290798, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:22:44", createdby = "tobiasko", deletable = "true", description = "input files:\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_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` = 2324465), list(`_classname` = "resource", `_id` = 2324464), list(`_classname` = "resource", `_id` = 2324463), list(`_classname` = "resource", `_id` = 2324462), list(`_classname` = "resource", `_id` = 2324461)), modified = "2023-07-03 09:22:44", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324476, container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:22:45", createdby = "tobiasko", deletable = "true", filechecksum = "aa9b33d4ec5b35d33893b356bab3f166", junk = "false", modified = "2023-07-03 09:22:45", modifiedby = "tobiasko", name = "WU290798-20230703-0922-rawDiag.pdf", relativepath = "container_32141/workunit_290798/WU290798-20230703-0922-rawDiag.pdf", size = "335359", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32141/workunit_290798/WU290798-20230703-0922-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32141/workunit_290798/WU290798-20230703-0922-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290798))) The current plot is available as workunit 290798 #rows are 532074 output$download 1... #rows are 532074 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 532074 output$download 2... #rows are 532074 output$download 2... Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). #rows are 532074 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee2a8b0d93.pdf Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee2a8b0d93.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290799, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:24:04", createdby = "tobiasko", deletable = "true", description = "input files:\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_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` = 2324465), list(`_classname` = "resource", `_id` = 2324464), list(`_classname` = "resource", `_id` = 2324463), list(`_classname` = "resource", `_id` = 2324462), list(`_classname` = "resource", `_id` = 2324461)), modified = "2023-07-03 09:24:04", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324477, container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:24:05", createdby = "tobiasko", deletable = "true", filechecksum = "e6e798490dfc9eabf5619ee335356322", junk = "false", modified = "2023-07-03 09:24:05", modifiedby = "tobiasko", name = "WU290799-20230703-0924-rawDiag.pdf", relativepath = "container_32141/workunit_290799/WU290799-20230703-0924-rawDiag.pdf", size = "177790", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32141/workunit_290799/WU290799-20230703-0924-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32141/workunit_290799/WU290799-20230703-0924-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290799))) The current plot is available as workunit 290799 #rows are 532074 output$download 1... #rows are 532074 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee595baa7.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee595baa7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290800, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:25:05", createdby = "tobiasko", deletable = "true", description = "input files:\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_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` = 2324465), list(`_classname` = "resource", `_id` = 2324464), list(`_classname` = "resource", `_id` = 2324463), list(`_classname` = "resource", `_id` = 2324462), list(`_classname` = "resource", `_id` = 2324461)), modified = "2023-07-03 09:25:05", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324478, container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:25:06", createdby = "tobiasko", deletable = "true", filechecksum = "8e4049caeeaa6a7798d4a4972b802364", junk = "false", modified = "2023-07-03 09:25:06", modifiedby = "tobiasko", name = "WU290800-20230703-0925-rawDiag.pdf", relativepath = "container_32141/workunit_290800/WU290800-20230703-0925-rawDiag.pdf", size = "1556707", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32141/workunit_290800/WU290800-20230703-0925-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32141/workunit_290800/WU290800-20230703-0925-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290800))) The current plot is available as workunit 290800 #rows are 532074 output$download 1... #rows are 532074 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee3f1fe154.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee3f1fe154.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290801, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:25:28", createdby = "tobiasko", deletable = "true", description = "input files:\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_Control_rep.raw\np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_003_S527671_BIRC6Control1_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_004_S527675_BIRC6KO2_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_005_S527676_BIRC6KO3_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_007_S527674_BIRC6KO1_Knock-out__KO_.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_006_S527673_BIRC6control3_Control.raw \np32141/Proteomics/EXPLORIS_2/analytic_20230630/20230630_C32141_002_S527672_BIRC6control2_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` = 2324465), list(`_classname` = "resource", `_id` = 2324464), list(`_classname` = "resource", `_id` = 2324463), list(`_classname` = "resource", `_id` = 2324462), list(`_classname` = "resource", `_id` = 2324461)), modified = "2023-07-03 09:25:28", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324479, container = list(`_classname` = "order", `_id` = 32141), created = "2023-07-03 09:25:30", createdby = "tobiasko", deletable = "true", filechecksum = "c544a765c1302f82b8547a4f67aa217f", junk = "false", modified = "2023-07-03 09:25:30", modifiedby = "tobiasko", name = "WU290801-20230703-0925-rawDiag.pdf", relativepath = "container_32141/workunit_290801/WU290801-20230703-0925-rawDiag.pdf", size = "10462", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32141/workunit_290801/WU290801-20230703-0925-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32141/workunit_290801/WU290801-20230703-0925-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290801))) The current plot is available as workunit 290801 #rows are 532074 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") 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 532074 output$download 1... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... #rows are 0 saving 'login and webservicepassword' ... output$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//p32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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 renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 83704 output$tic.basepeak <- renderPlot({ #rows are 83704 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee16710b2b.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee16710b2b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290811, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:14", createdby = "tobiasko", deletable = "true", description = "input files:\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw \np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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` = 2323459), list(`_classname` = "resource", `_id` = 2323458), list(`_classname` = "resource", `_id` = 2323457)), modified = "2023-07-03 10:23:14", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324610, container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:15", createdby = "tobiasko", deletable = "true", filechecksum = "1acdb8f52fb439268c8feabc204a9526", junk = "false", modified = "2023-07-03 10:23:15", modifiedby = "tobiasko", name = "WU290811-20230703-1023-rawDiag.pdf", relativepath = "container_32113/workunit_290811/WU290811-20230703-1023-rawDiag.pdf", size = "112179", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32113/workunit_290811/WU290811-20230703-1023-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32113/workunit_290811/WU290811-20230703-1023-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290811))) The current plot is available as workunit 290811 #rows are 83704 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 83704 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee375e3a93.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee375e3a93.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290812, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:35", createdby = "tobiasko", deletable = "true", description = "input files:\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw \np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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` = 2323459), list(`_classname` = "resource", `_id` = 2323458), list(`_classname` = "resource", `_id` = 2323457)), modified = "2023-07-03 10:23:35", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324611, container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:36", createdby = "tobiasko", deletable = "true", filechecksum = "7e6b84b16a57e38cab66cb0a24ba0f86", junk = "false", modified = "2023-07-03 10:23:36", modifiedby = "tobiasko", name = "WU290812-20230703-1023-rawDiag.pdf", relativepath = "container_32113/workunit_290812/WU290812-20230703-1023-rawDiag.pdf", size = "99970", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32113/workunit_290812/WU290812-20230703-1023-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32113/workunit_290812/WU290812-20230703-1023-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290812))) The current plot is available as workunit 290812 #rows are 83704 output$download 1... #rows are 83704 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee3fefca15.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee3fefca15.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290813, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:53", createdby = "tobiasko", deletable = "true", description = "input files:\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw \np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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` = 2323459), list(`_classname` = "resource", `_id` = 2323458), list(`_classname` = "resource", `_id` = 2323457)), modified = "2023-07-03 10:23:53", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324612, container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:23:55", createdby = "tobiasko", deletable = "true", filechecksum = "aafdc629f6e72815a466ff2334f3a0bf", junk = "false", modified = "2023-07-03 10:23:55", modifiedby = "tobiasko", name = "WU290813-20230703-1023-rawDiag.pdf", relativepath = "container_32113/workunit_290813/WU290813-20230703-1023-rawDiag.pdf", size = "56948", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32113/workunit_290813/WU290813-20230703-1023-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32113/workunit_290813/WU290813-20230703-1023-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290813))) The current plot is available as workunit 290813 #rows are 83704 output$download 1... #rows are 83704 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee7a4d59e1.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee7a4d59e1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290814, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:24:25", createdby = "tobiasko", deletable = "true", description = "input files:\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw \np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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` = 2323459), list(`_classname` = "resource", `_id` = 2323458), list(`_classname` = "resource", `_id` = 2323457)), modified = "2023-07-03 10:24:25", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324613, container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:24:27", createdby = "tobiasko", deletable = "true", filechecksum = "e9f38fda75035c0bf2dcce6567bcae70", junk = "false", modified = "2023-07-03 10:24:27", modifiedby = "tobiasko", name = "WU290814-20230703-1024-rawDiag.pdf", relativepath = "container_32113/workunit_290814/WU290814-20230703-1024-rawDiag.pdf", size = "377408", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32113/workunit_290814/WU290814-20230703-1024-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32113/workunit_290814/WU290814-20230703-1024-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290814))) The current plot is available as workunit 290814 #rows are 83704 output$download 1... #rows are 83704 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee1ade2654.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee1ade2654.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290815, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:24:42", createdby = "tobiasko", deletable = "true", description = "input files:\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_002_S526772_WT01_Group_1.raw \np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_003_S526773_CLF-GFP01_Group_2.raw\np32113/Proteomics/EXPLORIS_2/analytic_20230628/20230628_C32113_004_S526774_SWN-GFP01_Group_3.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` = 2323459), list(`_classname` = "resource", `_id` = 2323458), list(`_classname` = "resource", `_id` = 2323457)), modified = "2023-07-03 10:24:42", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324614, container = list(`_classname` = "order", `_id` = 32113), created = "2023-07-03 10:24:43", createdby = "tobiasko", deletable = "true", filechecksum = "160fe72afadb98820179b0342b4bbdfb", junk = "false", modified = "2023-07-03 10:24:43", modifiedby = "tobiasko", name = "WU290815-20230703-1024-rawDiag.pdf", relativepath = "container_32113/workunit_290815/WU290815-20230703-1024-rawDiag.pdf", size = "6860", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32113/workunit_290815/WU290815-20230703-1024-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32113/workunit_290815/WU290815-20230703-1024-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290815))) The current plot is available as workunit 290815 #rows are 83704 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") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 83704 output$download 1... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #rows are 83704 output$download 2... #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//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.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 renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber 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 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 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 LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 307141 output$tic.basepeak <- renderPlot({ #rows are 307141 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee7efcf9a8.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee7efcf9a8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290882, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:29:24", createdby = "tobiasko", deletable = "true", description = "input files:\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.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` = 2323677), list(`_classname` = "resource", `_id` = 2323676), list(`_classname` = "resource", `_id` = 2323675), list(`_classname` = "resource", `_id` = 2323674), list(`_classname` = "resource", `_id` = 2323673), list(`_classname` = "resource", `_id` = 2323672), list(`_classname` = "resource", `_id` = 2323671), list(`_classname` = "resource", `_id` = 2323670), list(`_classname` = "resource", `_id` = 2323669), list( `_classname` = "resource", `_id` = 2323668), list(`_classname` = "resource", `_id` = 2323667), list(`_classname` = "resource", `_id` = 2323666)), modified = "2023-07-04 10:29:24", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324870, container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:29:25", createdby = "tobiasko", deletable = "true", filechecksum = "555bcb19fbf39b18faf4e321ee758e74", junk = "false", modified = "2023-07-04 10:29:25", modifiedby = "tobiasko", name = "WU290882-20230704-1029-rawDiag.pdf", relativepath = "container_32068/workunit_290882/WU290882-20230704-1029-rawDiag.pdf", size = "456963", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32068/workunit_290882/WU290882-20230704-1029-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32068/workunit_290882/WU290882-20230704-1029-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290882))) The current plot is available as workunit 290882 #rows are 307141 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 307141 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee7c42583f.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee7c42583f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290883, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:29:49", createdby = "tobiasko", deletable = "true", description = "input files:\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.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` = 2323677), list(`_classname` = "resource", `_id` = 2323676), list(`_classname` = "resource", `_id` = 2323675), list(`_classname` = "resource", `_id` = 2323674), list(`_classname` = "resource", `_id` = 2323673), list(`_classname` = "resource", `_id` = 2323672), list(`_classname` = "resource", `_id` = 2323671), list(`_classname` = "resource", `_id` = 2323670), list(`_classname` = "resource", `_id` = 2323669), list( `_classname` = "resource", `_id` = 2323668), list(`_classname` = "resource", `_id` = 2323667), list(`_classname` = "resource", `_id` = 2323666)), modified = "2023-07-04 10:29:49", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324871, container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:29:50", createdby = "tobiasko", deletable = "true", filechecksum = "ca56fae3f3b5bc82f8dcb6f1ce763fc2", junk = "false", modified = "2023-07-04 10:29:50", modifiedby = "tobiasko", name = "WU290883-20230704-1029-rawDiag.pdf", relativepath = "container_32068/workunit_290883/WU290883-20230704-1029-rawDiag.pdf", size = "365181", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32068/workunit_290883/WU290883-20230704-1029-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32068/workunit_290883/WU290883-20230704-1029-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290883))) The current plot is available as workunit 290883 #rows are 307141 output$download 1... #rows are 307141 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee32046885.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee32046885.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290884, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:30:07", createdby = "tobiasko", deletable = "true", description = "input files:\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.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` = 2323677), list(`_classname` = "resource", `_id` = 2323676), list(`_classname` = "resource", `_id` = 2323675), list(`_classname` = "resource", `_id` = 2323674), list(`_classname` = "resource", `_id` = 2323673), list(`_classname` = "resource", `_id` = 2323672), list(`_classname` = "resource", `_id` = 2323671), list(`_classname` = "resource", `_id` = 2323670), list(`_classname` = "resource", `_id` = 2323669), list( `_classname` = "resource", `_id` = 2323668), list(`_classname` = "resource", `_id` = 2323667), list(`_classname` = "resource", `_id` = 2323666)), modified = "2023-07-04 10:30:07", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324872, container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:30:08", createdby = "tobiasko", deletable = "true", filechecksum = "6a12d195b85b61eb12be2c538a78ba40", junk = "false", modified = "2023-07-04 10:30:08", modifiedby = "tobiasko", name = "WU290884-20230704-1030-rawDiag.pdf", relativepath = "container_32068/workunit_290884/WU290884-20230704-1030-rawDiag.pdf", size = "273002", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32068/workunit_290884/WU290884-20230704-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32068/workunit_290884/WU290884-20230704-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290884))) The current plot is available as workunit 290884 #rows are 307141 output$download 1... #rows are 307141 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee38336ede.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee38336ede.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290886, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:30:38", createdby = "tobiasko", deletable = "true", description = "input files:\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.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` = 2323677), list(`_classname` = "resource", `_id` = 2323676), list(`_classname` = "resource", `_id` = 2323675), list(`_classname` = "resource", `_id` = 2323674), list(`_classname` = "resource", `_id` = 2323673), list(`_classname` = "resource", `_id` = 2323672), list(`_classname` = "resource", `_id` = 2323671), list(`_classname` = "resource", `_id` = 2323670), list(`_classname` = "resource", `_id` = 2323669), list( `_classname` = "resource", `_id` = 2323668), list(`_classname` = "resource", `_id` = 2323667), list(`_classname` = "resource", `_id` = 2323666)), modified = "2023-07-04 10:30:38", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324873, container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:30:40", createdby = "tobiasko", deletable = "true", filechecksum = "d3bfe5a10f136389c9c22ac7bc05e3fe", junk = "false", modified = "2023-07-04 10:30:40", modifiedby = "tobiasko", name = "WU290886-20230704-1030-rawDiag.pdf", relativepath = "container_32068/workunit_290886/WU290886-20230704-1030-rawDiag.pdf", size = "1371985", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32068/workunit_290886/WU290886-20230704-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32068/workunit_290886/WU290886-20230704-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290886))) The current plot is available as workunit 290886 #rows are 307141 output$download 1... #rows are 307141 output$download 2... ggsave to file /tmp/RtmplSR2B7/rawDiag-3e9bee667edbce.pdf generated pdf /tmp/RtmplSR2B7/rawDiag-3e9bee667edbce.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290887, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:31:38", createdby = "tobiasko", deletable = "true", description = "input files:\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_010_S525038_WT_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_009_S525034_Mut_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_012_S525029_EV_noUV_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_011_S525035_EV_noUV_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_014_S525033_Mut_noUV_1_Recombinant_protein.raw\np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_006_S525032_WT_1h_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_004_S525040_Mut_1h_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_013_S525030_EV_1h_1_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_003_S525036_EV_1h_2_Empty_Vector__EV_.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_005_S525031_WT_noUV_1_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_007_S525037_WT_noUV_2_Recombinant_protein.raw \np32068/Proteomics/EXPLORIS_2/analytic_20230629/20230629_C32068_002_S525039_Mut_noUV_2_Recombinant_protein.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` = 2323677), list(`_classname` = "resource", `_id` = 2323676), list(`_classname` = "resource", `_id` = 2323675), list(`_classname` = "resource", `_id` = 2323674), list(`_classname` = "resource", `_id` = 2323673), list(`_classname` = "resource", `_id` = 2323672), list(`_classname` = "resource", `_id` = 2323671), list(`_classname` = "resource", `_id` = 2323670), list(`_classname` = "resource", `_id` = 2323669), list( `_classname` = "resource", `_id` = 2323668), list(`_classname` = "resource", `_id` = 2323667), list(`_classname` = "resource", `_id` = 2323666)), modified = "2023-07-04 10:31:38", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2324877, container = list(`_classname` = "order", `_id` = 32068), created = "2023-07-04 10:31:39", createdby = "tobiasko", deletable = "true", filechecksum = "26523ef49ede39a7a6225af4ea30b43a", junk = "false", modified = "2023-07-04 10:31:39", modifiedby = "tobiasko", name = "WU290887-20230704-1031-rawDiag.pdf", relativepath = "container_32068/workunit_290887/WU290887-20230704-1031-rawDiag.pdf", size = "12573", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32068/workunit_290887/WU290887-20230704-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32068/workunit_290887/WU290887-20230704-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290887))) The current plot is available as workunit 290887 #rows are 307141 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 307141 output$download 1... 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 307141 output$download 2...