Listening on http://127.0.0.1:44703 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 51211 output$tic.basepeak <- renderPlot({ #rows are 51211 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed1856156d24.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed1856156d24.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292414, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:25:42", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:25:42", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345612, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:25:43", createdby = "tobiasko", deletable = "true", filechecksum = "6557df9263dee7e5fbb472bd16b63745", junk = "false", modified = "2023-08-14 10:25:43", modifiedby = "tobiasko", name = "WU292414-20230814-1025-rawDiag.pdf", relativepath = "container_31929/workunit_292414/WU292414-20230814-1025-rawDiag.pdf", size = "85843", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292414/WU292414-20230814-1025-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292414/WU292414-20230814-1025-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292414))) The current plot is available as workunit 292414 #rows are 51211 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 51211 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed18220cd890.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpiWj56h/rawDiag-2bed18220cd890.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292415, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:25:54", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:25:54", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345613, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:25:55", createdby = "tobiasko", deletable = "true", filechecksum = "ab4cae7c9d44ec10be06defcd3fec959", junk = "false", modified = "2023-08-14 10:25:55", modifiedby = "tobiasko", name = "WU292415-20230814-1025-rawDiag.pdf", relativepath = "container_31929/workunit_292415/WU292415-20230814-1025-rawDiag.pdf", size = "65728", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292415/WU292415-20230814-1025-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292415/WU292415-20230814-1025-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292415))) The current plot is available as workunit 292415 #rows are 51211 output$download 1... Warning: Removed 5 rows containing non-finite values (`stat_smooth()`). #rows are 51211 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed1833b686d1.pdf Warning: Removed 5 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpiWj56h/rawDiag-2bed1833b686d1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292416, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:07", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:26:07", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345614, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:08", createdby = "tobiasko", deletable = "true", filechecksum = "3e638766570a6342306d528d5b00c88c", junk = "false", modified = "2023-08-14 10:26:08", modifiedby = "tobiasko", name = "WU292416-20230814-1026-rawDiag.pdf", relativepath = "container_31929/workunit_292416/WU292416-20230814-1026-rawDiag.pdf", size = "47459", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292416/WU292416-20230814-1026-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292416/WU292416-20230814-1026-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292416))) The current plot is available as workunit 292416 #rows are 51211 output$download 1... #rows are 51211 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed18690d43b7.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed18690d43b7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292417, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:21", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:26:21", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345615, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:22", createdby = "tobiasko", deletable = "true", filechecksum = "8a831f7c9727dd87793301882d6d5232", junk = "false", modified = "2023-08-14 10:26:22", modifiedby = "tobiasko", name = "WU292417-20230814-1026-rawDiag.pdf", relativepath = "container_31929/workunit_292417/WU292417-20230814-1026-rawDiag.pdf", size = "228901", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292417/WU292417-20230814-1026-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292417/WU292417-20230814-1026-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292417))) The current plot is available as workunit 292417 #rows are 51211 output$download 1... #rows are 51211 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed182cc89119.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed182cc89119.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292418, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:37", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:26:37", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345616, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:38", createdby = "tobiasko", deletable = "true", filechecksum = "d268b116de805eb6eb11c3864a46a769", junk = "false", modified = "2023-08-14 10:26:38", modifiedby = "tobiasko", name = "WU292418-20230814-1026-rawDiag.pdf", relativepath = "container_31929/workunit_292418/WU292418-20230814-1026-rawDiag.pdf", size = "6406", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292418/WU292418-20230814-1026-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292418/WU292418-20230814-1026-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292418))) The current plot is available as workunit 292418 #rows are 51211 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 51211 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed1884f29f0.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed1884f29f0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292419, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:56", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_005_S517153_FOXO4Ub_Group_2_dda.raw \np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_002_S517152_FOXO4control_Group_1_dda_rep.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` = 2345611), list(`_classname` = "resource", `_id` = 2345610)), modified = "2023-08-14 10:26:56", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345617, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:26:57", createdby = "tobiasko", deletable = "true", filechecksum = "1e7e61d2071aab7acda05581794b3fb4", junk = "false", modified = "2023-08-14 10:26:57", modifiedby = "tobiasko", name = "WU292419-20230814-1026-rawDiag.pdf", relativepath = "container_31929/workunit_292419/WU292419-20230814-1026-rawDiag.pdf", size = "17874", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292419/WU292419-20230814-1026-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292419/WU292419-20230814-1026-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292419))) The current plot is available as workunit 292419 #rows are 51211 output$download 1... #rows are 51211 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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 173437 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 173437 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed1877630243.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed1877630243.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292420, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:30:47", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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` = 2345609), list(`_classname` = "resource", `_id` = 2345608)), modified = "2023-08-14 10:30:47", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345618, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:30:49", createdby = "tobiasko", deletable = "true", filechecksum = "b9dfd636f48aa544aa3c74bc4f5a8308", junk = "false", modified = "2023-08-14 10:30:49", modifiedby = "tobiasko", name = "WU292420-20230814-1030-rawDiag.pdf", relativepath = "container_31929/workunit_292420/WU292420-20230814-1030-rawDiag.pdf", size = "36106", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292420/WU292420-20230814-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292420/WU292420-20230814-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292420))) The current plot is available as workunit 292420 #rows are 173437 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 173437 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed184de1a54a.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpiWj56h/rawDiag-2bed184de1a54a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292421, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:30:55", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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` = 2345609), list(`_classname` = "resource", `_id` = 2345608)), modified = "2023-08-14 10:30:55", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345619, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:30:57", createdby = "tobiasko", deletable = "true", filechecksum = "09e6cdc7dca0f91961553a69c1f3dc6c", junk = "false", modified = "2023-08-14 10:30:57", modifiedby = "tobiasko", name = "WU292421-20230814-1030-rawDiag.pdf", relativepath = "container_31929/workunit_292421/WU292421-20230814-1030-rawDiag.pdf", size = "56851", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292421/WU292421-20230814-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292421/WU292421-20230814-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292421))) The current plot is available as workunit 292421 #rows are 173437 output$download 1... Warning: Removed 9 rows containing non-finite values (`stat_smooth()`). #rows are 173437 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed182f0e5655.pdf Warning: Removed 9 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpiWj56h/rawDiag-2bed182f0e5655.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292422, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:16", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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` = 2345609), list(`_classname` = "resource", `_id` = 2345608)), modified = "2023-08-14 10:31:16", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345620, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:17", createdby = "tobiasko", deletable = "true", filechecksum = "978f71d8cef8aaab4660bd4d100e14e4", junk = "false", modified = "2023-08-14 10:31:17", modifiedby = "tobiasko", name = "WU292422-20230814-1031-rawDiag.pdf", relativepath = "container_31929/workunit_292422/WU292422-20230814-1031-rawDiag.pdf", size = "20740", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292422/WU292422-20230814-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292422/WU292422-20230814-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292422))) The current plot is available as workunit 292422 #rows are 173437 output$download 1... #rows are 173437 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed18523c379.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed18523c379.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292423, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:34", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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` = 2345609), list(`_classname` = "resource", `_id` = 2345608)), modified = "2023-08-14 10:31:34", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345621, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:35", createdby = "tobiasko", deletable = "true", filechecksum = "8a4f0a26d82e6e1eee6cb5bfaef17a91", junk = "false", modified = "2023-08-14 10:31:35", modifiedby = "tobiasko", name = "WU292423-20230814-1031-rawDiag.pdf", relativepath = "container_31929/workunit_292423/WU292423-20230814-1031-rawDiag.pdf", size = "304483", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292423/WU292423-20230814-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292423/WU292423-20230814-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292423))) The current plot is available as workunit 292423 #rows are 173437 output$download 1... #rows are 173437 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 173437 output$download 2... ggsave to file /tmp/RtmpiWj56h/rawDiag-2bed187a41f212.pdf generated pdf /tmp/RtmpiWj56h/rawDiag-2bed187a41f212.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292424, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:58", createdby = "tobiasko", deletable = "true", description = "input files:\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_003_S517152_FOXO4control_Group_1_dia.raw\np31929/Proteomics/EXPLORIS_2/analytic_20230811/20230811_C31929_006_S517153_FOXO4Ub_Group_2_dia.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` = 2345609), list(`_classname` = "resource", `_id` = 2345608)), modified = "2023-08-14 10:31:58", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2345622, container = list(`_classname` = "order", `_id` = 31929), created = "2023-08-14 10:31:59", createdby = "tobiasko", deletable = "true", filechecksum = "0ce79042967be1e0a2db519ede575f58", junk = "false", modified = "2023-08-14 10:31:59", modifiedby = "tobiasko", name = "WU292424-20230814-1031-rawDiag.pdf", relativepath = "container_31929/workunit_292424/WU292424-20230814-1031-rawDiag.pdf", size = "17493", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31929/workunit_292424/WU292424-20230814-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31929/workunit_292424/WU292424-20230814-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292424))) The current plot is available as workunit 292424 #rows are 173437 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({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE saving 'login and webservicepassword' ... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE saving 'login and webservicepassword' ... #rows are 173437 output$download 2... Execution halted