Listening on http://127.0.0.1:43815 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 40229 output$tic.basepeak <- renderPlot({ #rows are 40229 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpU73UJT/rawDiag-2cb7c913ecf429.pdf generated pdf /tmp/RtmpU73UJT/rawDiag-2cb7c913ecf429.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293231, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:04:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.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` = 2355134), list(`_classname` = "resource", `_id` = 2355133)), modified = "2023-09-06 11:04:58", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2355145, container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:04:59", createdby = "tobiasko", deletable = "true", filechecksum = "952a930ef932d1471b630aa73818997a", junk = "false", modified = "2023-09-06 11:04:59", modifiedby = "tobiasko", name = "WU293231-20230906-1104-rawDiag.pdf", relativepath = "container_32718/workunit_293231/WU293231-20230906-1104-rawDiag.pdf", size = "88718", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32718/workunit_293231/WU293231-20230906-1104-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32718/workunit_293231/WU293231-20230906-1104-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293231))) The current plot is available as workunit 293231 #rows are 40229 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 40229 output$download 2... ggsave to file /tmp/RtmpU73UJT/rawDiag-2cb7c920a1e398.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpU73UJT/rawDiag-2cb7c920a1e398.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293232, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:05:18", createdby = "tobiasko", deletable = "true", description = "input files:\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.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` = 2355134), list(`_classname` = "resource", `_id` = 2355133)), modified = "2023-09-06 11:05:18", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2355147, container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:05:19", createdby = "tobiasko", deletable = "true", filechecksum = "f38ca9d31702adb6bd0848770c1ac09f", junk = "false", modified = "2023-09-06 11:05:20", modifiedby = "tobiasko", name = "WU293232-20230906-1105-rawDiag.pdf", relativepath = "container_32718/workunit_293232/WU293232-20230906-1105-rawDiag.pdf", size = "58409", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32718/workunit_293232/WU293232-20230906-1105-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32718/workunit_293232/WU293232-20230906-1105-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293232))) The current plot is available as workunit 293232 #rows are 40229 output$download 1... #rows are 40229 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 40229 output$download 2... ggsave to file /tmp/RtmpU73UJT/rawDiag-2cb7c944f9ecda.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpU73UJT/rawDiag-2cb7c944f9ecda.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293233, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:05:36", createdby = "tobiasko", deletable = "true", description = "input files:\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.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` = 2355134), list(`_classname` = "resource", `_id` = 2355133)), modified = "2023-09-06 11:05:36", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2355148, container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:05:38", createdby = "tobiasko", deletable = "true", filechecksum = "e19f0146aed8c7ab706c389b85bc6e0f", junk = "false", modified = "2023-09-06 11:05:38", modifiedby = "tobiasko", name = "WU293233-20230906-1105-rawDiag.pdf", relativepath = "container_32718/workunit_293233/WU293233-20230906-1105-rawDiag.pdf", size = "34936", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32718/workunit_293233/WU293233-20230906-1105-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32718/workunit_293233/WU293233-20230906-1105-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293233))) The current plot is available as workunit 293233 #rows are 40229 output$download 1... #rows are 40229 output$download 2... ggsave to file /tmp/RtmpU73UJT/rawDiag-2cb7c96f66dd4c.pdf generated pdf /tmp/RtmpU73UJT/rawDiag-2cb7c96f66dd4c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293234, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:06:16", createdby = "tobiasko", deletable = "true", description = "input files:\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.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` = 2355134), list(`_classname` = "resource", `_id` = 2355133)), modified = "2023-09-06 11:06:16", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2355149, container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:06:17", createdby = "tobiasko", deletable = "true", filechecksum = "bdf4e5e7a81406fe900da7e49047ad8c", junk = "false", modified = "2023-09-06 11:06:17", modifiedby = "tobiasko", name = "WU293234-20230906-1106-rawDiag.pdf", relativepath = "container_32718/workunit_293234/WU293234-20230906-1106-rawDiag.pdf", size = "50486", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32718/workunit_293234/WU293234-20230906-1106-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32718/workunit_293234/WU293234-20230906-1106-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293234))) The current plot is available as workunit 293234 #rows are 40229 output$download 1... #rows are 40229 output$download 2... ggsave to file /tmp/RtmpU73UJT/rawDiag-2cb7c97da7cc4e.pdf generated pdf /tmp/RtmpU73UJT/rawDiag-2cb7c97da7cc4e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293235, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:06:42", createdby = "tobiasko", deletable = "true", description = "input files:\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_003_S554535_MFM-X256-1_H2O2_Treated_DDA.raw\np32718/Proteomics/QEXACTIVE_1/tobiasko_20230905/20230905_002_S554534_MFM-X256-1_mock_Control_DDA.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` = 2355134), list(`_classname` = "resource", `_id` = 2355133)), modified = "2023-09-06 11:06:42", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2355150, container = list(`_classname` = "order", `_id` = 32718), created = "2023-09-06 11:06:43", createdby = "tobiasko", deletable = "true", filechecksum = "65a87e5b021b2c85ed563c3fb52cfab5", junk = "false", modified = "2023-09-06 11:06:43", modifiedby = "tobiasko", name = "WU293235-20230906-1106-rawDiag.pdf", relativepath = "container_32718/workunit_293235/WU293235-20230906-1106-rawDiag.pdf", size = "7611", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32718/workunit_293235/WU293235-20230906-1106-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32718/workunit_293235/WU293235-20230906-1106-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293235))) The current plot is available as workunit 293235 #rows are 40229 output$download 1... Execution halted