Listening on http://127.0.0.1:41553 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are 0 saving 'login and webservicepassword' ... output$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//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw qc ... 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 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 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 #rows are 170029 output$tic.basepeak <- renderPlot({ #rows are 170029 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a86c37aa8d.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a86c37aa8d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294095, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:02:52", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:02:52", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362566, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:02:53", createdby = "tobiasko", deletable = "true", filechecksum = "4e2182bf7b941bef4d4144301c8e43eb", junk = "false", modified = "2023-09-29 10:02:53", modifiedby = "tobiasko", name = "WU294095-20230929-1002-rawDiag.pdf", relativepath = "container_32943/workunit_294095/WU294095-20230929-1002-rawDiag.pdf", size = "188007", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294095/WU294095-20230929-1002-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294095/WU294095-20230929-1002-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294095))) The current plot is available as workunit 294095 #rows are 170029 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a813056d1c.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a813056d1c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294096, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:08", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:03:08", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362567, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:09", createdby = "tobiasko", deletable = "true", filechecksum = "10edb7c6cc4ca63b16cb50a2cd59acb1", junk = "false", modified = "2023-09-29 10:03:09", modifiedby = "tobiasko", name = "WU294096-20230929-1003-rawDiag.pdf", relativepath = "container_32943/workunit_294096/WU294096-20230929-1003-rawDiag.pdf", size = "181456", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294096/WU294096-20230929-1003-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294096/WU294096-20230929-1003-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294096))) The current plot is available as workunit 294096 #rows are 170029 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a876ddd9b8.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a876ddd9b8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294097, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:21", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:03:21", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362568, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:22", createdby = "tobiasko", deletable = "true", filechecksum = "d7e204abd2b574b479b03ad0150c66e7", junk = "false", modified = "2023-09-29 10:03:22", modifiedby = "tobiasko", name = "WU294097-20230929-1003-rawDiag.pdf", relativepath = "container_32943/workunit_294097/WU294097-20230929-1003-rawDiag.pdf", size = "288412", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294097/WU294097-20230929-1003-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294097/WU294097-20230929-1003-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294097))) The current plot is available as workunit 294097 #rows are 170029 output$download 1... Warning: Removed 3 rows containing non-finite values (`stat_smooth()`). #rows are 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a81ed7a6fe.pdf Warning: Removed 3 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a81ed7a6fe.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294098, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:29", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:03:29", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362569, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:30", createdby = "tobiasko", deletable = "true", filechecksum = "393010a13cf2d0fb0f5bc73ef5bddd6f", junk = "false", modified = "2023-09-29 10:03:30", modifiedby = "tobiasko", name = "WU294098-20230929-1003-rawDiag.pdf", relativepath = "container_32943/workunit_294098/WU294098-20230929-1003-rawDiag.pdf", size = "109550", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294098/WU294098-20230929-1003-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294098/WU294098-20230929-1003-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294098))) The current plot is available as workunit 294098 #rows are 170029 output$download 1... #rows are 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a83972645d.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a83972645d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294099, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:49", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:03:49", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362570, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:03:51", createdby = "tobiasko", deletable = "true", filechecksum = "9bf418abc2933b35ede260c47d7293b5", junk = "false", modified = "2023-09-29 10:03:51", modifiedby = "tobiasko", name = "WU294099-20230929-1003-rawDiag.pdf", relativepath = "container_32943/workunit_294099/WU294099-20230929-1003-rawDiag.pdf", size = "774086", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294099/WU294099-20230929-1003-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294099/WU294099-20230929-1003-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294099))) The current plot is available as workunit 294099 #rows are 170029 output$download 1... #rows are 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a823ac4696.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a823ac4696.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294100, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:05:12", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:05:12", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362571, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:05:14", createdby = "tobiasko", deletable = "true", filechecksum = "66f70ef609ad1534254e33b5a29325d2", junk = "false", modified = "2023-09-29 10:05:14", modifiedby = "tobiasko", name = "WU294100-20230929-1005-rawDiag.pdf", relativepath = "container_32943/workunit_294100/WU294100-20230929-1005-rawDiag.pdf", size = "8632", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294100/WU294100-20230929-1005-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294100/WU294100-20230929-1005-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294100))) The current plot is available as workunit 294100 #rows are 170029 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: '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: `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 170029 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a86114df06.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a86114df06.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294101, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:05:22", createdby = "tobiasko", deletable = "true", description = "input files:\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_004_S566029_Tplus2_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_003_S566025_T-1_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_006_S566027_T-3_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_008_S566026_T-2_Control.raw \np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_007_S566028_Tplus1_Sample.raw\np32943/Proteomics/EXPLORIS_1/analytic_20230927/20230927_C32943_002_S566030_Tplus3_Sample.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` = 2362168), list(`_classname` = "resource", `_id` = 2362167), list(`_classname` = "resource", `_id` = 2362166), list(`_classname` = "resource", `_id` = 2362165), list(`_classname` = "resource", `_id` = 2362164), list(`_classname` = "resource", `_id` = 2362163)), modified = "2023-09-29 10:05:22", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2362572, container = list(`_classname` = "order", `_id` = 32943), created = "2023-09-29 10:05:24", createdby = "tobiasko", deletable = "true", filechecksum = "d9f4db16ff18f9f0b8814486bdeef5aa", junk = "false", modified = "2023-09-29 10:05:24", modifiedby = "tobiasko", name = "WU294101-20230929-1005-rawDiag.pdf", relativepath = "container_32943/workunit_294101/WU294101-20230929-1005-rawDiag.pdf", size = "31480", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32943/workunit_294101/WU294101-20230929-1005-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32943/workunit_294101/WU294101-20230929-1005-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294101))) The current plot is available as workunit 294101 #rows are 170029 output$download 1... 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$xic 1: runApp #rows are 170029 output$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$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 21339 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a868e2d89b.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a868e2d89b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294118, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:38:57", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:38:57", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363182, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:38:58", createdby = "tobiasko", deletable = "true", filechecksum = "aff3e810618a01622cf971d5cd656d8c", junk = "false", modified = "2023-09-29 12:38:58", modifiedby = "tobiasko", name = "WU294118-20230929-1238-rawDiag.pdf", relativepath = "container_32998/workunit_294118/WU294118-20230929-1238-rawDiag.pdf", size = "106367", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294118/WU294118-20230929-1238-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294118/WU294118-20230929-1238-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294118))) The current plot is available as workunit 294118 #rows are 21339 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a87f2a4bf5.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a87f2a4bf5.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294119, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:39:26", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:39:26", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363183, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:39:27", createdby = "tobiasko", deletable = "true", filechecksum = "345a8fe4fdba62bdf2ee67f99ea7a95c", junk = "false", modified = "2023-09-29 12:39:28", modifiedby = "tobiasko", name = "WU294119-20230929-1239-rawDiag.pdf", relativepath = "container_32998/workunit_294119/WU294119-20230929-1239-rawDiag.pdf", size = "41806", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294119/WU294119-20230929-1239-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294119/WU294119-20230929-1239-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294119))) The current plot is available as workunit 294119 #rows are 21339 output$download 1... #rows are 21339 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a867a5e546.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a867a5e546.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294120, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:40:15", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:40:15", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363184, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:40:16", createdby = "tobiasko", deletable = "true", filechecksum = "3ce33f6245bbe78444bbd4b013da38a9", junk = "false", modified = "2023-09-29 12:40:16", modifiedby = "tobiasko", name = "WU294120-20230929-1240-rawDiag.pdf", relativepath = "container_32998/workunit_294120/WU294120-20230929-1240-rawDiag.pdf", size = "35613", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294120/WU294120-20230929-1240-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294120/WU294120-20230929-1240-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294120))) The current plot is available as workunit 294120 #rows are 21339 output$download 1... #rows are 21339 output$download 2... #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a85821b569.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a85821b569.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294121, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:40:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:40:58", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363185, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:40:59", createdby = "tobiasko", deletable = "true", filechecksum = "2ace9efba290896a9d9e295850b28e0c", junk = "false", modified = "2023-09-29 12:40:59", modifiedby = "tobiasko", name = "WU294121-20230929-1240-rawDiag.pdf", relativepath = "container_32998/workunit_294121/WU294121-20230929-1240-rawDiag.pdf", size = "46683", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294121/WU294121-20230929-1240-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294121/WU294121-20230929-1240-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294121))) The current plot is available as workunit 294121 #rows are 21339 output$download 1... #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a84eff8f22.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a84eff8f22.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294122, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:41:45", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:41:45", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363186, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:41:46", createdby = "tobiasko", deletable = "true", filechecksum = "c80b98f8479282f5d079bbb82a8ca84f", junk = "false", modified = "2023-09-29 12:41:46", modifiedby = "tobiasko", name = "WU294122-20230929-1241-rawDiag.pdf", relativepath = "container_32998/workunit_294122/WU294122-20230929-1241-rawDiag.pdf", size = "97427", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294122/WU294122-20230929-1241-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294122/WU294122-20230929-1241-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294122))) The current plot is available as workunit 294122 #rows are 21339 output$download 1... #rows are 21339 output$download 2... #rows are 21339 output$download 2... #rows are 21339 output$download 2... #rows are 21339 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a827499a7e.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a827499a7e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294123, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:43:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_010_Enolase_5ul_DDA.raw \np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_015_Enolase_5ul_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_011_Enolase_5ul_PepMap.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` = 2362541), list(`_classname` = "resource", `_id` = 2362540), list(`_classname` = "resource", `_id` = 2362539)), modified = "2023-09-29 12:43:27", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363187, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 12:43:29", createdby = "tobiasko", deletable = "true", filechecksum = "cc26781a80b138215b89a2a067d5e4d7", junk = "false", modified = "2023-09-29 12:43:29", modifiedby = "tobiasko", name = "WU294123-20230929-1243-rawDiag.pdf", relativepath = "container_32998/workunit_294123/WU294123-20230929-1243-rawDiag.pdf", size = "6246", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294123/WU294123-20230929-1243-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294123/WU294123-20230929-1243-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294123))) The current plot is available as workunit 294123 #rows are 21339 output$download 1... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 18225 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a8223318e3.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a8223318e3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294125, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:32", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:02:32", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363191, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:34", createdby = "tobiasko", deletable = "true", filechecksum = "79566e8fd67899b7710e5f0d123289d5", junk = "false", modified = "2023-09-29 13:02:34", modifiedby = "tobiasko", name = "WU294125-20230929-1302-rawDiag.pdf", relativepath = "container_32998/workunit_294125/WU294125-20230929-1302-rawDiag.pdf", size = "62832", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294125/WU294125-20230929-1302-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294125/WU294125-20230929-1302-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294125))) The current plot is available as workunit 294125 #rows are 18225 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a87b17b6a3.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a87b17b6a3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294126, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:45", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:02:45", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363192, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:46", createdby = "tobiasko", deletable = "true", filechecksum = "709a7f55c28564aa52cf07584a4d2bfe", junk = "false", modified = "2023-09-29 13:02:46", modifiedby = "tobiasko", name = "WU294126-20230929-1302-rawDiag.pdf", relativepath = "container_32998/workunit_294126/WU294126-20230929-1302-rawDiag.pdf", size = "29538", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294126/WU294126-20230929-1302-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294126/WU294126-20230929-1302-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294126))) The current plot is available as workunit 294126 #rows are 18225 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a84033fef1.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a84033fef1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294127, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:54", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:02:54", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363193, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:02:55", createdby = "tobiasko", deletable = "true", filechecksum = "264e63dd655e526c5988924e43d1594c", junk = "false", modified = "2023-09-29 13:02:55", modifiedby = "tobiasko", name = "WU294127-20230929-1302-rawDiag.pdf", relativepath = "container_32998/workunit_294127/WU294127-20230929-1302-rawDiag.pdf", size = "18455", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294127/WU294127-20230929-1302-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294127/WU294127-20230929-1302-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294127))) The current plot is available as workunit 294127 #rows are 18225 output$download 1... #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a81855b45a.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a81855b45a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294128, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:03:08", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:03:08", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363194, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:03:09", createdby = "tobiasko", deletable = "true", filechecksum = "459759778adc571134bdffcb3f8de893", junk = "false", modified = "2023-09-29 13:03:09", modifiedby = "tobiasko", name = "WU294128-20230929-1303-rawDiag.pdf", relativepath = "container_32998/workunit_294128/WU294128-20230929-1303-rawDiag.pdf", size = "28212", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294128/WU294128-20230929-1303-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294128/WU294128-20230929-1303-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294128))) The current plot is available as workunit 294128 #rows are 18225 output$download 1... #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a86755437c.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a86755437c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294129, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:03:30", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:03:30", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363195, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:03:32", createdby = "tobiasko", deletable = "true", filechecksum = "45dc35d2bcda91c00bd85c132451fa33", junk = "false", modified = "2023-09-29 13:03:32", modifiedby = "tobiasko", name = "WU294129-20230929-1303-rawDiag.pdf", relativepath = "container_32998/workunit_294129/WU294129-20230929-1303-rawDiag.pdf", size = "72314", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294129/WU294129-20230929-1303-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294129/WU294129-20230929-1303-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294129))) The current plot is available as workunit 294129 #rows are 18225 output$download 1... #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a8552c799d.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a8552c799d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294130, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:04:04", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:04:04", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363196, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:04:05", createdby = "tobiasko", deletable = "true", filechecksum = "161f7db6e2f2df7344734c9e8200ff0b", junk = "false", modified = "2023-09-29 13:04:05", modifiedby = "tobiasko", name = "WU294130-20230929-1304-rawDiag.pdf", relativepath = "container_32998/workunit_294130/WU294130-20230929-1304-rawDiag.pdf", size = "39218", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294130/WU294130-20230929-1304-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294130/WU294130-20230929-1304-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294130))) The current plot is available as workunit 294130 #rows are 18225 output$download 1... #rows are 18225 output$download 2... ggsave to file /tmp/RtmpQP2Bv0/rawDiag-1874a87c76141b.pdf generated pdf /tmp/RtmpQP2Bv0/rawDiag-1874a87c76141b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294131, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:04:19", createdby = "tobiasko", deletable = "true", description = "input files:\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_017_HeLaProteinDigest_2ug_PepMapDMSO.raw\np32998/Proteomics/LUMOS_1/tobiasko_20230926/20230926_014_HeLaProteinDigest_2ug_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` = 2362546), list(`_classname` = "resource", `_id` = 2362545)), modified = "2023-09-29 13:04:19", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2363197, container = list(`_classname` = "order", `_id` = 32998), created = "2023-09-29 13:04:20", createdby = "tobiasko", deletable = "true", filechecksum = "9d4ce3c2968c916e74e22a67c10b25e6", junk = "false", modified = "2023-09-29 13:04:20", modifiedby = "tobiasko", name = "WU294131-20230929-1304-rawDiag.pdf", relativepath = "container_32998/workunit_294131/WU294131-20230929-1304-rawDiag.pdf", size = "5654", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32998/workunit_294131/WU294131-20230929-1304-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32998/workunit_294131/WU294131-20230929-1304-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294131))) The current plot is available as workunit 294131 #rows are 18225 output$download 1... #rows are 18225 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 18225 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 18225 output$download 2... Execution halted