Listening on http://127.0.0.1:34259 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 #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//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 1091106 output$tic.basepeak <- renderPlot({ #rows are 1091106 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e2d210666.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e2d210666.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297882, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:30:17", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:30:17", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415328, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:30:19", createdby = "tobiasko", filechecksum = "eccb152ce107fe94e5c31cb2eb4eb9f5", junk = "false", modified = "2023-12-18 09:30:19", modifiedby = "tobiasko", name = "WU297882-20231218-0930-rawDiag.pdf", relativepath = "container_33709/workunit_297882/WU297882-20231218-0930-rawDiag.pdf", size = "194507", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297882/WU297882-20231218-0930-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297882/WU297882-20231218-0930-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297882))) The current plot is available as workunit 297882 #rows are 1091106 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 1091106 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e38177642.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e38177642.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297883, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:30:43", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:30:43", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415329, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:30:45", createdby = "tobiasko", filechecksum = "43daa3d27e69ab9c6b3d82019556e2c2", junk = "false", modified = "2023-12-18 09:30:45", modifiedby = "tobiasko", name = "WU297883-20231218-0930-rawDiag.pdf", relativepath = "container_33709/workunit_297883/WU297883-20231218-0930-rawDiag.pdf", size = "309420", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297883/WU297883-20231218-0930-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297883/WU297883-20231218-0930-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297883))) The current plot is available as workunit 297883 #rows are 1091106 output$download 1... #rows are 1091106 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31ef2fa94e.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31ef2fa94e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297884, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:31:10", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:31:10", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415330, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:31:11", createdby = "tobiasko", filechecksum = "767bd7338097731e779ede572d70c464", junk = "false", modified = "2023-12-18 09:31:11", modifiedby = "tobiasko", name = "WU297884-20231218-0931-rawDiag.pdf", relativepath = "container_33709/workunit_297884/WU297884-20231218-0931-rawDiag.pdf", size = "95417", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297884/WU297884-20231218-0931-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297884/WU297884-20231218-0931-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297884))) The current plot is available as workunit 297884 #rows are 1091106 output$download 1... #rows are 1091106 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e2c7b2438.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e2c7b2438.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297885, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:32:25", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:32:25", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415331, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:32:27", createdby = "tobiasko", filechecksum = "470553a747bb3bfc3db1d721ee4f0fd0", junk = "false", modified = "2023-12-18 09:32:27", modifiedby = "tobiasko", name = "WU297885-20231218-0932-rawDiag.pdf", relativepath = "container_33709/workunit_297885/WU297885-20231218-0932-rawDiag.pdf", size = "1960838", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297885/WU297885-20231218-0932-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297885/WU297885-20231218-0932-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297885))) The current plot is available as workunit 297885 #rows are 1091106 output$download 1... #rows are 1091106 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31ebf456ec.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31ebf456ec.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297886, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:32:47", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:32:47", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415333, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:32:50", createdby = "tobiasko", filechecksum = "31698b5f5fc2e2117da7dad5f0bfed1e", junk = "false", modified = "2023-12-18 09:32:50", modifiedby = "tobiasko", name = "WU297886-20231218-0932-rawDiag.pdf", relativepath = "container_33709/workunit_297886/WU297886-20231218-0932-rawDiag.pdf", size = "127959", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297886/WU297886-20231218-0932-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297886/WU297886-20231218-0932-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297886))) The current plot is available as workunit 297886 #rows are 1091106 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 1091106 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31edabf2a3.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31edabf2a3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297887, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:33:15", createdby = "tobiasko", description = "input files:\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_004_S607633_SMB451-3-3_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_007_S607610_SMB451-2-3_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_014_S607635_SMB451-4-2_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_002_S607608_SMB451-2-1_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_015_S607607_SMB451-1-3_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_003_S607632_SMB451-3-2_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_011_S607609_SMB451-2-2_Group_1.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_006_S607631_SMB451-3-1_Group_2.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_013_S607606_SMB451-1-2_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_012_S607586_SMB451-1-1_Control.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_010_S607636_SMB451-4-3_Group_3.raw\np33709/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33709_005_S607634_SMB451-4-1_Group_3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415309), list(`_classname` = "resource", `_id` = 2415308), list(`_classname` = "resource", `_id` = 2415307), list(`_classname` = "resource", `_id` = 2415306), list(`_classname` = "resource", `_id` = 2415305), list(`_classname` = "resource", `_id` = 2415304), list(`_classname` = "resource", `_id` = 2415303), list(`_classname` = "resource", `_id` = 2415302), list(`_classname` = "resource", `_id` = 2415301), list( `_classname` = "resource", `_id` = 2415300), list(`_classname` = "resource", `_id` = 2415299), list(`_classname` = "resource", `_id` = 2415298)), modified = "2023-12-18 09:33:15", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415336, container = list(`_classname` = "order", `_id` = 33709), created = "2023-12-18 09:33:16", createdby = "tobiasko", filechecksum = "1f0d16ca9067981a906226ae9649310c", junk = "false", modified = "2023-12-18 09:33:16", modifiedby = "tobiasko", name = "WU297887-20231218-0933-rawDiag.pdf", relativepath = "container_33709/workunit_297887/WU297887-20231218-0933-rawDiag.pdf", size = "50084", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33709/workunit_297887/WU297887-20231218-0933-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33709/workunit_297887/WU297887-20231218-0933-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297887))) The current plot is available as workunit 297887 #rows are 1091106 output$download 1... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#840] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp #rows are 1091106 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#840] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 1093414 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 1093414 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e3323b0aa.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e3323b0aa.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297890, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:49:01", createdby = "tobiasko", description = "input files:\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415325), list(`_classname` = "resource", `_id` = 2415324), list(`_classname` = "resource", `_id` = 2415323), list(`_classname` = "resource", `_id` = 2415322), list(`_classname` = "resource", `_id` = 2415321), list(`_classname` = "resource", `_id` = 2415320), list(`_classname` = "resource", `_id` = 2415319), list(`_classname` = "resource", `_id` = 2415318), list(`_classname` = "resource", `_id` = 2415317), list( `_classname` = "resource", `_id` = 2415316), list(`_classname` = "resource", `_id` = 2415315), list(`_classname` = "resource", `_id` = 2415314)), modified = "2023-12-18 09:49:01", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415362, container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:49:02", createdby = "tobiasko", filechecksum = "b2036b811a19e612e5852f53d12aaf9a", junk = "false", modified = "2023-12-18 09:49:02", modifiedby = "tobiasko", name = "WU297890-20231218-0949-rawDiag.pdf", relativepath = "container_33727/workunit_297890/WU297890-20231218-0949-rawDiag.pdf", size = "199049", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33727/workunit_297890/WU297890-20231218-0949-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33727/workunit_297890/WU297890-20231218-0949-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297890))) The current plot is available as workunit 297890 #rows are 1093414 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 1093414 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e30fe8146.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e30fe8146.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297891, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:49:30", createdby = "tobiasko", description = "input files:\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415325), list(`_classname` = "resource", `_id` = 2415324), list(`_classname` = "resource", `_id` = 2415323), list(`_classname` = "resource", `_id` = 2415322), list(`_classname` = "resource", `_id` = 2415321), list(`_classname` = "resource", `_id` = 2415320), list(`_classname` = "resource", `_id` = 2415319), list(`_classname` = "resource", `_id` = 2415318), list(`_classname` = "resource", `_id` = 2415317), list( `_classname` = "resource", `_id` = 2415316), list(`_classname` = "resource", `_id` = 2415315), list(`_classname` = "resource", `_id` = 2415314)), modified = "2023-12-18 09:49:30", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415366, container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:49:32", createdby = "tobiasko", filechecksum = "98c0aaebb34016f3809363eed0ff6c84", junk = "false", modified = "2023-12-18 09:49:32", modifiedby = "tobiasko", name = "WU297891-20231218-0949-rawDiag.pdf", relativepath = "container_33727/workunit_297891/WU297891-20231218-0949-rawDiag.pdf", size = "306217", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33727/workunit_297891/WU297891-20231218-0949-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33727/workunit_297891/WU297891-20231218-0949-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297891))) The current plot is available as workunit 297891 #rows are 1093414 output$download 1... #rows are 1093414 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e1ea1e3d6.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e1ea1e3d6.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297892, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:50:06", createdby = "tobiasko", description = "input files:\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415325), list(`_classname` = "resource", `_id` = 2415324), list(`_classname` = "resource", `_id` = 2415323), list(`_classname` = "resource", `_id` = 2415322), list(`_classname` = "resource", `_id` = 2415321), list(`_classname` = "resource", `_id` = 2415320), list(`_classname` = "resource", `_id` = 2415319), list(`_classname` = "resource", `_id` = 2415318), list(`_classname` = "resource", `_id` = 2415317), list( `_classname` = "resource", `_id` = 2415316), list(`_classname` = "resource", `_id` = 2415315), list(`_classname` = "resource", `_id` = 2415314)), modified = "2023-12-18 09:50:06", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415367, container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:50:08", createdby = "tobiasko", filechecksum = "d77481ebe7ed4c457338e6b692f79b58", junk = "false", modified = "2023-12-18 09:50:08", modifiedby = "tobiasko", name = "WU297892-20231218-0950-rawDiag.pdf", relativepath = "container_33727/workunit_297892/WU297892-20231218-0950-rawDiag.pdf", size = "91309", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33727/workunit_297892/WU297892-20231218-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33727/workunit_297892/WU297892-20231218-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297892))) The current plot is available as workunit 297892 #rows are 1093414 output$download 1... #rows are 1093414 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e2062fe70.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e2062fe70.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297893, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:52:08", createdby = "tobiasko", description = "input files:\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415325), list(`_classname` = "resource", `_id` = 2415324), list(`_classname` = "resource", `_id` = 2415323), list(`_classname` = "resource", `_id` = 2415322), list(`_classname` = "resource", `_id` = 2415321), list(`_classname` = "resource", `_id` = 2415320), list(`_classname` = "resource", `_id` = 2415319), list(`_classname` = "resource", `_id` = 2415318), list(`_classname` = "resource", `_id` = 2415317), list( `_classname` = "resource", `_id` = 2415316), list(`_classname` = "resource", `_id` = 2415315), list(`_classname` = "resource", `_id` = 2415314)), modified = "2023-12-18 09:52:08", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415368, container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:52:09", createdby = "tobiasko", filechecksum = "ef8475b47c94441fb565aedbeb44edae", junk = "false", modified = "2023-12-18 09:52:09", modifiedby = "tobiasko", name = "WU297893-20231218-0952-rawDiag.pdf", relativepath = "container_33727/workunit_297893/WU297893-20231218-0952-rawDiag.pdf", size = "1989796", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33727/workunit_297893/WU297893-20231218-0952-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33727/workunit_297893/WU297893-20231218-0952-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297893))) The current plot is available as workunit 297893 #rows are 1093414 output$download 1... #rows are 1093414 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 1093414 output$download 2... ggsave to file /tmp/RtmpcmZbAQ/rawDiag-38b31e7066114d.pdf generated pdf /tmp/RtmpcmZbAQ/rawDiag-38b31e7066114d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297894, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:53:08", createdby = "tobiasko", description = "input files:\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_010_S608365_KO-SRB705-3_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_016_S608362_WT-SRB705-3_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_014_S608359_KO-DMSO-3_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_004_S608355_WT-DMSO-2_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_002_S608360_WT-SRB705-1_Group_3_rep.raw\np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_003_S608364_KO-SRB705-2_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_011_S608363_KO-SRB705-1_Group_4.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_017_S608361_WT-SRB705-2_Group_3.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_015_S608357_KO-DMSO-1_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_008_S608354_WT-DMSO-1_Group_1.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_009_S608358_KO-DMSO-2_Group_2.raw \np33727/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33727_005_S608356_WT-DMSO-3_Group_1.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2415325), list(`_classname` = "resource", `_id` = 2415324), list(`_classname` = "resource", `_id` = 2415323), list(`_classname` = "resource", `_id` = 2415322), list(`_classname` = "resource", `_id` = 2415321), list(`_classname` = "resource", `_id` = 2415320), list(`_classname` = "resource", `_id` = 2415319), list(`_classname` = "resource", `_id` = 2415318), list(`_classname` = "resource", `_id` = 2415317), list( `_classname` = "resource", `_id` = 2415316), list(`_classname` = "resource", `_id` = 2415315), list(`_classname` = "resource", `_id` = 2415314)), modified = "2023-12-18 09:53:08", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2415369, container = list(`_classname` = "order", `_id` = 33727), created = "2023-12-18 09:53:09", createdby = "tobiasko", filechecksum = "9d809df3aa847f30afebf2df74959289", junk = "false", modified = "2023-12-18 09:53:09", modifiedby = "tobiasko", name = "WU297894-20231218-0953-rawDiag.pdf", relativepath = "container_33727/workunit_297894/WU297894-20231218-0953-rawDiag.pdf", size = "60367", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33727/workunit_297894/WU297894-20231218-0953-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33727/workunit_297894/WU297894-20231218-0953-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297894))) The current plot is available as workunit 297894 #rows are 1093414 output$download 1... DEBUG renderPlot plotQCs #rows are 1093414 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 1093414 output$download 2... output$tic.basepeak <- renderPlot({ executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_003_S609866_SPEN_4_ctrl_LZ_Group_2_rep.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33751/Proteomics/EXPLORIS_2/analytic_20231215/20231215_C33751_002_S609865_SPEN_4_LZ_Group_1_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