Listening on http://127.0.0.1:42859 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_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 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 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 250136 output$tic.basepeak <- renderPlot({ #rows are 250136 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e5063a956.pdf generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e5063a956.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294685, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:33:34", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:33:34", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369385, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:33:36", createdby = "tobiasko", deletable = "true", filechecksum = "0ce804d42c6b5348670288e7b10386ac", junk = "false", modified = "2023-10-13 10:33:36", modifiedby = "tobiasko", name = "WU294685-20231013-1033-rawDiag.pdf", relativepath = "container_33103/workunit_294685/WU294685-20231013-1033-rawDiag.pdf", size = "319306", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294685/WU294685-20231013-1033-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294685/WU294685-20231013-1033-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294685))) The current plot is available as workunit 294685 #rows are 250136 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 250136 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e753e54da.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e753e54da.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294686, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:33:55", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:33:55", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369386, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:33:56", createdby = "tobiasko", deletable = "true", filechecksum = "e9adfb0d3b672e1cdd7cb47435fd3185", junk = "false", modified = "2023-10-13 10:33:56", modifiedby = "tobiasko", name = "WU294686-20231013-1033-rawDiag.pdf", relativepath = "container_33103/workunit_294686/WU294686-20231013-1033-rawDiag.pdf", size = "271231", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294686/WU294686-20231013-1033-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294686/WU294686-20231013-1033-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294686))) The current plot is available as workunit 294686 #rows are 250136 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 250136 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e3bca0cd7.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e3bca0cd7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294687, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:34:28", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:34:28", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369387, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:34:29", createdby = "tobiasko", deletable = "true", filechecksum = "81d460a6d5eab8cd877feab09a95fe66", junk = "false", modified = "2023-10-13 10:34:29", modifiedby = "tobiasko", name = "WU294687-20231013-1034-rawDiag.pdf", relativepath = "container_33103/workunit_294687/WU294687-20231013-1034-rawDiag.pdf", size = "769824", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294687/WU294687-20231013-1034-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294687/WU294687-20231013-1034-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294687))) The current plot is available as workunit 294687 #rows are 250136 output$download 1... Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). #rows are 250136 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e9b6274.pdf Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e9b6274.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294688, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:34:46", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:34:46", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369388, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:34:47", createdby = "tobiasko", deletable = "true", filechecksum = "12ee5c34ad1fcd7b4086f4ce4b6e7904", junk = "false", modified = "2023-10-13 10:34:47", modifiedby = "tobiasko", name = "WU294688-20231013-1034-rawDiag.pdf", relativepath = "container_33103/workunit_294688/WU294688-20231013-1034-rawDiag.pdf", size = "183125", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294688/WU294688-20231013-1034-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294688/WU294688-20231013-1034-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294688))) The current plot is available as workunit 294688 #rows are 250136 output$download 1... #rows are 250136 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e57f95967.pdf generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e57f95967.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294689, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:35:30", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:35:30", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369389, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:35:32", createdby = "tobiasko", deletable = "true", filechecksum = "f47fcb699ec83ae137c2a5ec73287140", junk = "false", modified = "2023-10-13 10:35:32", modifiedby = "tobiasko", name = "WU294689-20231013-1035-rawDiag.pdf", relativepath = "container_33103/workunit_294689/WU294689-20231013-1035-rawDiag.pdf", size = "1142560", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294689/WU294689-20231013-1035-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294689/WU294689-20231013-1035-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294689))) The current plot is available as workunit 294689 #rows are 250136 output$download 1... #rows are 250136 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e52c44d8c.pdf generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e52c44d8c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294690, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:35:45", createdby = "tobiasko", deletable = "true", description = "input files:\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_003_S574376_SWN-GFP_replica_1_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_002_S574375_CLF-GFP_replica_3_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_006_S574377_SWN-GFP_replica_2_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_010_S574370_WT_replica_1_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_007_S574378_SWN-GFP_replica_3_Group_3.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_004_S574373_CLF-GFP_replica_1_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_012_S574374_CLF-GFP_replica_2_Group_2.raw\np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_011_S574372_WT_replica_3_Group_1.raw \np33103/Proteomics/EXPLORIS_2/analytic_20231012/20231012_C33103_008_S574371_WT_replica_2_Group_1.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` = 2369384), list(`_classname` = "resource", `_id` = 2369383), list(`_classname` = "resource", `_id` = 2369382), list(`_classname` = "resource", `_id` = 2369381), list(`_classname` = "resource", `_id` = 2369380), list(`_classname` = "resource", `_id` = 2369379), list(`_classname` = "resource", `_id` = 2369378), list(`_classname` = "resource", `_id` = 2369377), list(`_classname` = "resource", `_id` = 2369376)), modified = "2023-10-13 10:35:45", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369390, container = list(`_classname` = "order", `_id` = 33103), created = "2023-10-13 10:35:46", createdby = "tobiasko", deletable = "true", filechecksum = "c7775eab941a8d44f97595980df7ecf6", junk = "false", modified = "2023-10-13 10:35:46", modifiedby = "tobiasko", name = "WU294690-20231013-1035-rawDiag.pdf", relativepath = "container_33103/workunit_294690/WU294690-20231013-1035-rawDiag.pdf", size = "9795", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33103/workunit_294690/WU294690-20231013-1035-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33103/workunit_294690/WU294690-20231013-1035-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294690))) The current plot is available as workunit 294690 #rows are 250136 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 250136 output$download 2... DEBUG renderPlot plotQCs #rows are 250136 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE '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//p33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_002_S574507_B1-HT-HA-VP2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_008_S574510_B4-HT-HA-VP2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_004_S574508_B2-HT-HA-VP2_Recombinant_protein.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_006_S574509_B3-HT-HA-VP2_Recombinant_protein.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 67365 output$tic.basepeak <- renderPlot({ #rows are 67365 output$download 2... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 67365 output$download 2... ggsave to file /tmp/Rtmp1smZNl/rawDiag-11c88e301ffb8d.pdf generated pdf /tmp/Rtmp1smZNl/rawDiag-11c88e301ffb8d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294715, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33109), created = "2023-10-13 15:23:37", createdby = "spfammatter", deletable = "true", description = "input files:\np33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_002_S574507_B1-HT-HA-VP2_Recombinant_protein.raw\np33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_004_S574508_B2-HT-HA-VP2_Recombinant_protein.raw\np33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_006_S574509_B3-HT-HA-VP2_Recombinant_protein.raw\np33109/Proteomics/QEXACTIVE_1/analytic_20231011/20231011_C33109_008_S574510_B4-HT-HA-VP2_Recombinant_protein.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", modified = "2023-10-13 15:23:37", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2369452, container = list(`_classname` = "order", `_id` = 33109), created = "2023-10-13 15:23:39", createdby = "spfammatter", deletable = "true", filechecksum = "03bdf4569d3aa7b45137a369647f644c", junk = "false", modified = "2023-10-13 15:23:39", modifiedby = "spfammatter", name = "WU294715-20231013-1523-rawDiag.pdf", relativepath = "container_33109/workunit_294715/WU294715-20231013-1523-rawDiag.pdf", size = "239117", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33109/workunit_294715/WU294715-20231013-1523-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33109/workunit_294715/WU294715-20231013-1523-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294715))) The current plot is available as workunit 294715 #rows are 67365 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 67365 output$download 2... #rows are 67365 output$download 2... #rows are 67365 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 67365 output$download 2... DEBUG renderPlot plotQCs #rows are 250136 output$download 2... Execution halted