Listening on http://127.0.0.1:37441 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({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.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 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 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 331970 output$tic.basepeak <- renderPlot({ #rows are 331970 output$download 2... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7f41e21b5d.pdf generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7f41e21b5d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296766, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:04:15", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:04:15", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402410, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:04:16", createdby = "tobiasko", filechecksum = "0454639af574d41776f6b60e4d91f381", junk = "false", modified = "2023-11-28 18:04:16", modifiedby = "tobiasko", name = "WU296766-20231128-1804-rawDiag.pdf", relativepath = "container_33274/workunit_296766/WU296766-20231128-1804-rawDiag.pdf", size = "279145", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296766/WU296766-20231128-1804-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296766/WU296766-20231128-1804-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296766))) The current plot is available as workunit 296766 #rows are 331970 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 331970 output$download 2... ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7f5d58931.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7f5d58931.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296767, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:04:41", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:04:41", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402411, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:04:43", createdby = "tobiasko", filechecksum = "dfc90b755654acc17b70a007575027d4", junk = "false", modified = "2023-11-28 18:04:43", modifiedby = "tobiasko", name = "WU296767-20231128-1804-rawDiag.pdf", relativepath = "container_33274/workunit_296767/WU296767-20231128-1804-rawDiag.pdf", size = "363203", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296767/WU296767-20231128-1804-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296767/WU296767-20231128-1804-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296767))) The current plot is available as workunit 296767 #rows are 331970 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 331970 output$download 2... ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7f46f7654c.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7f46f7654c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296768, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:05:12", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:05:12", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402412, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:05:13", createdby = "tobiasko", filechecksum = "41643d9066367bb724e2bce36bc3d89b", junk = "false", modified = "2023-11-28 18:05:13", modifiedby = "tobiasko", name = "WU296768-20231128-1805-rawDiag.pdf", relativepath = "container_33274/workunit_296768/WU296768-20231128-1805-rawDiag.pdf", size = "883950", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296768/WU296768-20231128-1805-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296768/WU296768-20231128-1805-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296768))) The current plot is available as workunit 296768 #rows are 331970 output$download 1... #rows are 331970 output$download 2... Warning: Removed 27534 rows containing non-finite values (`stat_smooth()`). Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Removed 3692 rows containing missing values (`geom_line()`). #rows are 331970 output$download 2... ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7f575bda43.pdf Warning: Removed 27534 rows containing non-finite values (`stat_smooth()`). Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Removed 3692 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7f575bda43.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296769, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:05:26", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:05:26", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402413, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:05:28", createdby = "tobiasko", filechecksum = "a23171b92eabbfdb07451fc1ba7234a8", junk = "false", modified = "2023-11-28 18:05:28", modifiedby = "tobiasko", name = "WU296769-20231128-1805-rawDiag.pdf", relativepath = "container_33274/workunit_296769/WU296769-20231128-1805-rawDiag.pdf", size = "11880", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296769/WU296769-20231128-1805-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296769/WU296769-20231128-1805-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296769))) The current plot is available as workunit 296769 #rows are 331970 output$download 1... #rows are 331970 output$download 2... ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7f738c34ab.pdf generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7f738c34ab.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296770, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:06:04", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:06:04", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402414, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:06:06", createdby = "tobiasko", filechecksum = "a5b3eb50dd68ae65f4ee6397dcd13670", junk = "false", modified = "2023-11-28 18:06:06", modifiedby = "tobiasko", name = "WU296770-20231128-1806-rawDiag.pdf", relativepath = "container_33274/workunit_296770/WU296770-20231128-1806-rawDiag.pdf", size = "1226068", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296770/WU296770-20231128-1806-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296770/WU296770-20231128-1806-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296770))) The current plot is available as workunit 296770 #rows are 331970 output$download 1... #rows are 331970 output$download 2... ggsave to file /tmp/RtmpGNbl6j/rawDiag-388f7ffbbf55f.pdf generated pdf /tmp/RtmpGNbl6j/rawDiag-388f7ffbbf55f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296771, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:06:15", createdby = "tobiasko", description = "input files:\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_008_S583631_L_GFP_2_Control.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_010_S583628_L_TDPmNLS_1_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_004_S583637_TDPwt_2_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_007_S583636_TDPwt_1_basal.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_013_S583629_L_TDPmNLS_2_mNLS_L.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_015_S583626_L_TDPwt_1_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_003_S583633_S_TDPwt_2_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_009_S583627_L_TDPwt_2_WT_L.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_005_S583632_S_TDPwt_1_WT_S.raw \np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_002_S583634_S_TDPmNLS_1_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_012_S583635_S_TDPmNLS_2_mNLS_S.raw\np33274/Proteomics/EXPLORIS_2/analytic_20231123/20231123_C33274_014_S583630_L_GFP_1_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2402409), list(`_classname` = "resource", `_id` = 2402408), list(`_classname` = "resource", `_id` = 2402407), list(`_classname` = "resource", `_id` = 2402406), list(`_classname` = "resource", `_id` = 2402405), list(`_classname` = "resource", `_id` = 2402404), list(`_classname` = "resource", `_id` = 2402403), list(`_classname` = "resource", `_id` = 2402402), list(`_classname` = "resource", `_id` = 2402401), list( `_classname` = "resource", `_id` = 2402400), list(`_classname` = "resource", `_id` = 2402399), list(`_classname` = "resource", `_id` = 2402398)), modified = "2023-11-28 18:06:15", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402415, container = list(`_classname` = "order", `_id` = 33274), created = "2023-11-28 18:06:16", createdby = "tobiasko", filechecksum = "e4e3d2e98f74a9f856958dd105385e77", junk = "false", modified = "2023-11-28 18:06:16", modifiedby = "tobiasko", name = "WU296771-20231128-1806-rawDiag.pdf", relativepath = "container_33274/workunit_296771/WU296771-20231128-1806-rawDiag.pdf", size = "13029", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33274/workunit_296771/WU296771-20231128-1806-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33274/workunit_296771/WU296771-20231128-1806-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296771))) The current plot is available as workunit 296771 #rows are 331970 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 331970 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 331970 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 331970 output$download 2... Execution halted