Listening on http://127.0.0.1:43671 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 /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 #rows are 0 /scratch/cpanse/ Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:04065072:rsa routines:rsa_ossl_private_decrypt:padding check failed') Passing through unaltered. 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$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$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$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in value[[3L]](cond) : Error decrypting field. (#999, 'error:0407109F:rsa routines:RSA_padding_check_PKCS1_type_2:pkcs decoding error') Passing through unaltered. Warning in shinyStore::updateStore(session, "login", isolate(input$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$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33176/Proteomics/FUSION_2/chiawei_20231023/20231023_006_S579981_IFmix_200ng_DIA_all.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33176/Proteomics/FUSION_2/chiawei_20231023/20231023_006_S579981_IFmix_200ng_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33176/Proteomics/FUSION_2/chiawei_20231023/20231023_006_S579981_IFmix_200ng_DIA_50ms.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 144395 output$tic.basepeak <- renderPlot({ #rows are 144395 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. #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... 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: `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 144395 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. Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp #rows are 144395 output$download 2... #rows are 144395 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 144395 output$download 2... #rows are 144395 output$download 2... #rows are 144395 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 144395 output$download 2... #rows are 144395 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 87 rows containing missing values (`geom_line()`). #rows are 144395 output$download 2... #rows are 144395 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33176/Proteomics/FUSION_2/chiawei_20231027/20231027_003_S583624_IFmix_200ng_Hela_60ngDIA_dynamic.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33176/Proteomics/FUSION_2/chiawei_20231027/20231027_003_S583624_IFmix_200ng_Hela_60ngDIA.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 142195 output$download 2... #rows are 142195 output$download 2... #rows are 0 saving 'login and webservicepassword' ... output$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. 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//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_Control.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 #rows are 190906 output$tic.basepeak <- renderPlot({ #rows are 190906 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0446a73fcbe.pdf generated pdf /tmp/RtmpAZur2o/rawDiag-24a0446a73fcbe.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295506, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:28", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:56:28", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382008, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:29", createdby = "tobiasko", filechecksum = "c13fefc239342657598fe811206d2ea2", junk = "false", modified = "2023-10-31 10:56:29", modifiedby = "tobiasko", name = "WU295506-20231031-1056-rawDiag.pdf", relativepath = "container_33122/workunit_295506/WU295506-20231031-1056-rawDiag.pdf", size = "147206", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295506/WU295506-20231031-1056-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295506/WU295506-20231031-1056-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295506))) The current plot is available as workunit 295506 #rows are 190906 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a044612445ba.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpAZur2o/rawDiag-24a044612445ba.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295507, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:42", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:56:42", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382009, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:43", createdby = "tobiasko", filechecksum = "d8833d1173e871453a0893b383722358", junk = "false", modified = "2023-10-31 10:56:43", modifiedby = "tobiasko", name = "WU295507-20231031-1056-rawDiag.pdf", relativepath = "container_33122/workunit_295507/WU295507-20231031-1056-rawDiag.pdf", size = "182224", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295507/WU295507-20231031-1056-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295507/WU295507-20231031-1056-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295507))) The current plot is available as workunit 295507 #rows are 190906 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0445e5f2c89.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpAZur2o/rawDiag-24a0445e5f2c89.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295508, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:57", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:56:57", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382010, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:56:58", createdby = "tobiasko", filechecksum = "098f654a1eb28247fac661b3f5a4ebe7", junk = "false", modified = "2023-10-31 10:56:58", modifiedby = "tobiasko", name = "WU295508-20231031-1056-rawDiag.pdf", relativepath = "container_33122/workunit_295508/WU295508-20231031-1056-rawDiag.pdf", size = "319278", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295508/WU295508-20231031-1056-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295508/WU295508-20231031-1056-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295508))) The current plot is available as workunit 295508 #rows are 190906 output$download 1... Warning: Removed 206 rows containing non-finite values (`stat_smooth()`). #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0441e91d79e.pdf Warning: Removed 206 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpAZur2o/rawDiag-24a0441e91d79e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295509, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:05", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:57:05", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382011, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:06", createdby = "tobiasko", filechecksum = "30a23325edb8788f37eed17ad1690a10", junk = "false", modified = "2023-10-31 10:57:06", modifiedby = "tobiasko", name = "WU295509-20231031-1057-rawDiag.pdf", relativepath = "container_33122/workunit_295509/WU295509-20231031-1057-rawDiag.pdf", size = "86129", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295509/WU295509-20231031-1057-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295509/WU295509-20231031-1057-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295509))) The current plot is available as workunit 295509 #rows are 190906 output$download 1... #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a044439e0e6c.pdf generated pdf /tmp/RtmpAZur2o/rawDiag-24a044439e0e6c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295510, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:38", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:57:38", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382012, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:39", createdby = "tobiasko", filechecksum = "213f9aa418c7ad3433803528c2c86832", junk = "false", modified = "2023-10-31 10:57:39", modifiedby = "tobiasko", name = "WU295510-20231031-1057-rawDiag.pdf", relativepath = "container_33122/workunit_295510/WU295510-20231031-1057-rawDiag.pdf", size = "937249", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295510/WU295510-20231031-1057-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295510/WU295510-20231031-1057-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295510))) The current plot is available as workunit 295510 #rows are 190906 output$download 1... #rows are 190906 output$download 2... #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0444fd77e00.pdf generated pdf /tmp/RtmpAZur2o/rawDiag-24a0444fd77e00.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295511, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:51", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:57:51", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382013, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:57:52", createdby = "tobiasko", filechecksum = "db932533e1a3b631f8f03bfca72f3d3d", junk = "false", modified = "2023-10-31 10:57:52", modifiedby = "tobiasko", name = "WU295511-20231031-1057-rawDiag.pdf", relativepath = "container_33122/workunit_295511/WU295511-20231031-1057-rawDiag.pdf", size = "8782", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295511/WU295511-20231031-1057-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295511/WU295511-20231031-1057-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295511))) The current plot is available as workunit 295511 #rows are 190906 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") #rows are 190906 output$download 2... ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0442d5ef252.pdf generated pdf /tmp/RtmpAZur2o/rawDiag-24a0442d5ef252.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 295512, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:58:10", createdby = "tobiasko", description = "input files:\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_008_S574902_WT-uv1_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_006_S574903_WT-uv2_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_007_S574901_WT3_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_002_S574904_WT-uv3_Sample.raw\np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_004_S574899_WT1_Control.raw \np33122/Proteomics/EXPLORIS_2/analytic_20231025/20231025_C33122_003_S574900_WT2_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` = 2379567), list(`_classname` = "resource", `_id` = 2379566), list(`_classname` = "resource", `_id` = 2379565), list(`_classname` = "resource", `_id` = 2379564), list(`_classname` = "resource", `_id` = 2379563), list(`_classname` = "resource", `_id` = 2379562)), modified = "2023-10-31 10:58:10", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2382014, container = list(`_classname` = "order", `_id` = 33122), created = "2023-10-31 10:58:11", createdby = "tobiasko", filechecksum = "0a4e83939ef8b165ee5dabc137de2d7d", junk = "false", modified = "2023-10-31 10:58:11", modifiedby = "tobiasko", name = "WU295512-20231031-1058-rawDiag.pdf", relativepath = "container_33122/workunit_295512/WU295512-20231031-1058-rawDiag.pdf", size = "37814", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33122/workunit_295512/WU295512-20231031-1058-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33122/workunit_295512/WU295512-20231031-1058-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 295512))) The current plot is available as workunit 295512 #rows are 190906 output$download 1... DEBUG renderPlot plotQCs #rows are 190906 output$download 1... saving 'login and webservicepassword' ... #rows are 142195 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 142195 output$download 2... #rows are 142195 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 58 rows containing missing values (`geom_line()`). #rows are 142195 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 142195 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 58 rows containing missing values (`geom_line()`). #rows are 142195 output$download 2... #rows are 142195 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 142195 output$download 2... #rows are 142195 output$download 2... Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) #rows are 142195 output$download 2... #rows are 142195 output$download 2... #rows are 142195 output$download 2... #rows are 142195 output$download 2... #rows are 142195 output$download 2... #rows are 142195 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 142195 output$download 2... DEBUG renderPlot plotQCs #rows are 142195 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp ggsave to file /tmp/RtmpAZur2o/rawDiag-24a0443584eb48.pdf Warning: Error in +: non-numeric argument to binary operator 1: runApp #rows are 0 /scratch/cpanse/ Execution halted