Listening on http://127.0.0.1:40053 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. 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//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.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 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 293226 output$tic.basepeak <- renderPlot({ #rows are 293226 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpkaeMho/rawDiag-117d997c655caa.pdf generated pdf /tmp/RtmpkaeMho/rawDiag-117d997c655caa.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296291, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:18:33", createdby = "tobiasko", description = "input files:\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw \np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.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` = 2396440), list(`_classname` = "resource", `_id` = 2396439), list(`_classname` = "resource", `_id` = 2396438), list(`_classname` = "resource", `_id` = 2396437)), modified = "2023-11-20 09:18:33", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2396490, container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:18:34", createdby = "tobiasko", filechecksum = "6bbd82bb84846809c0197cff2415f53a", junk = "false", modified = "2023-11-20 09:18:34", modifiedby = "tobiasko", name = "WU296291-20231120-0918-rawDiag.pdf", relativepath = "container_33212/workunit_296291/WU296291-20231120-0918-rawDiag.pdf", size = "57800", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33212/workunit_296291/WU296291-20231120-0918-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33212/workunit_296291/WU296291-20231120-0918-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296291))) The current plot is available as workunit 296291 #rows are 293226 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 293226 output$download 2... ggsave to file /tmp/RtmpkaeMho/rawDiag-117d994fc6faee.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpkaeMho/rawDiag-117d994fc6faee.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296292, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:19:30", createdby = "tobiasko", description = "input files:\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw \np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.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` = 2396440), list(`_classname` = "resource", `_id` = 2396439), list(`_classname` = "resource", `_id` = 2396438), list(`_classname` = "resource", `_id` = 2396437)), modified = "2023-11-20 09:19:30", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2396491, container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:19:32", createdby = "tobiasko", filechecksum = "b0818be4b6a5bb5df01679925d8a83fe", junk = "false", modified = "2023-11-20 09:19:32", modifiedby = "tobiasko", name = "WU296292-20231120-0919-rawDiag.pdf", relativepath = "container_33212/workunit_296292/WU296292-20231120-0919-rawDiag.pdf", size = "99752", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33212/workunit_296292/WU296292-20231120-0919-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33212/workunit_296292/WU296292-20231120-0919-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296292))) The current plot is available as workunit 296292 #rows are 293226 output$download 1... #rows are 293226 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf Warning: Error in combine_vars: Faceting variables must have at least one value 184: 183: signalCondition 182: signal_abort 181: rlang::abort 180: cli::cli_abort 179: combine_vars 178: compute_layout 177: self$facet$compute_layout 176: setup 175: layout$setup 174: ggplot_build.ggplot 172: print.ggplot 167: func 165: f 164: Reduce 155: do 154: hybrid_chain 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cycle.load 1: runApp #rows are 293226 output$download 2... #rows are 293226 output$download 2... ggsave to file /tmp/RtmpkaeMho/rawDiag-117d9935f0d743.pdf generated pdf /tmp/RtmpkaeMho/rawDiag-117d9935f0d743.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296293, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:20:33", createdby = "tobiasko", description = "input files:\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw \np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.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` = 2396440), list(`_classname` = "resource", `_id` = 2396439), list(`_classname` = "resource", `_id` = 2396438), list(`_classname` = "resource", `_id` = 2396437)), modified = "2023-11-20 09:20:33", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2396492, container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:20:34", createdby = "tobiasko", filechecksum = "214d38b1b1de827a1c6db9ca2e031789", junk = "false", modified = "2023-11-20 09:20:34", modifiedby = "tobiasko", name = "WU296293-20231120-0920-rawDiag.pdf", relativepath = "container_33212/workunit_296293/WU296293-20231120-0920-rawDiag.pdf", size = "30653", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33212/workunit_296293/WU296293-20231120-0920-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33212/workunit_296293/WU296293-20231120-0920-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296293))) The current plot is available as workunit 296293 #rows are 293226 output$download 1... #rows are 293226 output$download 2... #rows are 293226 output$download 2... #rows are 293226 output$download 2... ggsave to file /tmp/RtmpkaeMho/rawDiag-117d996aed6ec0.pdf generated pdf /tmp/RtmpkaeMho/rawDiag-117d996aed6ec0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296294, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:21:52", createdby = "tobiasko", description = "input files:\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_009_S580219_K562_incl_iRT_autoQC03dia.raw \np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_005_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_002_S580219_K562_incl_iRT_1_autoQC03dia.raw\np33212/Proteomics/LUMOS_1/roschi_20231117_K562_DIA_autoQC/20231117_007_S580219_K562_incl_iRT_2_autoQC03dia.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` = 2396440), list(`_classname` = "resource", `_id` = 2396439), list(`_classname` = "resource", `_id` = 2396438), list(`_classname` = "resource", `_id` = 2396437)), modified = "2023-11-20 09:21:52", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2396493, container = list(`_classname` = "order", `_id` = 33212), created = "2023-11-20 09:21:54", createdby = "tobiasko", filechecksum = "cf6837d3f639f7399a98fa138a3e3d83", junk = "false", modified = "2023-11-20 09:21:54", modifiedby = "tobiasko", name = "WU296294-20231120-0921-rawDiag.pdf", relativepath = "container_33212/workunit_296294/WU296294-20231120-0921-rawDiag.pdf", size = "670295", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33212/workunit_296294/WU296294-20231120-0921-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33212/workunit_296294/WU296294-20231120-0921-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296294))) The current plot is available as workunit 296294 #rows are 293226 output$download 1... #rows are 293226 output$download 2... #rows are 293226 output$download 2... #rows are 293226 output$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: '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 293226 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp Execution halted