Listening on http://127.0.0.1:39621 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({ 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//p32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_003_S559196_WT_HB_1_01.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_005_S559197_WT_HB_2_02.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 114839 output$tic.basepeak <- renderPlot({ #rows are 114839 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb45a20901.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb45a20901.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293781, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32808), created = "2023-09-21 08:33:02", createdby = "spfammatter", deletable = "true", description = "input files:\np32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_003_S559196_WT_HB_1_01.raw\np32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_005_S559197_WT_HB_2_02.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` = 2359175), list(`_classname` = "resource", `_id` = 2359174)), modified = "2023-09-21 08:33:02", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359190, container = list(`_classname` = "order", `_id` = 32808), created = "2023-09-21 08:33:03", createdby = "spfammatter", deletable = "true", filechecksum = "2a1dd29c0766ee1da0fb0f7def1d3e73", junk = "false", modified = "2023-09-21 08:33:03", modifiedby = "spfammatter", name = "WU293781-20230921-0833-rawDiag.pdf", relativepath = "container_32808/workunit_293781/WU293781-20230921-0833-rawDiag.pdf", size = "39825", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32808/workunit_293781/WU293781-20230921-0833-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32808/workunit_293781/WU293781-20230921-0833-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293781))) The current plot is available as workunit 293781 #rows are 114839 output$download 1... saving 'login and webservicepassword' ... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp 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: `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 114839 output$download 2... DEBUG renderPlot plotQCs #rows are 114839 output$download 2... saving 'login and webservicepassword' ... 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$tableInfo 1: runApp #rows are 114839 output$download 2... #rows are 114839 output$download 2... #rows are 114839 output$download 2... #rows are 114839 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$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$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//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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 174728 output$tic.basepeak <- renderPlot({ #rows are 174728 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb42fa44df1.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb42fa44df1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293787, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:01:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:01:27", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359207, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:01:28", createdby = "tobiasko", deletable = "true", filechecksum = "04cc6ea330cb4feeff603dca7f87ae2a", junk = "false", modified = "2023-09-21 09:01:28", modifiedby = "tobiasko", name = "WU293787-20230921-0901-rawDiag.pdf", relativepath = "container_32897/workunit_293787/WU293787-20230921-0901-rawDiag.pdf", size = "188078", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293787/WU293787-20230921-0901-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293787/WU293787-20230921-0901-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293787))) The current plot is available as workunit 293787 #rows are 174728 output$download 1... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb45b467373.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb45b467373.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293788, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:01:42", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:01:42", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359208, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:01:44", createdby = "tobiasko", deletable = "true", filechecksum = "f3912c0ad6983673f67c47dc7424a142", junk = "false", modified = "2023-09-21 09:01:44", modifiedby = "tobiasko", name = "WU293788-20230921-0901-rawDiag.pdf", relativepath = "container_32897/workunit_293788/WU293788-20230921-0901-rawDiag.pdf", size = "171625", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293788/WU293788-20230921-0901-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293788/WU293788-20230921-0901-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293788))) The current plot is available as workunit 293788 #rows are 174728 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb474f03605.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb474f03605.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293789, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:06", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:02:06", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359209, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:07", createdby = "tobiasko", deletable = "true", filechecksum = "09d3fcc340e4b97c537a6c7f574fd99c", junk = "false", modified = "2023-09-21 09:02:07", modifiedby = "tobiasko", name = "WU293789-20230921-0902-rawDiag.pdf", relativepath = "container_32897/workunit_293789/WU293789-20230921-0902-rawDiag.pdf", size = "180794", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293789/WU293789-20230921-0902-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293789/WU293789-20230921-0902-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293789))) The current plot is available as workunit 293789 #rows are 174728 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb471f69822.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb471f69822.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293790, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:26", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:02:26", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359210, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:27", createdby = "tobiasko", deletable = "true", filechecksum = "e106ea0ccb68c8c73b9fd3c251fa892a", junk = "false", modified = "2023-09-21 09:02:27", modifiedby = "tobiasko", name = "WU293790-20230921-0902-rawDiag.pdf", relativepath = "container_32897/workunit_293790/WU293790-20230921-0902-rawDiag.pdf", size = "311208", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293790/WU293790-20230921-0902-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293790/WU293790-20230921-0902-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293790))) The current plot is available as workunit 293790 #rows are 174728 output$download 1... Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb4264ebfd1.pdf Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb4264ebfd1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293791, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:41", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:02:41", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359211, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:02:42", createdby = "tobiasko", deletable = "true", filechecksum = "066240497af6e474a53d796add58b0d5", junk = "false", modified = "2023-09-21 09:02:42", modifiedby = "tobiasko", name = "WU293791-20230921-0902-rawDiag.pdf", relativepath = "container_32897/workunit_293791/WU293791-20230921-0902-rawDiag.pdf", size = "105308", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293791/WU293791-20230921-0902-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293791/WU293791-20230921-0902-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293791))) The current plot is available as workunit 293791 #rows are 174728 output$download 1... #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb4c756de7.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb4c756de7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293792, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:05", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:03:05", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359212, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:06", createdby = "tobiasko", deletable = "true", filechecksum = "b1c68bf537c887410c36b24307141e50", junk = "false", modified = "2023-09-21 09:03:06", modifiedby = "tobiasko", name = "WU293792-20230921-0903-rawDiag.pdf", relativepath = "container_32897/workunit_293792/WU293792-20230921-0903-rawDiag.pdf", size = "804119", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293792/WU293792-20230921-0903-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293792/WU293792-20230921-0903-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293792))) The current plot is available as workunit 293792 #rows are 174728 output$download 1... #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb450c05644.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb450c05644.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293793, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:17", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:03:17", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359213, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:19", createdby = "tobiasko", deletable = "true", filechecksum = "1643379c1571cd7c5e74324c96c221d8", junk = "false", modified = "2023-09-21 09:03:19", modifiedby = "tobiasko", name = "WU293793-20230921-0903-rawDiag.pdf", relativepath = "container_32897/workunit_293793/WU293793-20230921-0903-rawDiag.pdf", size = "8581", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293793/WU293793-20230921-0903-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293793/WU293793-20230921-0903-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293793))) The current plot is available as workunit 293793 #rows are 174728 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 174728 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb456625f45.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb456625f45.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293794, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:33", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_009_S564240_E586Q_2_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_008_S564238_WT_3_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_002_S564239_E586Q_1_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_003_S564241_E586Q_3_Mutant_DDA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_004_S564237_WT_2_WT_DDA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_007_S564236_WT_1_WT_DDA.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` = 2359173), list(`_classname` = "resource", `_id` = 2359172), list(`_classname` = "resource", `_id` = 2359171), list(`_classname` = "resource", `_id` = 2359170), list(`_classname` = "resource", `_id` = 2359169), list(`_classname` = "resource", `_id` = 2359168)), modified = "2023-09-21 09:03:33", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359214, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:03:34", createdby = "tobiasko", deletable = "true", filechecksum = "d8c5070d6a2e957d9fe902ec57c66d24", junk = "false", modified = "2023-09-21 09:03:34", modifiedby = "tobiasko", name = "WU293794-20230921-0903-rawDiag.pdf", relativepath = "container_32897/workunit_293794/WU293794-20230921-0903-rawDiag.pdf", size = "35327", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293794/WU293794-20230921-0903-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293794/WU293794-20230921-0903-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293794))) The current plot is available as workunit 293794 #rows are 174728 output$download 1... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$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$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_005_S559197_WT_HB_2_02.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_003_S559196_WT_HB_1_01.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 114839 output$tic.basepeak <- renderPlot({ #rows are 114839 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/RtmpEJEKdC/rawDiag-10cb4316e7b2b.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb4316e7b2b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293796, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32808), created = "2023-09-21 09:13:48", createdby = "spfammatter", deletable = "true", description = "input files:\np32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_003_S559196_WT_HB_1_01.raw\np32808/Proteomics/LUMOS_1/analytic_20230920/20230920_C32808_005_S559197_WT_HB_2_02.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` = 2359175), list(`_classname` = "resource", `_id` = 2359174)), modified = "2023-09-21 09:13:48", modifiedby = "spfammatter", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359218, container = list(`_classname` = "order", `_id` = 32808), created = "2023-09-21 09:13:49", createdby = "spfammatter", deletable = "true", filechecksum = "2360ccac0b27b3d3f38e225da6189a95", junk = "false", modified = "2023-09-21 09:13:49", modifiedby = "spfammatter", name = "WU293796-20230921-0913-rawDiag.pdf", relativepath = "container_32808/workunit_293796/WU293796-20230921-0913-rawDiag.pdf", size = "39825", status = "available", storage = list( `_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32808/workunit_293796/WU293796-20230921-0913-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32808/workunit_293796/WU293796-20230921-0913-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293796))) The current plot is available as workunit 293796 #rows are 114839 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. Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp #rows are 174728 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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 544606 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({ 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//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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 544606 output$tic.basepeak <- renderPlot({ #rows are 544606 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb464301163.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb464301163.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293799, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:27:25", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:27:25", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359231, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:27:26", createdby = "tobiasko", deletable = "true", filechecksum = "0727d88e65adbce1e60d1e9f62d6dc83", junk = "false", modified = "2023-09-21 09:27:26", modifiedby = "tobiasko", name = "WU293799-20230921-0927-rawDiag.pdf", relativepath = "container_32897/workunit_293799/WU293799-20230921-0927-rawDiag.pdf", size = "98229", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293799/WU293799-20230921-0927-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293799/WU293799-20230921-0927-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293799))) The current plot is available as workunit 293799 #rows are 544606 output$download 1... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 544606 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb45ded745e.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb45ded745e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293800, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:27:42", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:27:42", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359232, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:27:43", createdby = "tobiasko", deletable = "true", filechecksum = "73f627dba901eb5e1d8735443a8453f1", junk = "false", modified = "2023-09-21 09:27:43", modifiedby = "tobiasko", name = "WU293800-20230921-0927-rawDiag.pdf", relativepath = "container_32897/workunit_293800/WU293800-20230921-0927-rawDiag.pdf", size = "95623", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293800/WU293800-20230921-0927-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293800/WU293800-20230921-0927-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293800))) The current plot is available as workunit 293800 #rows are 544606 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 544606 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb45208fd6f.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb45208fd6f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293801, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:28:14", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:28:14", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359233, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:28:16", createdby = "tobiasko", deletable = "true", filechecksum = "c3a933baf9ffc5ed7b866b2571de247e", junk = "false", modified = "2023-09-21 09:28:16", modifiedby = "tobiasko", name = "WU293801-20230921-0928-rawDiag.pdf", relativepath = "container_32897/workunit_293801/WU293801-20230921-0928-rawDiag.pdf", size = "156650", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293801/WU293801-20230921-0928-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293801/WU293801-20230921-0928-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293801))) The current plot is available as workunit 293801 #rows are 544606 output$download 1... #rows are 544606 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb43b1a20f8.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb43b1a20f8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293802, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:28:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:28:27", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359234, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:28:28", createdby = "tobiasko", deletable = "true", filechecksum = "82c26806295339221d96c9b4bacc52ec", junk = "false", modified = "2023-09-21 09:28:28", modifiedby = "tobiasko", name = "WU293802-20230921-0928-rawDiag.pdf", relativepath = "container_32897/workunit_293802/WU293802-20230921-0928-rawDiag.pdf", size = "51496", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293802/WU293802-20230921-0928-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293802/WU293802-20230921-0928-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293802))) The current plot is available as workunit 293802 #rows are 544606 output$download 1... #rows are 544606 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb423764d72.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb423764d72.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293803, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:29:26", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:29:26", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359235, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:29:29", createdby = "tobiasko", deletable = "true", filechecksum = "f3b5161ecbb8f79e4b22c79f18089af0", junk = "false", modified = "2023-09-21 09:29:29", modifiedby = "tobiasko", name = "WU293803-20230921-0929-rawDiag.pdf", relativepath = "container_32897/workunit_293803/WU293803-20230921-0929-rawDiag.pdf", size = "988154", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293803/WU293803-20230921-0929-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293803/WU293803-20230921-0929-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293803))) The current plot is available as workunit 293803 #rows are 544606 output$download 1... #rows are 544606 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 544606 output$download 2... ggsave to file /tmp/RtmpEJEKdC/rawDiag-10cb41a678295.pdf generated pdf /tmp/RtmpEJEKdC/rawDiag-10cb41a678295.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 293804, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:30:03", createdby = "tobiasko", deletable = "true", description = "input files:\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_014_S564237_WT_2_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_019_S564240_E586Q_2_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_012_S564239_E586Q_1_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_018_S564238_WT_3_WT_DIA.raw \np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_013_S564241_E586Q_3_Mutant_DIA.raw\np32897/Proteomics/EXPLORIS_2/analytic_20230920/20230920_C32897_017_S564236_WT_1_WT_DIA.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` = 2359199), list(`_classname` = "resource", `_id` = 2359198), list(`_classname` = "resource", `_id` = 2359197), list(`_classname` = "resource", `_id` = 2359196), list(`_classname` = "resource", `_id` = 2359195), list(`_classname` = "resource", `_id` = 2359194)), modified = "2023-09-21 09:30:03", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2359236, container = list(`_classname` = "order", `_id` = 32897), created = "2023-09-21 09:30:04", createdby = "tobiasko", deletable = "true", filechecksum = "9c6ac15918da5f9a868835c4efbe6495", junk = "false", modified = "2023-09-21 09:30:04", modifiedby = "tobiasko", name = "WU293804-20230921-0930-rawDiag.pdf", relativepath = "container_32897/workunit_293804/WU293804-20230921-0930-rawDiag.pdf", size = "27821", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32897/workunit_293804/WU293804-20230921-0930-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32897/workunit_293804/WU293804-20230921-0930-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 293804))) The current plot is available as workunit 293804 #rows are 544606 output$download 1... Execution halted