Listening on http://127.0.0.1:38853 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/ 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. 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. 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... output$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$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE #rows are 0 saving 'login and webservicepassword' ... output$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//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_006_S542455_WT02_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_002_S542459_CLF-GFP03_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_005_S542458_WT03_Group_1.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 missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode 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 521841 output$tic.basepeak <- renderPlot({ #rows are 521841 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 521841 output$download 2... #rows are 521841 output$download 2... #rows are 521841 output$download 2... #rows are 521841 output$download 2... Warning: Removed 46 rows containing non-finite values (`stat_smooth()`). Warning: Removed 9 rows containing missing values (`geom_line()`). #rows are 521841 output$download 2... #rows are 521841 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 521841 output$download 2... #rows are 521841 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 521841 output$download 2... ggsave to file /tmp/Rtmp6alSGh/rawDiag-16172c522a2920.pdf generated pdf /tmp/Rtmp6alSGh/rawDiag-16172c522a2920.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292329, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:56:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_002_S542459_CLF-GFP03_Group_2.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` = 2344418), list(`_classname` = "resource", `_id` = 2344417), list(`_classname` = "resource", `_id` = 2344416), list(`_classname` = "resource", `_id` = 2344415), list(`_classname` = "resource", `_id` = 2344414), list(`_classname` = "resource", `_id` = 2344413)), modified = "2023-08-11 07:56:27", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344421, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:56:28", createdby = "tobiasko", deletable = "true", filechecksum = "e893037ec88d17b56b7786242c40d6aa", junk = "false", modified = "2023-08-11 07:56:28", modifiedby = "tobiasko", name = "WU292329-20230811-0756-rawDiag.pdf", relativepath = "container_32479/workunit_292329/WU292329-20230811-0756-rawDiag.pdf", size = "91681", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292329/WU292329-20230811-0756-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292329/WU292329-20230811-0756-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292329))) The current plot is available as workunit 292329 #rows are 521841 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 521841 output$download 2... #rows are 521841 output$download 2... ggsave to file /tmp/Rtmp6alSGh/rawDiag-16172c55e8f1d9.pdf generated pdf /tmp/Rtmp6alSGh/rawDiag-16172c55e8f1d9.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292330, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:58:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_002_S542459_CLF-GFP03_Group_2.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` = 2344418), list(`_classname` = "resource", `_id` = 2344417), list(`_classname` = "resource", `_id` = 2344416), list(`_classname` = "resource", `_id` = 2344415), list(`_classname` = "resource", `_id` = 2344414), list(`_classname` = "resource", `_id` = 2344413)), modified = "2023-08-11 07:58:58", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344422, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:59:00", createdby = "tobiasko", deletable = "true", filechecksum = "cb621cf0ee48e8b12e84ea75468098b4", junk = "false", modified = "2023-08-11 07:59:00", modifiedby = "tobiasko", name = "WU292330-20230811-0758-rawDiag.pdf", relativepath = "container_32479/workunit_292330/WU292330-20230811-0758-rawDiag.pdf", size = "909533", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292330/WU292330-20230811-0758-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292330/WU292330-20230811-0758-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292330))) The current plot is available as workunit 292330 #rows are 521841 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 521841 output$download 2... ggsave to file /tmp/Rtmp6alSGh/rawDiag-16172c114a0c1a.pdf generated pdf /tmp/Rtmp6alSGh/rawDiag-16172c114a0c1a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292331, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:59:53", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230809/20230803_C32479_002_S542459_CLF-GFP03_Group_2.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` = 2344418), list(`_classname` = "resource", `_id` = 2344417), list(`_classname` = "resource", `_id` = 2344416), list(`_classname` = "resource", `_id` = 2344415), list(`_classname` = "resource", `_id` = 2344414), list(`_classname` = "resource", `_id` = 2344413)), modified = "2023-08-11 07:59:53", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344423, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-11 07:59:55", createdby = "tobiasko", deletable = "true", filechecksum = "726c57085b23f4b424872f0b4a4b0986", junk = "false", modified = "2023-08-11 07:59:55", modifiedby = "tobiasko", name = "WU292331-20230811-0759-rawDiag.pdf", relativepath = "container_32479/workunit_292331/WU292331-20230811-0759-rawDiag.pdf", size = "43735", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292331/WU292331-20230811-0759-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292331/WU292331-20230811-0759-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292331))) The current plot is available as workunit 292331 #rows are 521841 output$download 1... saving 'login and webservicepassword' ... Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp Execution halted