Listening on http://127.0.0.1:40491 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({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 54649 #rows are 54649 output$download 2... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f062d079237.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f062d079237.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294345, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:11", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:33:11", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365681, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:12", createdby = "tobiasko", deletable = "true", filechecksum = "d2679464df5555ea263013bcfd87bd3a", junk = "false", modified = "2023-10-05 09:33:12", modifiedby = "tobiasko", name = "WU294345-20231005-0933-rawDiag.pdf", relativepath = "container_33022/workunit_294345/WU294345-20231005-0933-rawDiag.pdf", size = "59773", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294345/WU294345-20231005-0933-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294345/WU294345-20231005-0933-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294345))) The current plot is available as workunit 294345 #rows are 54649 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f06540c1662.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f06540c1662.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294346, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:30", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:33:30", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365682, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:32", createdby = "tobiasko", deletable = "true", filechecksum = "c3ea1c1bc00fde281575d5f6d867de70", junk = "false", modified = "2023-10-05 09:33:32", modifiedby = "tobiasko", name = "WU294346-20231005-0933-rawDiag.pdf", relativepath = "container_33022/workunit_294346/WU294346-20231005-0933-rawDiag.pdf", size = "66649", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294346/WU294346-20231005-0933-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294346/WU294346-20231005-0933-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294346))) The current plot is available as workunit 294346 #rows are 54649 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f067f5ae68.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f067f5ae68.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294347, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:42", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:33:42", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365683, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:43", createdby = "tobiasko", deletable = "true", filechecksum = "b185192e9b7e191e0e73381e916382cd", junk = "false", modified = "2023-10-05 09:33:43", modifiedby = "tobiasko", name = "WU294347-20231005-0933-rawDiag.pdf", relativepath = "container_33022/workunit_294347/WU294347-20231005-0933-rawDiag.pdf", size = "41686", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294347/WU294347-20231005-0933-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294347/WU294347-20231005-0933-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294347))) The current plot is available as workunit 294347 #rows are 54649 output$download 1... #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f066b6030a9.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f066b6030a9.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294348, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:50", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:33:50", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365684, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:33:51", createdby = "tobiasko", deletable = "true", filechecksum = "467c753b46bc202fc1852c8e6a1156f2", junk = "false", modified = "2023-10-05 09:33:52", modifiedby = "tobiasko", name = "WU294348-20231005-0933-rawDiag.pdf", relativepath = "container_33022/workunit_294348/WU294348-20231005-0933-rawDiag.pdf", size = "34525", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294348/WU294348-20231005-0933-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294348/WU294348-20231005-0933-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294348))) The current plot is available as workunit 294348 #rows are 54649 output$download 1... #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f06163a92.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f06163a92.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294349, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:03", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:34:03", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365685, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:05", createdby = "tobiasko", deletable = "true", filechecksum = "154ed4db34037ace1b2e3fbd0a4ba6ef", junk = "false", modified = "2023-10-05 09:34:05", modifiedby = "tobiasko", name = "WU294349-20231005-0934-rawDiag.pdf", relativepath = "container_33022/workunit_294349/WU294349-20231005-0934-rawDiag.pdf", size = "209911", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294349/WU294349-20231005-0934-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294349/WU294349-20231005-0934-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294349))) The current plot is available as workunit 294349 #rows are 54649 output$download 1... #rows are 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f065cf12466.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f065cf12466.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294350, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:20", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:34:20", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365686, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:22", createdby = "tobiasko", deletable = "true", filechecksum = "5150bada4c14acf10ad09ba448e60619", junk = "false", modified = "2023-10-05 09:34:22", modifiedby = "tobiasko", name = "WU294350-20231005-0934-rawDiag.pdf", relativepath = "container_33022/workunit_294350/WU294350-20231005-0934-rawDiag.pdf", size = "6533", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294350/WU294350-20231005-0934-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294350/WU294350-20231005-0934-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294350))) The current plot is available as workunit 294350 #rows are 54649 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: `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 54649 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f065b2efe22.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f065b2efe22.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294351, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:38", createdby = "tobiasko", deletable = "true", description = "input files:\np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_004_S570717_LanCL1_GSH_negctrl_Group_2.raw \np33022/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33022_002_S570716_LanCL1_PraGSH_posctrl_Group_1.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` = 2365675), list(`_classname` = "resource", `_id` = 2365674)), modified = "2023-10-05 09:34:38", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365687, container = list(`_classname` = "order", `_id` = 33022), created = "2023-10-05 09:34:39", createdby = "tobiasko", deletable = "true", filechecksum = "3f3c8fc1934918b01691425dbfccb994", junk = "false", modified = "2023-10-05 09:34:39", modifiedby = "tobiasko", name = "WU294351-20231005-0934-rawDiag.pdf", relativepath = "container_33022/workunit_294351/WU294351-20231005-0934-rawDiag.pdf", size = "16540", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33022/workunit_294351/WU294351-20231005-0934-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33022/workunit_294351/WU294351-20231005-0934-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294351))) The current plot is available as workunit 294351 #rows are 54649 output$download 1... DEBUG renderPlot plotQCs #rows are 54649 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 54649 output$download 2... #rows are 54649 output$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$xic 1: runApp Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.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 #rows are 56263 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f0620e7566.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f0620e7566.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294355, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:29:49", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:29:49", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365696, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:29:50", createdby = "tobiasko", deletable = "true", filechecksum = "f8ca8acaf2d77c83f0c0c2464992d76e", junk = "false", modified = "2023-10-05 10:29:50", modifiedby = "tobiasko", name = "WU294355-20231005-1029-rawDiag.pdf", relativepath = "container_33000/workunit_294355/WU294355-20231005-1029-rawDiag.pdf", size = "70757", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294355/WU294355-20231005-1029-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294355/WU294355-20231005-1029-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294355))) The current plot is available as workunit 294355 #rows are 56263 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f065b4a6965.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f065b4a6965.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294356, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:12", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:30:12", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365697, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:13", createdby = "tobiasko", deletable = "true", filechecksum = "a2f8e68ecc0416de07ab6d3ebd4ffb64", junk = "false", modified = "2023-10-05 10:30:13", modifiedby = "tobiasko", name = "WU294356-20231005-1030-rawDiag.pdf", relativepath = "container_33000/workunit_294356/WU294356-20231005-1030-rawDiag.pdf", size = "67581", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294356/WU294356-20231005-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294356/WU294356-20231005-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294356))) The current plot is available as workunit 294356 #rows are 56263 output$download 1... #rows are 56263 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f064871450b.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f064871450b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294357, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:28", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:30:28", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365698, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:30", createdby = "tobiasko", deletable = "true", filechecksum = "2347d86e83e7d2123e75f2124d94a512", junk = "false", modified = "2023-10-05 10:30:30", modifiedby = "tobiasko", name = "WU294357-20231005-1030-rawDiag.pdf", relativepath = "container_33000/workunit_294357/WU294357-20231005-1030-rawDiag.pdf", size = "45795", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294357/WU294357-20231005-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294357/WU294357-20231005-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294357))) The current plot is available as workunit 294357 #rows are 56263 output$download 1... #rows are 56263 output$download 2... Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f0612575288.pdf Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f0612575288.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294358, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:51", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:30:51", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365699, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:30:52", createdby = "tobiasko", deletable = "true", filechecksum = "7de7816c6e06a7c8ece3f0cc0a904060", junk = "false", modified = "2023-10-05 10:30:52", modifiedby = "tobiasko", name = "WU294358-20231005-1030-rawDiag.pdf", relativepath = "container_33000/workunit_294358/WU294358-20231005-1030-rawDiag.pdf", size = "41538", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294358/WU294358-20231005-1030-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294358/WU294358-20231005-1030-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294358))) The current plot is available as workunit 294358 #rows are 56263 output$download 1... #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f067db78331.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f067db78331.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294359, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:03", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:31:03", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365700, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:04", createdby = "tobiasko", deletable = "true", filechecksum = "7bf85573ba19cfa769b5fe02cd10c888", junk = "false", modified = "2023-10-05 10:31:04", modifiedby = "tobiasko", name = "WU294359-20231005-1031-rawDiag.pdf", relativepath = "container_33000/workunit_294359/WU294359-20231005-1031-rawDiag.pdf", size = "256022", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294359/WU294359-20231005-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294359/WU294359-20231005-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294359))) The current plot is available as workunit 294359 #rows are 56263 output$download 1... #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f067dcdbdc3.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f067dcdbdc3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294360, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:33", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:31:33", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365701, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:34", createdby = "tobiasko", deletable = "true", filechecksum = "9dc5fbd0872e3e2a88a3c9295d173c53", junk = "false", modified = "2023-10-05 10:31:34", modifiedby = "tobiasko", name = "WU294360-20231005-1031-rawDiag.pdf", relativepath = "container_33000/workunit_294360/WU294360-20231005-1031-rawDiag.pdf", size = "6304", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294360/WU294360-20231005-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294360/WU294360-20231005-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294360))) The current plot is available as workunit 294360 #rows are 56263 output$download 1... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 56263 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f065abee229.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f065abee229.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294361, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:48", createdby = "tobiasko", deletable = "true", description = "input files:\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_004_S568757_liver-KO-62_Knock-out__KO_.raw\np33000/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C33000_002_S568756_liver-WT-61_Wild_Type__WT_.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` = 2365680), list(`_classname` = "resource", `_id` = 2365679)), modified = "2023-10-05 10:31:48", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365702, container = list(`_classname` = "order", `_id` = 33000), created = "2023-10-05 10:31:49", createdby = "tobiasko", deletable = "true", filechecksum = "d1b36246546d539c0e5f72dafa5945f8", junk = "false", modified = "2023-10-05 10:31:49", modifiedby = "tobiasko", name = "WU294361-20231005-1031-rawDiag.pdf", relativepath = "container_33000/workunit_294361/WU294361-20231005-1031-rawDiag.pdf", size = "13648", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33000/workunit_294361/WU294361-20231005-1031-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33000/workunit_294361/WU294361-20231005-1031-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294361))) The current plot is available as workunit 294361 #rows are 56263 output$download 1... DEBUG renderPlot plotQCs #rows are 56263 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 56263 output$download 2... #rows are 56263 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 54966 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f06595ca997.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f06595ca997.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294367, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:19:53", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:19:53", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365717, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:19:54", createdby = "tobiasko", deletable = "true", filechecksum = "d20fd4951095ac78b8569d4aa689ab81", junk = "false", modified = "2023-10-05 11:19:54", modifiedby = "tobiasko", name = "WU294367-20231005-1119-rawDiag.pdf", relativepath = "container_32900/workunit_294367/WU294367-20231005-1119-rawDiag.pdf", size = "57505", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294367/WU294367-20231005-1119-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294367/WU294367-20231005-1119-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294367))) The current plot is available as workunit 294367 #rows are 54966 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f06ee1ccff.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f06ee1ccff.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294368, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:12", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:20:12", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365718, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:13", createdby = "tobiasko", deletable = "true", filechecksum = "badcbd7fb8ba33dcd21882a14ea83b4b", junk = "false", modified = "2023-10-05 11:20:13", modifiedby = "tobiasko", name = "WU294368-20231005-1120-rawDiag.pdf", relativepath = "container_32900/workunit_294368/WU294368-20231005-1120-rawDiag.pdf", size = "66094", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294368/WU294368-20231005-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294368/WU294368-20231005-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294368))) The current plot is available as workunit 294368 #rows are 54966 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f06182fc885.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f06182fc885.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294369, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:19", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:20:19", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365719, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:20", createdby = "tobiasko", deletable = "true", filechecksum = "aee4dab98e30f6ed39867da5913798e2", junk = "false", modified = "2023-10-05 11:20:20", modifiedby = "tobiasko", name = "WU294369-20231005-1120-rawDiag.pdf", relativepath = "container_32900/workunit_294369/WU294369-20231005-1120-rawDiag.pdf", size = "42528", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294369/WU294369-20231005-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294369/WU294369-20231005-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294369))) The current plot is available as workunit 294369 #rows are 54966 output$download 1... Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f064e855643.pdf Warning: Removed 2 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f064e855643.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294370, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:28", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:20:28", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365720, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:29", createdby = "tobiasko", deletable = "true", filechecksum = "9293afff38c3e4e394f3cf90a091d169", junk = "false", modified = "2023-10-05 11:20:29", modifiedby = "tobiasko", name = "WU294370-20231005-1120-rawDiag.pdf", relativepath = "container_32900/workunit_294370/WU294370-20231005-1120-rawDiag.pdf", size = "34784", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294370/WU294370-20231005-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294370/WU294370-20231005-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294370))) The current plot is available as workunit 294370 #rows are 54966 output$download 1... #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f0658e6fa63.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f0658e6fa63.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294371, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:53", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:20:53", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365721, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:20:54", createdby = "tobiasko", deletable = "true", filechecksum = "4afdbab0c30910b47ad250ec8151288c", junk = "false", modified = "2023-10-05 11:20:54", modifiedby = "tobiasko", name = "WU294371-20231005-1120-rawDiag.pdf", relativepath = "container_32900/workunit_294371/WU294371-20231005-1120-rawDiag.pdf", size = "211636", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294371/WU294371-20231005-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294371/WU294371-20231005-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294371))) The current plot is available as workunit 294371 #rows are 54966 output$download 1... #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f066b3e4ceb.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f066b3e4ceb.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294372, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:21:07", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:21:07", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365722, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:21:08", createdby = "tobiasko", deletable = "true", filechecksum = "8e69df60114feba4d29d5a44815949cb", junk = "false", modified = "2023-10-05 11:21:08", modifiedby = "tobiasko", name = "WU294372-20231005-1121-rawDiag.pdf", relativepath = "container_32900/workunit_294372/WU294372-20231005-1121-rawDiag.pdf", size = "6484", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294372/WU294372-20231005-1121-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294372/WU294372-20231005-1121-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294372))) The current plot is available as workunit 294372 #rows are 54966 output$download 1... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 54966 output$download 2... ggsave to file /tmp/RtmpvP6Qog/rawDiag-1b7f0668f5d01c.pdf generated pdf /tmp/RtmpvP6Qog/rawDiag-1b7f0668f5d01c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 294373, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:21:18", createdby = "tobiasko", deletable = "true", description = "input files:\np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_003_S565845_IP_CTRL_Control.raw \np32900/Proteomics/EXPLORIS_2/analytic_20231004/20231004_C32900_002_S565844_IP_hDASPO_Wild_Type__WT_.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` = 2365678), list(`_classname` = "resource", `_id` = 2365677)), modified = "2023-10-05 11:21:18", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2365723, container = list(`_classname` = "order", `_id` = 32900), created = "2023-10-05 11:21:19", createdby = "tobiasko", deletable = "true", filechecksum = "f0f474d640fc5830550a6b4947121981", junk = "false", modified = "2023-10-05 11:21:19", modifiedby = "tobiasko", name = "WU294373-20231005-1121-rawDiag.pdf", relativepath = "container_32900/workunit_294373/WU294373-20231005-1121-rawDiag.pdf", size = "15035", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32900/workunit_294373/WU294373-20231005-1121-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32900/workunit_294373/WU294373-20231005-1121-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 294373))) The current plot is available as workunit 294373 #rows are 54966 output$download 1... DEBUG renderPlot plotQCs #rows are 54966 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 54966 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 54966 output$download 2... Execution halted