Listening on http://127.0.0.1:33411 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//p32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_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 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 139892 output$tic.basepeak <- renderPlot({ #rows are 139892 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc1558e65c1.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc1558e65c1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290502, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:51:31", createdby = "tobiasko", deletable = "true", description = "input files:\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_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` = 2318931), list(`_classname` = "resource", `_id` = 2318930), list(`_classname` = "resource", `_id` = 2318929), list(`_classname` = "resource", `_id` = 2318928), list(`_classname` = "resource", `_id` = 2318927)), modified = "2023-06-26 09:51:31", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2319361, container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:51:32", createdby = "tobiasko", deletable = "true", filechecksum = "0c888a038c52675d0525ba403eac80d8", junk = "false", modified = "2023-06-26 09:51:32", modifiedby = "tobiasko", name = "WU290502-20230626-0951-rawDiag.pdf", relativepath = "container_32092/workunit_290502/WU290502-20230626-0951-rawDiag.pdf", size = "151631", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32092/workunit_290502/WU290502-20230626-0951-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32092/workunit_290502/WU290502-20230626-0951-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290502))) The current plot is available as workunit 290502 #rows are 139892 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 139892 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc130d956.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc130d956.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290503, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:00", createdby = "tobiasko", deletable = "true", description = "input files:\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_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` = 2318931), list(`_classname` = "resource", `_id` = 2318930), list(`_classname` = "resource", `_id` = 2318929), list(`_classname` = "resource", `_id` = 2318928), list(`_classname` = "resource", `_id` = 2318927)), modified = "2023-06-26 09:52:00", modifiedby = "tobiasko", name = "scan frequency plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2319367, container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:01", createdby = "tobiasko", deletable = "true", filechecksum = "29e68872772488dabb45fabdfd5fbb64", junk = "false", modified = "2023-06-26 09:52:01", modifiedby = "tobiasko", name = "WU290503-20230626-0952-rawDiag.pdf", relativepath = "container_32092/workunit_290503/WU290503-20230626-0952-rawDiag.pdf", size = "146915", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32092/workunit_290503/WU290503-20230626-0952-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32092/workunit_290503/WU290503-20230626-0952-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290503))) The current plot is available as workunit 290503 #rows are 139892 output$download 1... #rows are 139892 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc157e1a018.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc157e1a018.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290504, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:22", createdby = "tobiasko", deletable = "true", description = "input files:\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_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` = 2318931), list(`_classname` = "resource", `_id` = 2318930), list(`_classname` = "resource", `_id` = 2318929), list(`_classname` = "resource", `_id` = 2318928), list(`_classname` = "resource", `_id` = 2318927)), modified = "2023-06-26 09:52:22", modifiedby = "tobiasko", name = "lock mass correction plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2319371, container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:24", createdby = "tobiasko", deletable = "true", filechecksum = "9a72ec1962c33ca886ce61637f969f96", junk = "false", modified = "2023-06-26 09:52:24", modifiedby = "tobiasko", name = "WU290504-20230626-0952-rawDiag.pdf", relativepath = "container_32092/workunit_290504/WU290504-20230626-0952-rawDiag.pdf", size = "85301", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32092/workunit_290504/WU290504-20230626-0952-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32092/workunit_290504/WU290504-20230626-0952-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290504))) The current plot is available as workunit 290504 #rows are 139892 output$download 1... #rows are 139892 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc11f9adaf8.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc11f9adaf8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290505, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:51", createdby = "tobiasko", deletable = "true", description = "input files:\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_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` = 2318931), list(`_classname` = "resource", `_id` = 2318930), list(`_classname` = "resource", `_id` = 2318929), list(`_classname` = "resource", `_id` = 2318928), list(`_classname` = "resource", `_id` = 2318927)), modified = "2023-06-26 09:52:51", modifiedby = "tobiasko", name = "injection time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2319375, container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:52:53", createdby = "tobiasko", deletable = "true", filechecksum = "afb87fcee5e4625ae7545c69b1fa673e", junk = "false", modified = "2023-06-26 09:52:53", modifiedby = "tobiasko", name = "WU290505-20230626-0952-rawDiag.pdf", relativepath = "container_32092/workunit_290505/WU290505-20230626-0952-rawDiag.pdf", size = "609943", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32092/workunit_290505/WU290505-20230626-0952-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32092/workunit_290505/WU290505-20230626-0952-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290505))) The current plot is available as workunit 290505 #rows are 139892 output$download 1... #rows are 139892 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc1488eba81.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc1488eba81.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290506, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:53:34", createdby = "tobiasko", deletable = "true", description = "input files:\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_004_S526348_No_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_002_S526345_SEP_Ab_2.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_006_S526347_No_Ab_1.raw \np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_008r_S526346_SEP_Ab_3.raw\np32092/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32092_010_S526344_SEP_Ab_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` = 2318931), list(`_classname` = "resource", `_id` = 2318930), list(`_classname` = "resource", `_id` = 2318929), list(`_classname` = "resource", `_id` = 2318928), list(`_classname` = "resource", `_id` = 2318927)), modified = "2023-06-26 09:53:34", modifiedby = "tobiasko", name = "charge state plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2319383, container = list(`_classname` = "order", `_id` = 32092), created = "2023-06-26 09:53:36", createdby = "tobiasko", deletable = "true", filechecksum = "a956216ab8369b5d644fc1f71f1849b0", junk = "false", modified = "2023-06-26 09:53:36", modifiedby = "tobiasko", name = "WU290506-20230626-0953-rawDiag.pdf", relativepath = "container_32092/workunit_290506/WU290506-20230626-0953-rawDiag.pdf", size = "8361", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32092/workunit_290506/WU290506-20230626-0953-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32092/workunit_290506/WU290506-20230626-0953-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290506))) The current plot is available as workunit 290506 #rows are 139892 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 139892 output$download 2... DEBUG renderPlot plotQCs #rows are 139892 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc17cdded0d.pdf Warning: Error in +: non-numeric argument to binary operator 1: runApp #rows are 0 saving 'login and webservicepassword' ... output$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//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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 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 230100 output$tic.basepeak <- renderPlot({ #rows are 230100 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc17ea8ae60.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc17ea8ae60.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290514, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:20:36", createdby = "tobiasko", deletable = "true", description = "input files:\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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` = 2318926), list(`_classname` = "resource", `_id` = 2318925), list(`_classname` = "resource", `_id` = 2318924), list(`_classname` = "resource", `_id` = 2318923), list(`_classname` = "resource", `_id` = 2318922), list(`_classname` = "resource", `_id` = 2318921)), modified = "2023-06-26 10:20:36", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2320264, container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:20:38", createdby = "tobiasko", deletable = "true", filechecksum = "9efcd4dfd982326b211c10e5aebdf97a", junk = "false", modified = "2023-06-26 10:20:38", modifiedby = "tobiasko", name = "WU290514-20230626-1020-rawDiag.pdf", relativepath = "container_32088/workunit_290514/WU290514-20230626-1020-rawDiag.pdf", size = "161150", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32088/workunit_290514/WU290514-20230626-1020-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32088/workunit_290514/WU290514-20230626-1020-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290514))) The current plot is available as workunit 290514 #rows are 230100 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 230100 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc13b133d88.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc13b133d88.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290515, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:21:11", createdby = "tobiasko", deletable = "true", description = "input files:\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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` = 2318926), list(`_classname` = "resource", `_id` = 2318925), list(`_classname` = "resource", `_id` = 2318924), list(`_classname` = "resource", `_id` = 2318923), list(`_classname` = "resource", `_id` = 2318922), list(`_classname` = "resource", `_id` = 2318921)), modified = "2023-06-26 10:21:11", modifiedby = "tobiasko", name = "scan frequency plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2320267, container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:21:12", createdby = "tobiasko", deletable = "true", filechecksum = "4067e2a260b7be56ea5837885bfb0c18", junk = "false", modified = "2023-06-26 10:21:12", modifiedby = "tobiasko", name = "WU290515-20230626-1021-rawDiag.pdf", relativepath = "container_32088/workunit_290515/WU290515-20230626-1021-rawDiag.pdf", size = "179131", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32088/workunit_290515/WU290515-20230626-1021-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32088/workunit_290515/WU290515-20230626-1021-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290515))) The current plot is available as workunit 290515 #rows are 230100 output$download 1... #rows are 230100 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc111e063f5.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc111e063f5.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290516, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:22:01", createdby = "tobiasko", deletable = "true", description = "input files:\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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` = 2318926), list(`_classname` = "resource", `_id` = 2318925), list(`_classname` = "resource", `_id` = 2318924), list(`_classname` = "resource", `_id` = 2318923), list(`_classname` = "resource", `_id` = 2318922), list(`_classname` = "resource", `_id` = 2318921)), modified = "2023-06-26 10:22:01", modifiedby = "tobiasko", name = "lock mass correction plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2320272, container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:22:02", createdby = "tobiasko", deletable = "true", filechecksum = "8c1c6448e0fa9f416a02859b65aa06d4", junk = "false", modified = "2023-06-26 10:22:02", modifiedby = "tobiasko", name = "WU290516-20230626-1022-rawDiag.pdf", relativepath = "container_32088/workunit_290516/WU290516-20230626-1022-rawDiag.pdf", size = "70857", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32088/workunit_290516/WU290516-20230626-1022-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32088/workunit_290516/WU290516-20230626-1022-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290516))) The current plot is available as workunit 290516 #rows are 230100 output$download 1... #rows are 230100 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc12af7df06.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc12af7df06.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290518, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:22:41", createdby = "tobiasko", deletable = "true", description = "input files:\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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` = 2318926), list(`_classname` = "resource", `_id` = 2318925), list(`_classname` = "resource", `_id` = 2318924), list(`_classname` = "resource", `_id` = 2318923), list(`_classname` = "resource", `_id` = 2318922), list(`_classname` = "resource", `_id` = 2318921)), modified = "2023-06-26 10:22:41", modifiedby = "tobiasko", name = "injection time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2320290, container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:22:43", createdby = "tobiasko", deletable = "true", filechecksum = "44012256c1018bf125b8d5076faafbfb", junk = "false", modified = "2023-06-26 10:22:43", modifiedby = "tobiasko", name = "WU290518-20230626-1022-rawDiag.pdf", relativepath = "container_32088/workunit_290518/WU290518-20230626-1022-rawDiag.pdf", size = "1258200", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32088/workunit_290518/WU290518-20230626-1022-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32088/workunit_290518/WU290518-20230626-1022-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290518))) The current plot is available as workunit 290518 #rows are 230100 output$download 1... #rows are 230100 output$download 2... ggsave to file /tmp/RtmpdbmaSB/rawDiag-f5fc13c374d90.pdf generated pdf /tmp/RtmpdbmaSB/rawDiag-f5fc13c374d90.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290519, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:23:22", createdby = "tobiasko", deletable = "true", description = "input files:\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_012r_S526158_3_MITO_H2O2_Group_3.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_006_S526161_6_MITO_Group_6.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_010_S526159_4_aha-BACT_Group_4.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_002_S526156_1_aha-BACT_H2O2_Group_1.raw\np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_008_S526160_5_aha-MITO_Group_5.raw \np32088/Proteomics/EXPLORIS_1/analytic_20230623/20230623_C32088_004_S526157_2_aha-MITO_H2O2_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` = 2318926), list(`_classname` = "resource", `_id` = 2318925), list(`_classname` = "resource", `_id` = 2318924), list(`_classname` = "resource", `_id` = 2318923), list(`_classname` = "resource", `_id` = 2318922), list(`_classname` = "resource", `_id` = 2318921)), modified = "2023-06-26 10:23:22", modifiedby = "tobiasko", name = "charge state plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2320325, container = list(`_classname` = "order", `_id` = 32088), created = "2023-06-26 10:23:23", createdby = "tobiasko", deletable = "true", filechecksum = "b74b78e6c4f48921766ae0bb2d12eca7", junk = "false", modified = "2023-06-26 10:23:23", modifiedby = "tobiasko", name = "WU290519-20230626-1023-rawDiag.pdf", relativepath = "container_32088/workunit_290519/WU290519-20230626-1023-rawDiag.pdf", size = "8681", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32088/workunit_290519/WU290519-20230626-1023-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32088/workunit_290519/WU290519-20230626-1023-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290519))) The current plot is available as workunit 290519 #rows are 230100 output$download 1... DEBUG renderPlot 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") plotQCs #rows are 230100 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 230100 output$download 2... Execution halted