Listening on http://127.0.0.1:44001 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//p32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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_20230803/20230803_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_20230803/20230803_C32479_005_S542458_WT03_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_20230803/20230803_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_20230803/20230803_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_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.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 157129 output$tic.basepeak <- renderPlot({ #rows are 157129 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmporDRWC/rawDiag-11766efbaddd.pdf generated pdf /tmp/RtmporDRWC/rawDiag-11766efbaddd.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292115, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:13:36", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:13:36", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343425, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:13:37", createdby = "tobiasko", deletable = "true", filechecksum = "6763080494ea5fa480ec885997be13a6", junk = "false", modified = "2023-08-08 12:13:37", modifiedby = "tobiasko", name = "WU292115-20230808-1213-rawDiag.pdf", relativepath = "container_32479/workunit_292115/WU292115-20230808-1213-rawDiag.pdf", size = "206854", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292115/WU292115-20230808-1213-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292115/WU292115-20230808-1213-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292115))) The current plot is available as workunit 292115 #rows are 157129 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-117666581569f.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmporDRWC/rawDiag-117666581569f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292116, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:13:50", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:13:50", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343426, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:13:52", createdby = "tobiasko", deletable = "true", filechecksum = "207854868ddd31a10e7a625f6ca51245", junk = "false", modified = "2023-08-08 12:13:52", modifiedby = "tobiasko", name = "WU292116-20230808-1213-rawDiag.pdf", relativepath = "container_32479/workunit_292116/WU292116-20230808-1213-rawDiag.pdf", size = "190513", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292116/WU292116-20230808-1213-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292116/WU292116-20230808-1213-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292116))) The current plot is available as workunit 292116 #rows are 157129 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-11766427e84bf.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmporDRWC/rawDiag-11766427e84bf.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292117, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:10", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:14:10", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343427, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:11", createdby = "tobiasko", deletable = "true", filechecksum = "9c1083f41a464bff1811882a70538dad", junk = "false", modified = "2023-08-08 12:14:11", modifiedby = "tobiasko", name = "WU292117-20230808-1214-rawDiag.pdf", relativepath = "container_32479/workunit_292117/WU292117-20230808-1214-rawDiag.pdf", size = "322060", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292117/WU292117-20230808-1214-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292117/WU292117-20230808-1214-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292117))) The current plot is available as workunit 292117 #rows are 157129 output$download 1... Warning: Removed 37 rows containing non-finite values (`stat_smooth()`). #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-11766bc3a663.pdf Warning: Removed 37 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmporDRWC/rawDiag-11766bc3a663.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292118, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:19", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:14:19", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343428, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:20", createdby = "tobiasko", deletable = "true", filechecksum = "a7e72381ca792c0ae46e817982fccab6", junk = "false", modified = "2023-08-08 12:14:20", modifiedby = "tobiasko", name = "WU292118-20230808-1214-rawDiag.pdf", relativepath = "container_32479/workunit_292118/WU292118-20230808-1214-rawDiag.pdf", size = "125518", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292118/WU292118-20230808-1214-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292118/WU292118-20230808-1214-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292118))) The current plot is available as workunit 292118 #rows are 157129 output$download 1... #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-1176646cd97e9.pdf generated pdf /tmp/RtmporDRWC/rawDiag-1176646cd97e9.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292119, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:34", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:14:34", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343429, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:35", createdby = "tobiasko", deletable = "true", filechecksum = "df2d693e670129427c272d88090f2797", junk = "false", modified = "2023-08-08 12:14:35", modifiedby = "tobiasko", name = "WU292119-20230808-1214-rawDiag.pdf", relativepath = "container_32479/workunit_292119/WU292119-20230808-1214-rawDiag.pdf", size = "670492", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292119/WU292119-20230808-1214-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292119/WU292119-20230808-1214-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292119))) The current plot is available as workunit 292119 #rows are 157129 output$download 1... #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-117664efd0efa.pdf generated pdf /tmp/RtmporDRWC/rawDiag-117664efd0efa.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292120, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:43", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:14:43", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343430, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:44", createdby = "tobiasko", deletable = "true", filechecksum = "abbda6d4e410740f6d97c89afc87608d", junk = "false", modified = "2023-08-08 12:14:44", modifiedby = "tobiasko", name = "WU292120-20230808-1214-rawDiag.pdf", relativepath = "container_32479/workunit_292120/WU292120-20230808-1214-rawDiag.pdf", size = "8603", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292120/WU292120-20230808-1214-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292120/WU292120-20230808-1214-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292120))) The current plot is available as workunit 292120 #rows are 157129 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 157129 output$download 2... ggsave to file /tmp/RtmporDRWC/rawDiag-117664be50723.pdf generated pdf /tmp/RtmporDRWC/rawDiag-117664be50723.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292121, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_005_S542458_WT03_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_007_S542460_SWN-GFP03_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_006_S542455_WT02_Group_1.raw \np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_004_S542456_CLF-GFP02_Group_2.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_C32479_003_S542457_SWN-GFP02_Group_3.raw\np32479/Proteomics/EXPLORIS_2/analytic_20230803/20230803_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` = 2340572), list(`_classname` = "resource", `_id` = 2340571), list(`_classname` = "resource", `_id` = 2340570), list(`_classname` = "resource", `_id` = 2340569), list(`_classname` = "resource", `_id` = 2340568), list(`_classname` = "resource", `_id` = 2340567)), modified = "2023-08-08 12:14:58", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2343431, container = list(`_classname` = "order", `_id` = 32479), created = "2023-08-08 12:14:59", createdby = "tobiasko", deletable = "true", filechecksum = "e5f3704ed671c318c8c5b73f9afba911", junk = "false", modified = "2023-08-08 12:14:59", modifiedby = "tobiasko", name = "WU292121-20230808-1214-rawDiag.pdf", relativepath = "container_32479/workunit_292121/WU292121-20230808-1214-rawDiag.pdf", size = "47502", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32479/workunit_292121/WU292121-20230808-1214-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32479/workunit_292121/WU292121-20230808-1214-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292121))) The current plot is available as workunit 292121 #rows are 157129 output$download 1... DEBUG renderPlot plotQCs #rows are 157129 output$download 1... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p26109/Proteomics/LUMOS_2/ackle_20230531_operator_training/20230531_001_autoQC01.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p26109/Proteomics/LUMOS_2/ackle_20230531_operator_training/20230531_006_autoQC01.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p26109/Proteomics/LUMOS_2/ackle_20230531_operator_training/20230531_012_autoQC01.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p26109/Proteomics/LUMOS_2/ackle_20230531_operator_training/20230531_013_autoQC4L.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p26109/Proteomics/LUMOS_2/ackle_20230531_operator_training/20230531_008_S427185_Glu1_Group_1.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 213738 output$tic.basepeak <- renderPlot({ #rows are 213738 output$download 2... saving 'login and webservicepassword' ... output$tic.basepeak <- renderPlot({ #rows are 213738 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 213738 output$download 2... #rows are 213738 output$download 2... #rows are 213738 output$download 2... #rows are 213738 output$download 2... #rows are 213738 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 213738 output$download 2... DEBUG renderPlot plotQCs #rows are 213738 output$download 2... DEBUG renderPlot plotQCs #rows are 157129 output$download 1... Execution halted