Listening on http://127.0.0.1:37979 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//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 158388 output$tic.basepeak <- renderPlot({ #rows are 158388 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpOjAjgR/rawDiag-3c40d7715dd25c.pdf generated pdf /tmp/RtmpOjAjgR/rawDiag-3c40d7715dd25c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292837, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:01", createdby = "tobiasko", deletable = "true", description = "input files:\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2350275), list(`_classname` = "resource", `_id` = 2350274), list(`_classname` = "resource", `_id` = 2350273), list(`_classname` = "resource", `_id` = 2350272), list(`_classname` = "resource", `_id` = 2350271), list(`_classname` = "resource", `_id` = 2350270)), modified = "2023-08-25 09:50:01", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2350283, container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:02", createdby = "tobiasko", deletable = "true", filechecksum = "eb973d460598c534c5e20859c46994f4", junk = "false", modified = "2023-08-25 09:50:02", modifiedby = "tobiasko", name = "WU292837-20230825-0950-rawDiag.pdf", relativepath = "container_32503/workunit_292837/WU292837-20230825-0950-rawDiag.pdf", size = "196640", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32503/workunit_292837/WU292837-20230825-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32503/workunit_292837/WU292837-20230825-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292837))) The current plot is available as workunit 292837 #rows are 158388 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 158388 output$download 2... ggsave to file /tmp/RtmpOjAjgR/rawDiag-3c40d74855dbc8.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpOjAjgR/rawDiag-3c40d74855dbc8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292838, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:23", createdby = "tobiasko", deletable = "true", description = "input files:\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2350275), list(`_classname` = "resource", `_id` = 2350274), list(`_classname` = "resource", `_id` = 2350273), list(`_classname` = "resource", `_id` = 2350272), list(`_classname` = "resource", `_id` = 2350271), list(`_classname` = "resource", `_id` = 2350270)), modified = "2023-08-25 09:50:23", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2350284, container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:24", createdby = "tobiasko", deletable = "true", filechecksum = "0ef80f026054c642b526a8dd6d6fd757", junk = "false", modified = "2023-08-25 09:50:24", modifiedby = "tobiasko", name = "WU292838-20230825-0950-rawDiag.pdf", relativepath = "container_32503/workunit_292838/WU292838-20230825-0950-rawDiag.pdf", size = "186905", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32503/workunit_292838/WU292838-20230825-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32503/workunit_292838/WU292838-20230825-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292838))) The current plot is available as workunit 292838 #rows are 158388 output$download 1... Warning: Removed 219 rows containing non-finite values (`stat_smooth()`). #rows are 158388 output$download 2... ggsave to file /tmp/RtmpOjAjgR/rawDiag-3c40d750299bd8.pdf Warning: Removed 219 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpOjAjgR/rawDiag-3c40d750299bd8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292839, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:44", createdby = "tobiasko", deletable = "true", description = "input files:\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2350275), list(`_classname` = "resource", `_id` = 2350274), list(`_classname` = "resource", `_id` = 2350273), list(`_classname` = "resource", `_id` = 2350272), list(`_classname` = "resource", `_id` = 2350271), list(`_classname` = "resource", `_id` = 2350270)), modified = "2023-08-25 09:50:44", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2350285, container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:50:45", createdby = "tobiasko", deletable = "true", filechecksum = "cc74340e4827074a4f739f7aa383658c", junk = "false", modified = "2023-08-25 09:50:45", modifiedby = "tobiasko", name = "WU292839-20230825-0950-rawDiag.pdf", relativepath = "container_32503/workunit_292839/WU292839-20230825-0950-rawDiag.pdf", size = "129787", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32503/workunit_292839/WU292839-20230825-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32503/workunit_292839/WU292839-20230825-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292839))) The current plot is available as workunit 292839 #rows are 158388 output$download 1... #rows are 158388 output$download 2... ggsave to file /tmp/RtmpOjAjgR/rawDiag-3c40d7125aeecc.pdf generated pdf /tmp/RtmpOjAjgR/rawDiag-3c40d7125aeecc.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292841, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:51:31", createdby = "tobiasko", deletable = "true", description = "input files:\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2350275), list(`_classname` = "resource", `_id` = 2350274), list(`_classname` = "resource", `_id` = 2350273), list(`_classname` = "resource", `_id` = 2350272), list(`_classname` = "resource", `_id` = 2350271), list(`_classname` = "resource", `_id` = 2350270)), modified = "2023-08-25 09:51:31", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2350354, container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:51:32", createdby = "tobiasko", deletable = "true", filechecksum = "a2c0bce33a7e410cedbca67e46d9e6d1", junk = "false", modified = "2023-08-25 09:51:32", modifiedby = "tobiasko", name = "WU292841-20230825-0951-rawDiag.pdf", relativepath = "container_32503/workunit_292841/WU292841-20230825-0951-rawDiag.pdf", size = "688646", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32503/workunit_292841/WU292841-20230825-0951-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32503/workunit_292841/WU292841-20230825-0951-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292841))) The current plot is available as workunit 292841 #rows are 158388 output$download 1... #rows are 158388 output$download 2... ggsave to file /tmp/RtmpOjAjgR/rawDiag-3c40d7296f7105.pdf generated pdf /tmp/RtmpOjAjgR/rawDiag-3c40d7296f7105.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292842, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:52:08", createdby = "tobiasko", deletable = "true", description = "input files:\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_007_S544360_IP_WT_3_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_002_S544358_IP_WT_1_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_006_S544362_IP_GFP_2_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_004_S544359_IP_WT_2_Wild_Type__WT_DDA.raw\np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_003_S544363_IP_GFP_3_Group_1_DDA.raw \np32503/Proteomics/EXPLORIS_2/analytic_20230824/20230824_C32503_008_S544361_IP_GFP_1_Group_1_DDA.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2350275), list(`_classname` = "resource", `_id` = 2350274), list(`_classname` = "resource", `_id` = 2350273), list(`_classname` = "resource", `_id` = 2350272), list(`_classname` = "resource", `_id` = 2350271), list(`_classname` = "resource", `_id` = 2350270)), modified = "2023-08-25 09:52:08", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2350355, container = list(`_classname` = "order", `_id` = 32503), created = "2023-08-25 09:52:09", createdby = "tobiasko", deletable = "true", filechecksum = "1c48b6fba08446a0bd7172363ddc469d", junk = "false", modified = "2023-08-25 09:52:09", modifiedby = "tobiasko", name = "WU292842-20230825-0952-rawDiag.pdf", relativepath = "container_32503/workunit_292842/WU292842-20230825-0952-rawDiag.pdf", size = "8422", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32503/workunit_292842/WU292842-20230825-0952-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32503/workunit_292842/WU292842-20230825-0952-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292842))) The current plot is available as workunit 292842 #rows are 158388 output$download 1... #rows are 158388 output$download 2... #rows are 158388 output$download 2... Execution halted