Listening on http://127.0.0.1:45105 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 /scratch/cpanse/ 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 78312 output$tic.basepeak <- renderPlot({ #rows are 78312 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 78312 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 78312 output$download 2... ggsave to file /tmp/RtmphZ4FDT/rawDiag-1f49a3386c7cc5.pdf generated pdf /tmp/RtmphZ4FDT/rawDiag-1f49a3386c7cc5.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292721, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:49:58", createdby = "tobiasko", deletable = "true", description = "input files:\np3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.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` = 2347739)), modified = "2023-08-21 09:49:58", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2347907, container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:49:59", createdby = "tobiasko", deletable = "true", filechecksum = "a7fd9bf426c01cad6ca14303b0991706", junk = "false", modified = "2023-08-21 09:49:59", modifiedby = "tobiasko", name = "WU292721-20230821-0949-rawDiag.pdf", relativepath = "container_3000/workunit_292721/WU292721-20230821-0949-rawDiag.pdf", size = "18681", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_3000/workunit_292721/WU292721-20230821-0949-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_3000/workunit_292721/WU292721-20230821-0949-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292721))) The current plot is available as workunit 292721 #rows are 78312 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 78312 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmphZ4FDT/rawDiag-1f49a32c7da667.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmphZ4FDT/rawDiag-1f49a32c7da667.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292722, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:06", createdby = "tobiasko", deletable = "true", description = "input files:\np3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.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` = 2347739)), modified = "2023-08-21 09:50:06", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2347908, container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:07", createdby = "tobiasko", deletable = "true", filechecksum = "c69c5dd515899caeb8e001ae6daafe7e", junk = "false", modified = "2023-08-21 09:50:07", modifiedby = "tobiasko", name = "WU292722-20230821-0950-rawDiag.pdf", relativepath = "container_3000/workunit_292722/WU292722-20230821-0950-rawDiag.pdf", size = "30223", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_3000/workunit_292722/WU292722-20230821-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_3000/workunit_292722/WU292722-20230821-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292722))) The current plot is available as workunit 292722 #rows are 78312 output$download 1... #rows are 78312 output$download 2... ggsave to file /tmp/RtmphZ4FDT/rawDiag-1f49a35f3bd5d6.pdf generated pdf /tmp/RtmphZ4FDT/rawDiag-1f49a35f3bd5d6.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292723, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:20", createdby = "tobiasko", deletable = "true", description = "input files:\np3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.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` = 2347739)), modified = "2023-08-21 09:50:20", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2347909, container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:22", createdby = "tobiasko", deletable = "true", filechecksum = "4aa2fd3328255ba075cf458497491fa3", junk = "false", modified = "2023-08-21 09:50:22", modifiedby = "tobiasko", name = "WU292723-20230821-0950-rawDiag.pdf", relativepath = "container_3000/workunit_292723/WU292723-20230821-0950-rawDiag.pdf", size = "12626", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_3000/workunit_292723/WU292723-20230821-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_3000/workunit_292723/WU292723-20230821-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292723))) The current plot is available as workunit 292723 #rows are 78312 output$download 1... #rows are 78312 output$download 2... ggsave to file /tmp/RtmphZ4FDT/rawDiag-1f49a323340c5b.pdf generated pdf /tmp/RtmphZ4FDT/rawDiag-1f49a323340c5b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292724, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:42", createdby = "tobiasko", deletable = "true", description = "input files:\np3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.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` = 2347739)), modified = "2023-08-21 09:50:42", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2347910, container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:44", createdby = "tobiasko", deletable = "true", filechecksum = "76b51a3151379be8b33e9daddc9233d7", junk = "false", modified = "2023-08-21 09:50:44", modifiedby = "tobiasko", name = "WU292724-20230821-0950-rawDiag.pdf", relativepath = "container_3000/workunit_292724/WU292724-20230821-0950-rawDiag.pdf", size = "2264343", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_3000/workunit_292724/WU292724-20230821-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_3000/workunit_292724/WU292724-20230821-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292724))) The current plot is available as workunit 292724 #rows are 78312 output$download 1... #rows are 78312 output$download 2... ggsave to file /tmp/RtmphZ4FDT/rawDiag-1f49a379d10536.pdf generated pdf /tmp/RtmphZ4FDT/rawDiag-1f49a379d10536.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292725, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:54", createdby = "tobiasko", deletable = "true", description = "input files:\np3000/Proteomics/LUMOS_2/tobiasko_20230818_DIA/20230818_005_autoQC4L.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` = 2347739)), modified = "2023-08-21 09:50:54", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2347911, container = list(`_classname` = "project", `_id` = 3000), created = "2023-08-21 09:50:56", createdby = "tobiasko", deletable = "true", filechecksum = "a824d9b413e8b2fca5f9b73ef4734598", junk = "false", modified = "2023-08-21 09:50:56", modifiedby = "tobiasko", name = "WU292725-20230821-0950-rawDiag.pdf", relativepath = "container_3000/workunit_292725/WU292725-20230821-0950-rawDiag.pdf", size = "68611", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_3000/workunit_292725/WU292725-20230821-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_3000/workunit_292725/WU292725-20230821-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292725))) The current plot is available as workunit 292725 #rows are 78312 output$download 1... #rows are 78312 output$download 2... DEBUG queryMass 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 78312 output$download 2... #rows are 0 /scratch/cpanse/ #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_052_S540824_45_WT_25uM-HbHp1-1_72_D.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 79622 #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... #rows are Warning: Error in if: argument is of length zero 97: renderUI [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#879] 96: func 83: renderFunc 82: output$rawDataStatus 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_052_S540824_45_WT_25uM-HbHp1-1_72_D.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_041_S540800_21_WT_25uM-HbHp1-1_24_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_027_S540794_15_CD163KO_25uM-HbHp1-1_72_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_014_S540782_3_CD163KO_ctrl_0_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_043_S540804_25_WT_25uM-HbHp1-1_72_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_018_S540798_19_WT_ctrl_0_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_038_S540826_47_WT_25uM-HbHp1-1_96_D.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_058_S540805_26_CD163KO_25uM-HbHp1-1_72_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_062_S540825_46_CD163KO_25uM-HbHp1-1_72_D.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_013_S540813_34_CD163KO_25uM-HbHp1-1_72_C.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_020_S540784_5_WT_25uM-HbHp1-1_24_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_053_S540803_24_CD163KO_25uM-HbHp1-1_48_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_063_S540823_44_CD163KO_25uM-HbHp1-1_48_D.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber copied AGC to AGCMode calculated PrescanMode values renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_002a_S540820_41_WT_25uM-HbHp1-1_24_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_030_S540786_7_CD163KO_25uM-HbHp1-1_24_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_010_S540802_23_WT_25uM-HbHp1-1_48_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_035_S540810_31_WT_25uM-HbHp1-1_48_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_048a_S540819_40_CD163KO_ctrl_0_E.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_024_S540788_9_WT_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_060_S540815_36_CD163KO_25uM-HbHp1-1_96_C.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_047_S540799_20_CD163KO_ctrl_0_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_026_S540816_37_WT_ctrl_0_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_009_S540817_38_CD163KO_ctrl_0_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_040_S540787_8_WT_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_019_S540808_29_WT_25uM-HbHp1-1_24_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_005_S540801_22_CD163KO_25uM-HbHp1-1_24_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_057_S540811_32_CD163KO_25uM-HbHp1-1_48_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_032_S540785_6_CD163KO_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_031_S540783_4_WT_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_051_S540818_39_WT_ctrl_0_E.raw qc ... copied AGC to AGCMode calculated PrescanMode values executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_065a_S540809_30_CD163KO_ctrl_0_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_036_S540795_16_WT_25uM-HbHp1-1_96_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_015_S540780_1_WT_25uM-HbHp1-1_0_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_042_S540793_14_CD163KO_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_021_S540791_12_WT_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_003_S540827_48_CD163KO_25uM-HbHp1-1_96_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_007_S540806_27_WT_25uM-HbHp1-1_96_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_016_S540781_2_CD163KO_ctrl_0_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_037_S540807_28_CD163KO_25uM-HbHp1-1_96_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_029_S540792_13_WT_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_054_S540812_33_WT_25uM-HbHp1-1_72_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_049_S540814_35_WT_25uM-HbHp1-1_96_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_004_S540822_43_WT_25uM-HbHp1-1_48_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_025_S540797_18_CD163KO_25uM-HbHp1-1_96_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_059_S540789_10_CD163KO_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_008_S540821_42_CD163KO_25uM-HbHp1-1_24_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_064_S540790_11_CD163KO_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_046_S540796_17_CD163KO_25uM-HbHp1-1_96_A.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 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 missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber copied AGC to AGCMode calculated PrescanMode values 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 3817655 output$tic.basepeak <- renderPlot({ #rows are 3817655 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 1392 rows containing missing values (`geom_line()`). #rows are 3817655 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 3817655 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 1392 rows containing missing values (`geom_line()`). #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 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") 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: '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: '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: '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: '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: '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: '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: '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 3817655 output$download 2... 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: '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: '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: '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: '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: '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: '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: '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") #rows are 3817655 output$download 2... DEBUG renderPlot plotQCs #rows are 3817655 output$download 2... 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: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp #rows are 3817655 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_052_S540824_45_WT_25uM-HbHp1-1_72_D.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_041_S540800_21_WT_25uM-HbHp1-1_24_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_027_S540794_15_CD163KO_25uM-HbHp1-1_72_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_014_S540782_3_CD163KO_ctrl_0_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_043_S540804_25_WT_25uM-HbHp1-1_72_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_018_S540798_19_WT_ctrl_0_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_038_S540826_47_WT_25uM-HbHp1-1_96_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_053_S540803_24_CD163KO_25uM-HbHp1-1_48_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_020_S540784_5_WT_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_058_S540805_26_CD163KO_25uM-HbHp1-1_72_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_013_S540813_34_CD163KO_25uM-HbHp1-1_72_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_035_S540810_31_WT_25uM-HbHp1-1_48_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_048a_S540819_40_CD163KO_ctrl_0_E.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_062_S540825_46_CD163KO_25uM-HbHp1-1_72_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_040_S540787_8_WT_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_009_S540817_38_CD163KO_ctrl_0_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_060_S540815_36_CD163KO_25uM-HbHp1-1_96_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_047_S540799_20_CD163KO_ctrl_0_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_026_S540816_37_WT_ctrl_0_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_024_S540788_9_WT_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_002a_S540820_41_WT_25uM-HbHp1-1_24_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_057_S540811_32_CD163KO_25uM-HbHp1-1_48_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_031_S540783_4_WT_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_019_S540808_29_WT_25uM-HbHp1-1_24_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_030_S540786_7_CD163KO_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_063_S540823_44_CD163KO_25uM-HbHp1-1_48_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_010_S540802_23_WT_25uM-HbHp1-1_48_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_051_S540818_39_WT_ctrl_0_E.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_036_S540795_16_WT_25uM-HbHp1-1_96_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_065a_S540809_30_CD163KO_ctrl_0_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_032_S540785_6_CD163KO_25uM-HbHp1-1_24_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_003_S540827_48_CD163KO_25uM-HbHp1-1_96_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_042_S540793_14_CD163KO_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_021_S540791_12_WT_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_005_S540801_22_CD163KO_25uM-HbHp1-1_24_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_029_S540792_13_WT_25uM-HbHp1-1_72_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_007_S540806_27_WT_25uM-HbHp1-1_96_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_046_S540796_17_CD163KO_25uM-HbHp1-1_96_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_016_S540781_2_CD163KO_ctrl_0_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_015_S540780_1_WT_25uM-HbHp1-1_0_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_064_S540790_11_CD163KO_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_004_S540822_43_WT_25uM-HbHp1-1_48_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_037_S540807_28_CD163KO_25uM-HbHp1-1_96_B.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_059_S540789_10_CD163KO_25uM-HbHp1-1_48_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_049_S540814_35_WT_25uM-HbHp1-1_96_C.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_025_S540797_18_CD163KO_25uM-HbHp1-1_96_A.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_008_S540821_42_CD163KO_25uM-HbHp1-1_24_D.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_054_S540812_33_WT_25uM-HbHp1-1_72_C.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 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 3817655 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 3817655 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 1392 rows containing missing values (`geom_line()`). #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... DEBUG renderPlot plotQCs #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... #rows are 3817655 output$download 2... saving 'login and webservicepassword' ... Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$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//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_052_S540824_45_WT_25uM-HbHp1-1_72_D.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_041_S540800_21_WT_25uM-HbHp1-1_24_B.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_027_S540794_15_CD163KO_25uM-HbHp1-1_72_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_014_S540782_3_CD163KO_ctrl_0_A.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32416/Proteomics/LUMOS_2/analytic_20230803/20230803_C32416_043_S540804_25_WT_25uM-HbHp1-1_72_B.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 398434 output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 145 rows containing missing values (`geom_line()`). #rows are 398434 output$download 2... output$scan.frequency <- renderPlot #rows are 398434 output$download 2... #rows are 398434 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 398434 output$download 2... #rows are 398434 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf Warning: Error in combine_vars: Faceting variables must have at least one value 184: 183: signalCondition 182: signal_abort 181: rlang::abort 180: cli::cli_abort 179: combine_vars 178: compute_layout 177: self$facet$compute_layout 176: setup 175: layout$setup 174: ggplot_build.ggplot 172: print.ggplot 167: func 165: f 164: Reduce 155: do 154: hybrid_chain 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$cycle.load 1: runApp #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 398434 output$download 2... DEBUG renderPlot plotQCs #rows are 398434 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp saving 'login and webservicepassword' ... Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG renderPlot plotQCs #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG renderPlot plotQCs #rows are 398434 output$download 2... DEBUG renderPlot plotQCs #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG renderPlot plotQCs #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 188: stop 187: plyr::rbind.fill 186: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#513] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: rawXICData 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$xic 1: runApp #rows are 398434 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG renderPlot Warning: Error in : All inputs to rbind.fill must be data.frames 172: 171: stop 170: rawXICData 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$download 2... #rows are 398434 output$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") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 188: stop 187: plyr::rbind.fill 186: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#513] 184: .func 181: contextFunc 180: env$runWith 173: ctx$run 172: self$.updateValue 170: rawXICData 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp DEBUG renderPlot Warning: Error in : All inputs to rbind.fill must be data.frames 172: 171: stop 170: rawXICData 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp Warning: Error in : All inputs to rbind.fill must be data.frames 107: 106: stop 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... #rows are 398434 output$download 2... DEBUG renderPlot Warning: Error in : All inputs to rbind.fill must be data.frames 172: 171: stop 170: rawXICData 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#644] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp output$tic.basepeak <- renderPlot({ #rows are 398434 output$download 2... #rows are 398434 output$download 2... Execution halted