Listening on http://127.0.0.1:33411 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ 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//p33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 115703 output$tic.basepeak <- renderPlot({ #rows are 115703 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f261e9167a.pdf generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f261e9167a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296047, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:17", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:36:17", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391741, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:18", createdby = "tobiasko", filechecksum = "f71c6400d6a2ded25fb9154fc456b227", junk = "false", modified = "2023-11-14 10:36:18", modifiedby = "tobiasko", name = "WU296047-20231114-1036-rawDiag.pdf", relativepath = "container_33356/workunit_296047/WU296047-20231114-1036-rawDiag.pdf", size = "80422", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296047/WU296047-20231114-1036-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296047/WU296047-20231114-1036-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296047))) The current plot is available as workunit 296047 #rows are 115703 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 115703 output$download 2... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f22db4e6e.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f22db4e6e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296048, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:31", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:36:31", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391742, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:32", createdby = "tobiasko", filechecksum = "db225c33ee192f7f7271dfbc93154877", junk = "false", modified = "2023-11-14 10:36:32", modifiedby = "tobiasko", name = "WU296048-20231114-1036-rawDiag.pdf", relativepath = "container_33356/workunit_296048/WU296048-20231114-1036-rawDiag.pdf", size = "113072", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296048/WU296048-20231114-1036-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296048/WU296048-20231114-1036-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296048))) The current plot is available as workunit 296048 #rows are 115703 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 115703 output$download 2... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f212b2d003.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f212b2d003.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296049, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:48", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:36:48", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391743, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:50", createdby = "tobiasko", filechecksum = "29640cf8c75d1b3458c70f3d67ce07b1", junk = "false", modified = "2023-11-14 10:36:50", modifiedby = "tobiasko", name = "WU296049-20231114-1036-rawDiag.pdf", relativepath = "container_33356/workunit_296049/WU296049-20231114-1036-rawDiag.pdf", size = "103990", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296049/WU296049-20231114-1036-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296049/WU296049-20231114-1036-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296049))) The current plot is available as workunit 296049 #rows are 115703 output$download 1... Warning: Removed 20 rows containing non-finite values (`stat_smooth()`). #rows are 115703 output$download 2... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f25ce6540f.pdf Warning: Removed 20 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f25ce6540f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296050, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:55", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:36:55", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391744, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:36:57", createdby = "tobiasko", filechecksum = "9744828b0a3fce2b0b58bc13ef236b6e", junk = "false", modified = "2023-11-14 10:36:57", modifiedby = "tobiasko", name = "WU296050-20231114-1036-rawDiag.pdf", relativepath = "container_33356/workunit_296050/WU296050-20231114-1036-rawDiag.pdf", size = "42021", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296050/WU296050-20231114-1036-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296050/WU296050-20231114-1036-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296050))) The current plot is available as workunit 296050 #rows are 115703 output$download 1... #rows are 115703 output$download 2... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f2300cb4f4.pdf generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f2300cb4f4.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296051, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:39:01", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:39:01", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391745, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:39:02", createdby = "tobiasko", filechecksum = "25209631852d160701a61f6c9f51499d", junk = "false", modified = "2023-11-14 10:39:02", modifiedby = "tobiasko", name = "WU296051-20231114-1039-rawDiag.pdf", relativepath = "container_33356/workunit_296051/WU296051-20231114-1039-rawDiag.pdf", size = "426429", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296051/WU296051-20231114-1039-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296051/WU296051-20231114-1039-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296051))) The current plot is available as workunit 296051 #rows are 115703 output$download 1... #rows are 115703 output$download 2... ggsave to file /tmp/RtmpqUTW4N/rawDiag-2df8f2663069cc.pdf generated pdf /tmp/RtmpqUTW4N/rawDiag-2df8f2663069cc.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296052, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:39:10", createdby = "tobiasko", description = "input files:\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_005_S587809_NI_nobiotin_beads_Control_noninfected.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_002_S587806_Ad5_biotin_beads_infected___biotin-azide.raw \np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_004_S587808_NI_biotin_beads_noninfected__biotin-azide.raw\np33356/Proteomics/EXPLORIS_2/analytic_20231113/20231113_C33356_003_S587807_Ad5_nobiotin_beads_Control_infected.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2391740), list(`_classname` = "resource", `_id` = 2391739), list(`_classname` = "resource", `_id` = 2391738), list(`_classname` = "resource", `_id` = 2391737)), modified = "2023-11-14 10:39:10", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2391746, container = list(`_classname` = "order", `_id` = 33356), created = "2023-11-14 10:39:11", createdby = "tobiasko", filechecksum = "0b2741b3c42d6c30d294e29144b5ff53", junk = "false", modified = "2023-11-14 10:39:11", modifiedby = "tobiasko", name = "WU296052-20231114-1039-rawDiag.pdf", relativepath = "container_33356/workunit_296052/WU296052-20231114-1039-rawDiag.pdf", size = "7322", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33356/workunit_296052/WU296052-20231114-1039-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33356/workunit_296052/WU296052-20231114-1039-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296052))) The current plot is available as workunit 296052 #rows are 115703 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `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 115703 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 115703 output$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") #rows are 115703 output$download 2... DEBUG renderPlot plotQCs #rows are 115703 output$download 2... DEBUG renderPlot plotQCs #rows are 115703 output$download 2... #rows are 0 /scratch/cpanse/ saving 'login and webservicepassword' ... output$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({ 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/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_004_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_008_S193756_K-562_N_A_tMS2new.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_007_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_003_S193756_K-562_N_A_DIA15k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_005_S193756_K-562_N_A_tMS2new.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_010_S193756_K-562_N_AtMS2org.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_009_S193756_K-562_N_A_DIA15k.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 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 468440 output$tic.basepeak <- renderPlot({ #rows are 468440 output$download 2... saving 'login and webservicepassword' ... #rows are 468440 output$download 2... #rows are 468440 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 468440 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_008_S193756_K-562_N_A_tMS2new.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_005_S193756_K-562_N_A_tMS2new.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_010_S193756_K-562_N_AtMS2org.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values output$tic.basepeak <- renderPlot({ #rows are 199709 output$download 2... #rows are 199709 output$download 2... #rows are 199709 output$download 2... output$scan.frequency <- renderPlot Warning: Removed 116 rows containing missing values (`geom_line()`). #rows are 199709 output$download 2... #rows are 199709 output$download 2... Warning in max(res$n) : no non-missing arguments to max; returning -Inf #rows are 199709 output$download 2... #rows are 199709 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_002_S193756_K-562_N_A_tMS2org.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_004_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_007_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_010_S193756_K-562_N_AtMS2org.raw qc ... missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values missing column name(s): FTResolution, LMCorrection, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMCorrectionppm to LMCorrection copied AGC to AGCMode calculated PrescanMode values #rows are 201647 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 201647 output$download 2... #rows are 201647 output$download 2... #rows are 201647 output$download 2... #rows are 201647 output$download 2... #rows are 201647 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_004_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_007_S193756_K-562_N_A_DIA30k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_003_S193756_K-562_N_A_DIA15k.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/LUMOS_2/roschi_20231113_DIA_K562/20231113_009_S193756_K-562_N_A_DIA15k.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 #rows are 268731 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 268731 output$download 2... #rows are 268731 output$download 2... DEBUG renderPlot plotQCs #rows are 115703 output$download 2...