Listening on http://127.0.0.1:45277 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//p33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 79636 output$tic.basepeak <- renderPlot({ #rows are 79636 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce45e93b65.pdf generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce45e93b65.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296466, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:55:34", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:55:34", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398237, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:55:35", createdby = "tobiasko", filechecksum = "2343fef109601fd95336f756102d32f0", junk = "false", modified = "2023-11-23 09:55:35", modifiedby = "tobiasko", name = "WU296466-20231123-0955-rawDiag.pdf", relativepath = "container_33434/workunit_296466/WU296466-20231123-0955-rawDiag.pdf", size = "130565", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296466/WU296466-20231123-0955-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296466/WU296466-20231123-0955-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296466))) The current plot is available as workunit 296466 #rows are 79636 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 79636 output$download 2... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce4518e20cf.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce4518e20cf.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296467, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:55:51", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:55:51", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398238, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:55:52", createdby = "tobiasko", filechecksum = "fed478c5964e934d134dbf4d9a85edea", junk = "false", modified = "2023-11-23 09:55:52", modifiedby = "tobiasko", name = "WU296467-20231123-0955-rawDiag.pdf", relativepath = "container_33434/workunit_296467/WU296467-20231123-0955-rawDiag.pdf", size = "115652", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296467/WU296467-20231123-0955-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296467/WU296467-20231123-0955-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296467))) The current plot is available as workunit 296467 #rows are 79636 output$download 1... #rows are 79636 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 79636 output$download 2... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce433f4c413.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce433f4c413.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296468, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:56:41", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:56:41", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398239, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:56:43", createdby = "tobiasko", filechecksum = "b2a0885d3de28f4ec378110653fc8cf8", junk = "false", modified = "2023-11-23 09:56:43", modifiedby = "tobiasko", name = "WU296468-20231123-0956-rawDiag.pdf", relativepath = "container_33434/workunit_296468/WU296468-20231123-0956-rawDiag.pdf", size = "103423", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296468/WU296468-20231123-0956-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296468/WU296468-20231123-0956-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296468))) The current plot is available as workunit 296468 #rows are 79636 output$download 1... Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). #rows are 79636 output$download 2... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce4632ab846.pdf Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce4632ab846.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296469, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:56:56", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:56:56", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398240, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:56:57", createdby = "tobiasko", filechecksum = "b7358713370639f5cbc8bebef1f6f853", junk = "false", modified = "2023-11-23 09:56:57", modifiedby = "tobiasko", name = "WU296469-20231123-0956-rawDiag.pdf", relativepath = "container_33434/workunit_296469/WU296469-20231123-0956-rawDiag.pdf", size = "77014", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296469/WU296469-20231123-0956-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296469/WU296469-20231123-0956-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296469))) The current plot is available as workunit 296469 #rows are 79636 output$download 1... #rows are 79636 output$download 2... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce47c4f51e4.pdf generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce47c4f51e4.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296470, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:57:16", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:57:16", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398241, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:57:17", createdby = "tobiasko", filechecksum = "29d27c1d328f1a7708a0e047afa1f210", junk = "false", modified = "2023-11-23 09:57:17", modifiedby = "tobiasko", name = "WU296470-20231123-0957-rawDiag.pdf", relativepath = "container_33434/workunit_296470/WU296470-20231123-0957-rawDiag.pdf", size = "323076", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296470/WU296470-20231123-0957-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296470/WU296470-20231123-0957-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296470))) The current plot is available as workunit 296470 #rows are 79636 output$download 1... #rows are 79636 output$download 2... #rows are 79636 output$download 2... #rows are 79636 output$download 2... ggsave to file /tmp/RtmpmYIrnL/rawDiag-2fdce41159f2f1.pdf generated pdf /tmp/RtmpmYIrnL/rawDiag-2fdce41159f2f1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296471, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:58:48", createdby = "tobiasko", description = "input files:\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_002_S594438_297_1_IP_IgG_CTRL_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_003_S594440_297_2_IP_IgG_FGF7_IgG_Control.raw \np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_004_S594437_297_1_IP_STAT2_CTRL_IP_experiment.raw\np33434/Proteomics/QEXACTIVE_1/analytic_20231122/20231122_C33434_005_S594439_297_2_IP_STAT2_FGF7_IP_experiment.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` = 2398188), list(`_classname` = "resource", `_id` = 2398187), list(`_classname` = "resource", `_id` = 2398186), list(`_classname` = "resource", `_id` = 2398185)), modified = "2023-11-23 09:58:48", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2398242, container = list(`_classname` = "order", `_id` = 33434), created = "2023-11-23 09:58:49", createdby = "tobiasko", filechecksum = "978079fa5294a26cf4456c0e03da45f7", junk = "false", modified = "2023-11-23 09:58:49", modifiedby = "tobiasko", name = "WU296471-20231123-0958-rawDiag.pdf", relativepath = "container_33434/workunit_296471/WU296471-20231123-0958-rawDiag.pdf", size = "10209", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33434/workunit_296471/WU296471-20231123-0958-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33434/workunit_296471/WU296471-20231123-0958-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296471))) The current plot is available as workunit 296471 #rows are 79636 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 79636 output$download 2... DEBUG renderPlot plotQCs #rows are 79636 output$download 2... Execution halted