Listening on http://127.0.0.1:38009 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' ... Warning: The select input "bfabric8-workunit" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 17951 output$tic.basepeak <- renderPlot({ #rows are 17951 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f05552d958c.pdf generated pdf /tmp/RtmpGACDfc/rawDiag-116f05552d958c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296807, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:23", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:45:23", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402565, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:24", createdby = "tobiasko", filechecksum = "37ffecbaba26c923f8ca244840694eab", junk = "false", modified = "2023-11-29 11:45:24", modifiedby = "tobiasko", name = "WU296807-20231129-1145-rawDiag.pdf", relativepath = "container_33528/workunit_296807/WU296807-20231129-1145-rawDiag.pdf", size = "43952", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296807/WU296807-20231129-1145-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296807/WU296807-20231129-1145-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296807))) The current plot is available as workunit 296807 #rows are 17951 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f054cd0b733.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpGACDfc/rawDiag-116f054cd0b733.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296808, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:33", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:45:33", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402566, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:34", createdby = "tobiasko", filechecksum = "fce0ed16c7b29970e5d8e252493b6b3d", junk = "false", modified = "2023-11-29 11:45:34", modifiedby = "tobiasko", name = "WU296808-20231129-1145-rawDiag.pdf", relativepath = "container_33528/workunit_296808/WU296808-20231129-1145-rawDiag.pdf", size = "32736", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296808/WU296808-20231129-1145-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296808/WU296808-20231129-1145-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296808))) The current plot is available as workunit 296808 #rows are 17951 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f053e773552.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpGACDfc/rawDiag-116f053e773552.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296809, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:44", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2402560)), modified = "2023-11-29 11:45:44", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402567, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:45:45", createdby = "tobiasko", filechecksum = "ea3e203517a88d5781d0b2178ef2aae1", junk = "false", modified = "2023-11-29 11:45:45", modifiedby = "tobiasko", name = "WU296809-20231129-1145-rawDiag.pdf", relativepath = "container_33528/workunit_296809/WU296809-20231129-1145-rawDiag.pdf", size = "12154", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296809/WU296809-20231129-1145-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296809/WU296809-20231129-1145-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296809))) The current plot is available as workunit 296809 #rows are 17951 output$download 1... #rows are 17951 output$download 2... Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f0573a60520.pdf Warning: Removed 1 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpGACDfc/rawDiag-116f0573a60520.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296810, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:00", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:46:00", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402568, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:01", createdby = "tobiasko", filechecksum = "44282d97f2322a371b4fe35b4dfa523d", junk = "false", modified = "2023-11-29 11:46:01", modifiedby = "tobiasko", name = "WU296810-20231129-1146-rawDiag.pdf", relativepath = "container_33528/workunit_296810/WU296810-20231129-1146-rawDiag.pdf", size = "29956", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296810/WU296810-20231129-1146-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296810/WU296810-20231129-1146-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296810))) The current plot is available as workunit 296810 #rows are 17951 output$download 1... #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f058a978df.pdf generated pdf /tmp/RtmpGACDfc/rawDiag-116f058a978df.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296811, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:12", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:46:12", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402569, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:13", createdby = "tobiasko", filechecksum = "c138128d0462463b3d0b5c6cb78bfaf7", junk = "false", modified = "2023-11-29 11:46:13", modifiedby = "tobiasko", name = "WU296811-20231129-1146-rawDiag.pdf", relativepath = "container_33528/workunit_296811/WU296811-20231129-1146-rawDiag.pdf", size = "83213", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296811/WU296811-20231129-1146-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296811/WU296811-20231129-1146-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296811))) The current plot is available as workunit 296811 #rows are 17951 output$download 1... #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f057adcde7.pdf generated pdf /tmp/RtmpGACDfc/rawDiag-116f057adcde7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296812, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:22", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:46:22", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402570, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:23", createdby = "tobiasko", filechecksum = "4a7bd6ebcce65cd033911f8d1e17f56e", junk = "false", modified = "2023-11-29 11:46:23", modifiedby = "tobiasko", name = "WU296812-20231129-1146-rawDiag.pdf", relativepath = "container_33528/workunit_296812/WU296812-20231129-1146-rawDiag.pdf", size = "32512", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296812/WU296812-20231129-1146-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296812/WU296812-20231129-1146-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296812))) The current plot is available as workunit 296812 #rows are 17951 output$download 1... #rows are 17951 output$download 2... ggsave to file /tmp/RtmpGACDfc/rawDiag-116f051a6e4329.pdf generated pdf /tmp/RtmpGACDfc/rawDiag-116f051a6e4329.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296813, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:42", createdby = "tobiasko", description = "input files:\np33528/Proteomics/QEXACTIVE_1/analytic_20231128/20231128_C33528_002_S599796_SUMOpep_Group_1_rep.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` = 2402560)), modified = "2023-11-29 11:46:42", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2402571, container = list(`_classname` = "order", `_id` = 33528), created = "2023-11-29 11:46:44", createdby = "tobiasko", filechecksum = "739870f4911d786189a267b462bcb89f", junk = "false", modified = "2023-11-29 11:46:44", modifiedby = "tobiasko", name = "WU296813-20231129-1146-rawDiag.pdf", relativepath = "container_33528/workunit_296813/WU296813-20231129-1146-rawDiag.pdf", size = "6612", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33528/workunit_296813/WU296813-20231129-1146-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33528/workunit_296813/WU296813-20231129-1146-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296813))) The current plot is available as workunit 296813 #rows are 17951 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 17951 output$download 2... DEBUG renderPlot plotQCs #rows are 17951 output$download 2...