Listening on http://127.0.0.1:33187 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 36952 output$tic.basepeak <- renderPlot({ #rows are 36952 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a294921459b.pdf generated pdf /tmp/RtmpP8S5IU/rawDiag-182a294921459b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290936, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:24:20", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:24:20", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325479, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:24:22", createdby = "tobiasko", deletable = "true", filechecksum = "335e550c43b2dd746c825ead92e07db6", junk = "false", modified = "2023-07-05 12:24:22", modifiedby = "tobiasko", name = "WU290936-20230705-1224-rawDiag.pdf", relativepath = "container_32211/workunit_290936/WU290936-20230705-1224-rawDiag.pdf", size = "110379", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290936/WU290936-20230705-1224-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290936/WU290936-20230705-1224-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290936))) The current plot is available as workunit 290936 #rows are 36952 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 36952 output$download 2... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a2925c31e82.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpP8S5IU/rawDiag-182a2925c31e82.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290937, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:24:40", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:24:40", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325480, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:24:42", createdby = "tobiasko", deletable = "true", filechecksum = "fd970c325ee30208462d0aa31fea3650", junk = "false", modified = "2023-07-05 12:24:42", modifiedby = "tobiasko", name = "WU290937-20230705-1224-rawDiag.pdf", relativepath = "container_32211/workunit_290937/WU290937-20230705-1224-rawDiag.pdf", size = "57258", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290937/WU290937-20230705-1224-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290937/WU290937-20230705-1224-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290937))) The current plot is available as workunit 290937 #rows are 36952 output$download 1... #rows are 36952 output$download 2... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a29a6676e4.pdf generated pdf /tmp/RtmpP8S5IU/rawDiag-182a29a6676e4.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290938, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:24", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:25:24", modifiedby = "tobiasko", name = "scan time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325481, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:25", createdby = "tobiasko", deletable = "true", filechecksum = "4b88f2047ca04b3c952004d8fcecebce", junk = "false", modified = "2023-07-05 12:25:25", modifiedby = "tobiasko", name = "WU290938-20230705-1225-rawDiag.pdf", relativepath = "container_32211/workunit_290938/WU290938-20230705-1225-rawDiag.pdf", size = "178954", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290938/WU290938-20230705-1225-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290938/WU290938-20230705-1225-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290938))) The current plot is available as workunit 290938 #rows are 36952 output$download 1... #rows are 36952 output$download 2... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a2941ecf989.pdf generated pdf /tmp/RtmpP8S5IU/rawDiag-182a2941ecf989.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290939, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:37", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:25:37", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325482, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:38", createdby = "tobiasko", deletable = "true", filechecksum = "cc664201529883feee11ea5bd267e2b2", junk = "false", modified = "2023-07-05 12:25:38", modifiedby = "tobiasko", name = "WU290939-20230705-1225-rawDiag.pdf", relativepath = "container_32211/workunit_290939/WU290939-20230705-1225-rawDiag.pdf", size = "59098", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290939/WU290939-20230705-1225-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290939/WU290939-20230705-1225-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290939))) The current plot is available as workunit 290939 #rows are 36952 output$download 1... #rows are 36952 output$download 2... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a297ffdeb8c.pdf generated pdf /tmp/RtmpP8S5IU/rawDiag-182a297ffdeb8c.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290940, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:25:58", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325483, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:25:59", createdby = "tobiasko", deletable = "true", filechecksum = "c1dc2313de7c07eb2da7ec9edc675951", junk = "false", modified = "2023-07-05 12:25:59", modifiedby = "tobiasko", name = "WU290940-20230705-1225-rawDiag.pdf", relativepath = "container_32211/workunit_290940/WU290940-20230705-1225-rawDiag.pdf", size = "194239", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290940/WU290940-20230705-1225-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290940/WU290940-20230705-1225-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290940))) The current plot is available as workunit 290940 #rows are 36952 output$download 1... #rows are 36952 output$download 2... ggsave to file /tmp/RtmpP8S5IU/rawDiag-182a295ade3dd1.pdf generated pdf /tmp/RtmpP8S5IU/rawDiag-182a295ade3dd1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290941, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:26:29", createdby = "tobiasko", deletable = "true", description = "input files:\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_004_S530799_CFTRSLC26A6PDZ1Coexpressed_Group_2.raw\np32211/Proteomics/QEXACTIVE_1/analytic_20230704/20230704_C32211_002_S530798_SLC26A6-PDZ1Alone_Group_1.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` = 2325476), list(`_classname` = "resource", `_id` = 2325475)), modified = "2023-07-05 12:26:29", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325484, container = list(`_classname` = "order", `_id` = 32211), created = "2023-07-05 12:26:30", createdby = "tobiasko", deletable = "true", filechecksum = "15139db116e0b70d5db6601e520d461b", junk = "false", modified = "2023-07-05 12:26:31", modifiedby = "tobiasko", name = "WU290941-20230705-1226-rawDiag.pdf", relativepath = "container_32211/workunit_290941/WU290941-20230705-1226-rawDiag.pdf", size = "6939", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32211/workunit_290941/WU290941-20230705-1226-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32211/workunit_290941/WU290941-20230705-1226-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290941))) The current plot is available as workunit 290941 #rows are 36952 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") plotQCs #rows are 36952 output$download 1... 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 36952 output$download 2... DEBUG renderPlot plotQCs #rows are 36952 output$download 2... Execution halted