Listening on http://127.0.0.1:37041 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... Warning: The select input "bfabric8-workunit" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 17937 output$tic.basepeak <- renderPlot({ #rows are 17937 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d4522272184.pdf generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d4522272184.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291014, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:19:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:19:27", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325964, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:19:28", createdby = "tobiasko", deletable = "true", filechecksum = "5ce358ecda67c2de892cf5355b49829b", junk = "false", modified = "2023-07-06 16:19:28", modifiedby = "tobiasko", name = "WU291014-20230706-1619-rawDiag.pdf", relativepath = "container_32217/workunit_291014/WU291014-20230706-1619-rawDiag.pdf", size = "55509", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291014/WU291014-20230706-1619-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291014/WU291014-20230706-1619-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291014))) The current plot is available as workunit 291014 #rows are 17937 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 17937 output$download 2... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d451dc025a7.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d451dc025a7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291015, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:19:51", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:19:51", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325965, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:19:52", createdby = "tobiasko", deletable = "true", filechecksum = "2d021c195dc6dfffc1406d4b1a7aaff8", junk = "false", modified = "2023-07-06 16:19:52", modifiedby = "tobiasko", name = "WU291015-20230706-1619-rawDiag.pdf", relativepath = "container_32217/workunit_291015/WU291015-20230706-1619-rawDiag.pdf", size = "31133", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291015/WU291015-20230706-1619-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291015/WU291015-20230706-1619-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291015))) The current plot is available as workunit 291015 #rows are 17937 output$download 1... #rows are 17937 output$download 2... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d454df12508.pdf generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d454df12508.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291016, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:08", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:20:08", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325966, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:09", createdby = "tobiasko", deletable = "true", filechecksum = "254523a5a0e9d9e7fd5f009827c75262", junk = "false", modified = "2023-07-06 16:20:09", modifiedby = "tobiasko", name = "WU291016-20230706-1620-rawDiag.pdf", relativepath = "container_32217/workunit_291016/WU291016-20230706-1620-rawDiag.pdf", size = "33756", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291016/WU291016-20230706-1620-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291016/WU291016-20230706-1620-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291016))) The current plot is available as workunit 291016 #rows are 17937 output$download 1... #rows are 17937 output$download 2... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d4562e670a8.pdf generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d4562e670a8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291017, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:20", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:20:20", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325967, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:22", createdby = "tobiasko", deletable = "true", filechecksum = "38dffd4e5a2e9614c0250e85e8fbd9c9", junk = "false", modified = "2023-07-06 16:20:22", modifiedby = "tobiasko", name = "WU291017-20230706-1620-rawDiag.pdf", relativepath = "container_32217/workunit_291017/WU291017-20230706-1620-rawDiag.pdf", size = "82649", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291017/WU291017-20230706-1620-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291017/WU291017-20230706-1620-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291017))) The current plot is available as workunit 291017 #rows are 17937 output$download 1... #rows are 17937 output$download 2... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d45bbcf537.pdf generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d45bbcf537.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291018, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:40", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:20:40", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325968, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:41", createdby = "tobiasko", deletable = "true", filechecksum = "d0e6b00dcd86869aa52e2bb3de0358af", junk = "false", modified = "2023-07-06 16:20:41", modifiedby = "tobiasko", name = "WU291018-20230706-1620-rawDiag.pdf", relativepath = "container_32217/workunit_291018/WU291018-20230706-1620-rawDiag.pdf", size = "5672", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291018/WU291018-20230706-1620-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291018/WU291018-20230706-1620-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291018))) The current plot is available as workunit 291018 #rows are 17937 output$download 1... DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. #rows are 17937 output$download 2... ggsave to file /tmp/Rtmp7jjX2d/rawDiag-271d45281efd35.pdf generated pdf /tmp/Rtmp7jjX2d/rawDiag-271d45281efd35.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 291019, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:49", createdby = "tobiasko", deletable = "true", description = "input files:\np32217/Proteomics/QEXACTIVE_1/analytic_20230706/20230706_C32217_002_S531714_H6-NAC-PD.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` = 2325963)), modified = "2023-07-06 16:20:49", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2325969, container = list(`_classname` = "order", `_id` = 32217), created = "2023-07-06 16:20:50", createdby = "tobiasko", deletable = "true", filechecksum = "26c64265455515f9b9b532992347370e", junk = "false", modified = "2023-07-06 16:20:50", modifiedby = "tobiasko", name = "WU291019-20230706-1620-rawDiag.pdf", relativepath = "container_32217/workunit_291019/WU291019-20230706-1620-rawDiag.pdf", size = "19876", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32217/workunit_291019/WU291019-20230706-1620-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32217/workunit_291019/WU291019-20230706-1620-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 291019))) The current plot is available as workunit 291019 #rows are 17937 output$download 1... #rows are 17937 output$download 2... Execution halted