Listening on http://127.0.0.1:32817 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 #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//p33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 50883 output$tic.basepeak <- renderPlot({ #rows are 50883 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816370ad2602.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816370ad2602.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297185, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:15:41", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:15:41", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405740, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:15:42", createdby = "tobiasko", filechecksum = "21d53733159d590daaad37d5961d7103", junk = "false", modified = "2023-12-05 11:15:42", modifiedby = "tobiasko", name = "WU297185-20231205-1115-rawDiag.pdf", relativepath = "container_33510/workunit_297185/WU297185-20231205-1115-rawDiag.pdf", size = "77833", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297185/WU297185-20231205-1115-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297185/WU297185-20231205-1115-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297185))) The current plot is available as workunit 297185 #rows are 50883 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816341b29938.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpY3CEeN/rawDiag-28816341b29938.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297186, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:15:55", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:15:55", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405741, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:15:57", createdby = "tobiasko", filechecksum = "af608a53c4acade31b5049b48ccdedb2", junk = "false", modified = "2023-12-05 11:15:57", modifiedby = "tobiasko", name = "WU297186-20231205-1115-rawDiag.pdf", relativepath = "container_33510/workunit_297186/WU297186-20231205-1115-rawDiag.pdf", size = "67570", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297186/WU297186-20231205-1115-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297186/WU297186-20231205-1115-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297186))) The current plot is available as workunit 297186 #rows are 50883 output$download 1... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881632169ea92.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881632169ea92.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297187, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:15", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:16:15", modifiedby = "tobiasko", name = "scan time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405742, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:16", createdby = "tobiasko", filechecksum = "c887ba1cfac226d9f5d25d9015ca479a", junk = "false", modified = "2023-12-05 11:16:16", modifiedby = "tobiasko", name = "WU297187-20231205-1116-rawDiag.pdf", relativepath = "container_33510/workunit_297187/WU297187-20231205-1116-rawDiag.pdf", size = "265802", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297187/WU297187-20231205-1116-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297187/WU297187-20231205-1116-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297187))) The current plot is available as workunit 297187 #rows are 50883 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163780aa696.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpY3CEeN/rawDiag-288163780aa696.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297188, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:29", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:16:29", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405743, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:30", createdby = "tobiasko", filechecksum = "4fc0ddae08f7c1c36f35ca0bb6fcf65d", junk = "false", modified = "2023-12-05 11:16:30", modifiedby = "tobiasko", name = "WU297188-20231205-1116-rawDiag.pdf", relativepath = "container_33510/workunit_297188/WU297188-20231205-1116-rawDiag.pdf", size = "43478", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297188/WU297188-20231205-1116-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297188/WU297188-20231205-1116-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297188))) The current plot is available as workunit 297188 #rows are 50883 output$download 1... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163713c4b49.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163713c4b49.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297189, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:43", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:16:43", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405744, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:44", createdby = "tobiasko", filechecksum = "308c5b3ceac8f2c73cff0cd28522fdd3", junk = "false", modified = "2023-12-05 11:16:44", modifiedby = "tobiasko", name = "WU297189-20231205-1116-rawDiag.pdf", relativepath = "container_33510/workunit_297189/WU297189-20231205-1116-rawDiag.pdf", size = "42386", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297189/WU297189-20231205-1116-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297189/WU297189-20231205-1116-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297189))) The current plot is available as workunit 297189 #rows are 50883 output$download 1... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163a55f0c3.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163a55f0c3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297190, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:53", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:16:53", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405745, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:16:54", createdby = "tobiasko", filechecksum = "b8b8a08cbbd6c244aa592c17e4601a0c", junk = "false", modified = "2023-12-05 11:16:54", modifiedby = "tobiasko", name = "WU297190-20231205-1116-rawDiag.pdf", relativepath = "container_33510/workunit_297190/WU297190-20231205-1116-rawDiag.pdf", size = "185005", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297190/WU297190-20231205-1116-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297190/WU297190-20231205-1116-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297190))) The current plot is available as workunit 297190 #rows are 50883 output$download 1... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881632b7c44d5.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881632b7c44d5.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297191, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:17:09", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:17:09", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405746, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:17:10", createdby = "tobiasko", filechecksum = "14a97e613c1eea7d75fc5edb1adeb727", junk = "false", modified = "2023-12-05 11:17:10", modifiedby = "tobiasko", name = "WU297191-20231205-1117-rawDiag.pdf", relativepath = "container_33510/workunit_297191/WU297191-20231205-1117-rawDiag.pdf", size = "46469", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297191/WU297191-20231205-1117-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297191/WU297191-20231205-1117-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297191))) The current plot is available as workunit 297191 #rows are 50883 output$download 1... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163674757ca.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163674757ca.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297192, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:17:21", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:17:21", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405747, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:17:22", createdby = "tobiasko", filechecksum = "c25033bf48e3c9a23f4abe307d0efa24", junk = "false", modified = "2023-12-05 11:17:22", modifiedby = "tobiasko", name = "WU297192-20231205-1117-rawDiag.pdf", relativepath = "container_33510/workunit_297192/WU297192-20231205-1117-rawDiag.pdf", size = "5860", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297192/WU297192-20231205-1117-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297192/WU297192-20231205-1117-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297192))) The current plot is available as workunit 297192 #rows are 50883 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: `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 50883 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 50883 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 50883 output$download 2... DEBUG renderPlot plotQCs #rows are 50883 output$download 2... #rows are 50883 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816375450627.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816375450627.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297195, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:25:29", createdby = "tobiasko", description = "input files:\np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_003_S599139_SPEN_3_LZ_Group_1.raw \np33510/Proteomics/EXPLORIS_1/analytic_20231130/20231130_C33510_002_S599140_SPEN_3_ctrl_LZ_Group_2.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403937), list(`_classname` = "resource", `_id` = 2403936)), modified = "2023-12-05 11:25:29", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405763, container = list(`_classname` = "order", `_id` = 33510), created = "2023-12-05 11:25:31", createdby = "tobiasko", filechecksum = "c9c66cc52c44a913d0384f62aaade30c", junk = "false", modified = "2023-12-05 11:25:31", modifiedby = "tobiasko", name = "WU297195-20231205-1125-rawDiag.pdf", relativepath = "container_33510/workunit_297195/WU297195-20231205-1125-rawDiag.pdf", size = "16169", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33510/workunit_297195/WU297195-20231205-1125-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33510/workunit_297195/WU297195-20231205-1125-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297195))) The current plot is available as workunit 297195 #rows are 50883 output$download 1... #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({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_004a_S602274_2_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_002_S602273_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_006_S602275_2_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 missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 40998 output$tic.basepeak <- renderPlot({ #rows are 40998 output$download 2... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. output$scan.frequency <- renderPlot Warning: Removed 87 rows containing missing values (`geom_line()`). #rows are 40998 output$download 2... #rows are 40998 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... #rows are 40998 output$download 2... 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") #rows are 40998 output$download 2... DEBUG renderPlot plotQCs #rows are 40998 output$download 2... #rows are 40998 output$download 2... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#423] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#859] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning: Error in : 'data' must be 2-dimensional (e.g. data frame or matrix) 107: stop 106: 104: processWidget 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableInfo 1: runApp DEBUG renderPlot plotQCs #rows are 40998 output$download 2... #rows are 40998 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 40998 output$download 2... #rows are 40998 output$download 2... DEBUG renderPlot plotQCs #rows are 40998 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 40998 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816317e5ea10.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816317e5ea10.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297199, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33566), created = "2023-12-05 12:35:20", createdby = "heinzmann", description = "input files:\np33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_004a_S602274_2_1.raw\np33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_002_S602273_1.raw \np33566/Proteomics/QEXACTIVE_1/analytic_20231129/20231129_C33566_006_S602275_2_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2403676), list(`_classname` = "resource", `_id` = 2403675), list(`_classname` = "resource", `_id` = 2403674)), modified = "2023-12-05 12:35:20", modifiedby = "heinzmann", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405774, container = list(`_classname` = "order", `_id` = 33566), created = "2023-12-05 12:35:21", createdby = "heinzmann", filechecksum = "3d8bcebe394315894bef9e425f6f25ba", junk = "false", modified = "2023-12-05 12:35:21", modifiedby = "heinzmann", name = "WU297199-20231205-1235-rawDiag.pdf", relativepath = "container_33566/workunit_297199/WU297199-20231205-1235-rawDiag.pdf", size = "252661", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33566/workunit_297199/WU297199-20231205-1235-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33566/workunit_297199/WU297199-20231205-1235-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297199))) The current plot is available as workunit 297199 #rows are 40998 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#840] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp #rows are 50883 output$download 2... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#840] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection 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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 452294 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 452294 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816318cc2ab.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816318cc2ab.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297201, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:42:11", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:42:11", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405776, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:42:12", createdby = "tobiasko", filechecksum = "7a97b72d0d221a66a98163c6e382c371", junk = "false", modified = "2023-12-05 12:42:12", modifiedby = "tobiasko", name = "WU297201-20231205-1242-rawDiag.pdf", relativepath = "container_33552/workunit_297201/WU297201-20231205-1242-rawDiag.pdf", size = "488577", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297201/WU297201-20231205-1242-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297201/WU297201-20231205-1242-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297201))) The current plot is available as workunit 297201 #rows are 452294 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881637bd8782d.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpY3CEeN/rawDiag-2881637bd8782d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297202, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:44:51", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:44:51", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405777, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:44:52", createdby = "tobiasko", filechecksum = "3da55766ce7fb63d5b2bf12123e21d79", junk = "false", modified = "2023-12-05 12:44:52", modifiedby = "tobiasko", name = "WU297202-20231205-1244-rawDiag.pdf", relativepath = "container_33552/workunit_297202/WU297202-20231205-1244-rawDiag.pdf", size = "450643", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297202/WU297202-20231205-1244-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297202/WU297202-20231205-1244-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297202))) The current plot is available as workunit 297202 #rows are 452294 output$download 1... #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881635cac9db3.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881635cac9db3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297203, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:47:28", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:47:28", modifiedby = "tobiasko", name = "scan time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405778, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:47:30", createdby = "tobiasko", filechecksum = "55d2afa8621d3c068ba248a889a7a0a7", junk = "false", modified = "2023-12-05 12:47:30", modifiedby = "tobiasko", name = "WU297203-20231205-1247-rawDiag.pdf", relativepath = "container_33552/workunit_297203/WU297203-20231205-1247-rawDiag.pdf", size = "2322504", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297203/WU297203-20231205-1247-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297203/WU297203-20231205-1247-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297203))) The current plot is available as workunit 297203 #rows are 452294 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881634ee8b9cf.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpY3CEeN/rawDiag-2881634ee8b9cf.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297204, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:48:44", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:48:44", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405779, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:48:46", createdby = "tobiasko", filechecksum = "6543bd1e4a88d33e3764c4d3d2494453", junk = "false", modified = "2023-12-05 12:48:46", modifiedby = "tobiasko", name = "WU297204-20231205-1248-rawDiag.pdf", relativepath = "container_33552/workunit_297204/WU297204-20231205-1248-rawDiag.pdf", size = "1913232", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297204/WU297204-20231205-1248-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297204/WU297204-20231205-1248-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297204))) The current plot is available as workunit 297204 #rows are 452294 output$download 1... #rows are 452294 output$download 2... #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163779d43f3.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163779d43f3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297205, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:49:07", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:49:07", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405780, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:49:08", createdby = "tobiasko", filechecksum = "f8609fc780e22ff4e49b6bf4d1091c92", junk = "false", modified = "2023-12-05 12:49:08", modifiedby = "tobiasko", name = "WU297205-20231205-1249-rawDiag.pdf", relativepath = "container_33552/workunit_297205/WU297205-20231205-1249-rawDiag.pdf", size = "250908", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297205/WU297205-20231205-1249-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297205/WU297205-20231205-1249-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297205))) The current plot is available as workunit 297205 #rows are 452294 output$download 1... #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816329f2e5c7.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816329f2e5c7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297206, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:49:47", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:49:47", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405781, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:49:49", createdby = "tobiasko", filechecksum = "f8b4154f8f1b54d53241eac0012fd516", junk = "false", modified = "2023-12-05 12:49:49", modifiedby = "tobiasko", name = "WU297206-20231205-1249-rawDiag.pdf", relativepath = "container_33552/workunit_297206/WU297206-20231205-1249-rawDiag.pdf", size = "2162379", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297206/WU297206-20231205-1249-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297206/WU297206-20231205-1249-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297206))) The current plot is available as workunit 297206 #rows are 452294 output$download 1... #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163669e785e.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163669e785e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297207, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:10", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:50:10", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405782, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:11", createdby = "tobiasko", filechecksum = "9f0609f999d69227819f1fb9b4cc9c9a", junk = "false", modified = "2023-12-05 12:50:11", modifiedby = "tobiasko", name = "WU297207-20231205-1250-rawDiag.pdf", relativepath = "container_33552/workunit_297207/WU297207-20231205-1250-rawDiag.pdf", size = "313196", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297207/WU297207-20231205-1250-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297207/WU297207-20231205-1250-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297207))) The current plot is available as workunit 297207 #rows are 452294 output$download 1... #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881634ec64fca.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881634ec64fca.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297208, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:27", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:50:27", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405783, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:28", createdby = "tobiasko", filechecksum = "5c9427011a6679dc1848dd5873e7665d", junk = "false", modified = "2023-12-05 12:50:28", modifiedby = "tobiasko", name = "WU297208-20231205-1250-rawDiag.pdf", relativepath = "container_33552/workunit_297208/WU297208-20231205-1250-rawDiag.pdf", size = "14020", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297208/WU297208-20231205-1250-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297208/WU297208-20231205-1250-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297208))) The current plot is available as workunit 297208 #rows are 452294 output$download 1... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 452294 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881631e357f01.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881631e357f01.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297209, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:51", createdby = "tobiasko", description = "input files:\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_017_S601084_Control_1_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_008_S601093_bFGF_2_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_004_S601096_C7_3_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_018_S601086_C7_1_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_002_S601088_bFGF_1_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_005_S601089_Control_2_Control.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_006_S601091_C7_2_C7.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw\np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_015_S601098_bFGF_3_bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_016_S601092_C-bFGF_2_C7___bFGF.raw \np33552/Proteomics/EXPLORIS_2/analytic_20231130/20231130_C33552_013_S601094_Control_3_Control.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405411), list(`_classname` = "resource", `_id` = 2405410), list(`_classname` = "resource", `_id` = 2405409), list(`_classname` = "resource", `_id` = 2405408), list(`_classname` = "resource", `_id` = 2405407), list(`_classname` = "resource", `_id` = 2405406), list(`_classname` = "resource", `_id` = 2405405), list(`_classname` = "resource", `_id` = 2405404), list(`_classname` = "resource", `_id` = 2405403), list( `_classname` = "resource", `_id` = 2405402), list(`_classname` = "resource", `_id` = 2405401), list(`_classname` = "resource", `_id` = 2405400), list(`_classname` = "resource", `_id` = 2405399), list(`_classname` = "resource", `_id` = 2405398), list(`_classname` = "resource", `_id` = 2405397)), modified = "2023-12-05 12:50:51", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2405784, container = list(`_classname` = "order", `_id` = 33552), created = "2023-12-05 12:50:52", createdby = "tobiasko", filechecksum = "8e3d02599269106ce6edbc182927c895", junk = "false", modified = "2023-12-05 12:50:52", modifiedby = "tobiasko", name = "WU297209-20231205-1250-rawDiag.pdf", relativepath = "container_33552/workunit_297209/WU297209-20231205-1250-rawDiag.pdf", size = "112580", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33552/workunit_297209/WU297209-20231205-1250-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33552/workunit_297209/WU297209-20231205-1250-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297209))) The current plot is available as workunit 297209 #rows are 452294 output$download 1... DEBUG renderPlot plotQCs #rows are 452294 output$download 1... #rows are 0 /scratch/cpanse/ DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#643] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp DEBUG renderPlot Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#643] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$qc 1: runApp 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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_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 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 102199 output$download 1... output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$tic.basepeak <- renderPlot({ #rows are 102199 output$download 2... output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816310d3acb9.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816310d3acb9.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297229, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 15:58:48", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 15:58:48", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406156, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 15:58:50", createdby = "tobiasko", filechecksum = "aa581f6b6b185f3ebb7b570615aa87ea", junk = "false", modified = "2023-12-05 15:58:50", modifiedby = "tobiasko", name = "WU297229-20231205-1558-rawDiag.pdf", relativepath = "container_33589/workunit_297229/WU297229-20231205-1558-rawDiag.pdf", size = "159792", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297229/WU297229-20231205-1558-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297229/WU297229-20231205-1558-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297229))) The current plot is available as workunit 297229 #rows are 102199 output$download 1... Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. 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. Warning in shinyStore::updateStore(session, "login", isolate(input$login), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "webservicepassword", isolate(input$webservicepassword), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. Warning in shinyStore::updateStore(session, "project", isolate(input$project), : Encryption requested, but the user is not authenticated. The encryption will be MUCH weaker without binding to a logged-in user. output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 102199 output$download 2... #rows are Warning: Error in if: argument is of length zero 97: renderUI [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#878] 96: func 83: renderFunc 82: output$rawDataStatus 1: runApp ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163cac24e6.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpY3CEeN/rawDiag-288163cac24e6.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297230, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 15:59:41", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 15:59:41", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406157, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 15:59:42", createdby = "tobiasko", filechecksum = "86af2723405b3549264a2b62cb29df09", junk = "false", modified = "2023-12-05 15:59:42", modifiedby = "tobiasko", name = "WU297230-20231205-1559-rawDiag.pdf", relativepath = "container_33589/workunit_297230/WU297230-20231205-1559-rawDiag.pdf", size = "145520", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297230/WU297230-20231205-1559-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297230/WU297230-20231205-1559-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297230))) The current plot is available as workunit 297230 #rows are 102199 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 102199 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881636958c299.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpY3CEeN/rawDiag-2881636958c299.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297231, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:00:23", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 16:00:23", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406158, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:00:25", createdby = "tobiasko", filechecksum = "cda1215fc31b47fe6e37086946d69360", junk = "false", modified = "2023-12-05 16:00:25", modifiedby = "tobiasko", name = "WU297231-20231205-1600-rawDiag.pdf", relativepath = "container_33589/workunit_297231/WU297231-20231205-1600-rawDiag.pdf", size = "140295", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297231/WU297231-20231205-1600-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297231/WU297231-20231205-1600-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297231))) The current plot is available as workunit 297231 #rows are 102199 output$download 1... #rows are 102199 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-28816338417c69.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-28816338417c69.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297232, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:00:40", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 16:00:40", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406159, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:00:41", createdby = "tobiasko", filechecksum = "58d830f2daf03c74e2b940edf866a999", junk = "false", modified = "2023-12-05 16:00:41", modifiedby = "tobiasko", name = "WU297232-20231205-1600-rawDiag.pdf", relativepath = "container_33589/workunit_297232/WU297232-20231205-1600-rawDiag.pdf", size = "84505", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297232/WU297232-20231205-1600-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297232/WU297232-20231205-1600-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297232))) The current plot is available as workunit 297232 #rows are 102199 output$download 1... #rows are 102199 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881635619d9e5.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881635619d9e5.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297233, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:01:11", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 16:01:11", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406160, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:01:12", createdby = "tobiasko", filechecksum = "0c1d5e07741ec03c5da2785a3794831b", junk = "false", modified = "2023-12-05 16:01:12", modifiedby = "tobiasko", name = "WU297233-20231205-1601-rawDiag.pdf", relativepath = "container_33589/workunit_297233/WU297233-20231205-1601-rawDiag.pdf", size = "508354", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297233/WU297233-20231205-1601-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297233/WU297233-20231205-1601-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297233))) The current plot is available as workunit 297233 #rows are 102199 output$download 1... #rows are 102199 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-2881635c202794.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-2881635c202794.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297234, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:01:31", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 16:01:31", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406161, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:01:32", createdby = "tobiasko", filechecksum = "ddafef2f0072ed0d1ae650b33e230f78", junk = "false", modified = "2023-12-05 16:01:32", modifiedby = "tobiasko", name = "WU297234-20231205-1601-rawDiag.pdf", relativepath = "container_33589/workunit_297234/WU297234-20231205-1601-rawDiag.pdf", size = "101483", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297234/WU297234-20231205-1601-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297234/WU297234-20231205-1601-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297234))) The current plot is available as workunit 297234 #rows are 102199 output$download 1... #rows are 102199 output$download 2... ggsave to file /tmp/RtmpY3CEeN/rawDiag-288163231b1a83.pdf generated pdf /tmp/RtmpY3CEeN/rawDiag-288163231b1a83.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 297235, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:02:42", createdby = "tobiasko", description = "input files:\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_006_S602863_NPHP3_Replicate1_Group_2.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_008_S602861_CEP290_Replicate1_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_004_S602862_CEP290_Replicate2_Group_1.raw\np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_002_S602865_IgGRabbit_Control_rep.raw \np33589/Proteomics/QEXACTIVE_1/analytic_20231201/20231201_C33589_011_S602864_NPHP3_Replicate2_Group_2.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.25.\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` = 2405660), list(`_classname` = "resource", `_id` = 2405659), list(`_classname` = "resource", `_id` = 2405658), list(`_classname` = "resource", `_id` = 2405657), list(`_classname` = "resource", `_id` = 2405656)), modified = "2023-12-05 16:02:42", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2406162, container = list(`_classname` = "order", `_id` = 33589), created = "2023-12-05 16:02:43", createdby = "tobiasko", filechecksum = "6823488b76ac533510c0a7ecb8a34ae1", junk = "false", modified = "2023-12-05 16:02:43", modifiedby = "tobiasko", name = "WU297235-20231205-1602-rawDiag.pdf", relativepath = "container_33589/workunit_297235/WU297235-20231205-1602-rawDiag.pdf", size = "12017", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33589/workunit_297235/WU297235-20231205-1602-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33589/workunit_297235/WU297235-20231205-1602-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 297235))) The current plot is available as workunit 297235 #rows are 102199 output$download 1... Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") #rows are 102199 output$download 2... DEBUG renderPlot plotQCs #rows are 102199 output$download 2... output$tic.basepeak <- renderPlot({ #rows are 102199 output$download 2... Execution halted