Listening on http://127.0.0.1:36837 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.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 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 LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode renamed AGCPSMode to PrescanMode 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 148477 output$tic.basepeak <- renderPlot({ #rows are 148477 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f928d34b.pdf generated pdf /tmp/RtmprkYF92/rawDiag-21470f928d34b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290216, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:19:39", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:19:39", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315583, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:19:40", createdby = "tobiasko", deletable = "true", filechecksum = "3350a5a48e26e1b28e74e00ac3fa8061", junk = "false", modified = "2023-06-19 10:19:40", modifiedby = "tobiasko", name = "WU290216-20230619-1019-rawDiag.pdf", relativepath = "container_32024/workunit_290216/WU290216-20230619-1019-rawDiag.pdf", size = "245197", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290216/WU290216-20230619-1019-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290216/WU290216-20230619-1019-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290216))) The current plot is available as workunit 290216 #rows are 148477 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 148477 output$download 2... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f2be78fa0.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmprkYF92/rawDiag-21470f2be78fa0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290217, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:20:01", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:20:01", modifiedby = "tobiasko", name = "scan frequency plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315596, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:20:03", createdby = "tobiasko", deletable = "true", filechecksum = "db71ba1ef267fa55db620f116caf0808", junk = "false", modified = "2023-06-19 10:20:03", modifiedby = "tobiasko", name = "WU290217-20230619-1020-rawDiag.pdf", relativepath = "container_32024/workunit_290217/WU290217-20230619-1020-rawDiag.pdf", size = "186373", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290217/WU290217-20230619-1020-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290217/WU290217-20230619-1020-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290217))) The current plot is available as workunit 290217 #rows are 148477 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 148477 output$download 2... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f2797a8db.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmprkYF92/rawDiag-21470f2797a8db.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290218, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:20:35", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:20:35", modifiedby = "tobiasko", name = "cycle load plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315623, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:20:45", createdby = "tobiasko", deletable = "true", filechecksum = "4b920e067b8aa84bad5c3e93ee6cbb44", junk = "false", modified = "2023-06-19 10:20:45", modifiedby = "tobiasko", name = "WU290218-20230619-1020-rawDiag.pdf", relativepath = "container_32024/workunit_290218/WU290218-20230619-1020-rawDiag.pdf", size = "269861", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290218/WU290218-20230619-1020-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290218/WU290218-20230619-1020-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290218))) The current plot is available as workunit 290218 #rows are 148477 output$download 1... #rows are 148477 output$download 2... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f21313aa6.pdf generated pdf /tmp/RtmprkYF92/rawDiag-21470f21313aa6.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290219, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:20:58", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:20:58", modifiedby = "tobiasko", name = "lock mass correction plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315636, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:21:00", createdby = "tobiasko", deletable = "true", filechecksum = "2ce0333ef6f226a55d1d23318cc9fc30", junk = "false", modified = "2023-06-19 10:21:00", modifiedby = "tobiasko", name = "WU290219-20230619-1020-rawDiag.pdf", relativepath = "container_32024/workunit_290219/WU290219-20230619-1020-rawDiag.pdf", size = "137628", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290219/WU290219-20230619-1020-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290219/WU290219-20230619-1020-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290219))) The current plot is available as workunit 290219 #rows are 148477 output$download 1... #rows are 148477 output$download 2... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f4571940d.pdf generated pdf /tmp/RtmprkYF92/rawDiag-21470f4571940d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290220, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:21:27", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:21:27", modifiedby = "tobiasko", name = "injection time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315659, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:21:28", createdby = "tobiasko", deletable = "true", filechecksum = "1c61ec94fc19ef91ad2efabf7ea06944", junk = "false", modified = "2023-06-19 10:21:28", modifiedby = "tobiasko", name = "WU290220-20230619-1021-rawDiag.pdf", relativepath = "container_32024/workunit_290220/WU290220-20230619-1021-rawDiag.pdf", size = "594441", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290220/WU290220-20230619-1021-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290220/WU290220-20230619-1021-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290220))) The current plot is available as workunit 290220 #rows are 148477 output$download 1... #rows are 148477 output$download 2... ggsave to file /tmp/RtmprkYF92/rawDiag-21470f1cc7fb4d.pdf generated pdf /tmp/RtmprkYF92/rawDiag-21470f1cc7fb4d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290221, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:21:38", createdby = "tobiasko", deletable = "true", description = "input files:\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_005_S522421_650_MatK_C_2_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_009_S522423_659_MatK_1_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_004_S522424_659_MatK_2_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_008_S522425_659_MatK_3_C-.raw \np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_002_S522420_650_MatK_C_1_C_.raw\np32024/Proteomics/EXPLORIS_2/analytic_20230616/20230616_C32024_003_S522422_650_MatK_C_3_C_.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.22.\nSystem information: Linux, 5.10.0-21-amd64, #1 SMP Debian 5.10.162-1 (2023-01-21), fgcz-c-072, x86_64, unknown, www-data, www-data\n\nTo help us funding further development, please cite:\n(bfabricSiny) PMID: 36073980 DOI: 10.1515/jib-2022-0031", exportable = "false", inputresource = list(list(`_classname` = "resource", `_id` = 2315229), list(`_classname` = "resource", `_id` = 2315228), list(`_classname` = "resource", `_id` = 2315227), list(`_classname` = "resource", `_id` = 2315226), list(`_classname` = "resource", `_id` = 2315225), list(`_classname` = "resource", `_id` = 2315224)), modified = "2023-06-19 10:21:38", modifiedby = "tobiasko", name = "charge state plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2315667, container = list(`_classname` = "order", `_id` = 32024), created = "2023-06-19 10:21:39", createdby = "tobiasko", deletable = "true", filechecksum = "dee5c7282716703ceb2c131a911693ec", junk = "false", modified = "2023-06-19 10:21:39", modifiedby = "tobiasko", name = "WU290221-20230619-1021-rawDiag.pdf", relativepath = "container_32024/workunit_290221/WU290221-20230619-1021-rawDiag.pdf", size = "8666", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32024/workunit_290221/WU290221-20230619-1021-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32024/workunit_290221/WU290221-20230619-1021-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290221))) The current plot is available as workunit 290221 #rows are 148477 output$download 1... DEBUG renderPlot DEBUG queryMass Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") Warning: 'readXICs' is deprecated. Use 'rawrr::readChromatogram' instead. See help("Deprecated") 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") plotQCs #rows are 148477 output$download 1... Execution halted