Listening on http://127.0.0.1:37553 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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 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 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 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 renamed AGCPSMode to PrescanMode #rows are 216432 output$tic.basepeak <- renderPlot({ #rows are 216432 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c3536f910.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c3536f910.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292347, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:40:31", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:40:31", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344588, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:40:32", createdby = "tobiasko", deletable = "true", filechecksum = "9b6e27f142397ec3823c98373946948d", junk = "false", modified = "2023-08-11 09:40:32", modifiedby = "tobiasko", name = "WU292347-20230811-0940-rawDiag.pdf", relativepath = "container_32266/workunit_292347/WU292347-20230811-0940-rawDiag.pdf", size = "270207", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292347/WU292347-20230811-0940-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292347/WU292347-20230811-0940-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292347))) The current plot is available as workunit 292347 #rows are 216432 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 216432 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c61792f0.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpgffsTo/rawDiag-17188c61792f0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292348, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:01", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:41:01", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344590, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:03", createdby = "tobiasko", deletable = "true", filechecksum = "d21eef039b346679dc9c43bd3904f8e9", junk = "false", modified = "2023-08-11 09:41:03", modifiedby = "tobiasko", name = "WU292348-20230811-0941-rawDiag.pdf", relativepath = "container_32266/workunit_292348/WU292348-20230811-0941-rawDiag.pdf", size = "236306", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292348/WU292348-20230811-0941-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292348/WU292348-20230811-0941-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292348))) The current plot is available as workunit 292348 #rows are 216432 output$download 1... Warning: Removed 50 rows containing non-finite values (`stat_smooth()`). Warning: Removed 9 rows containing missing values (`geom_line()`). #rows are 216432 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c32e8844d.pdf Warning: Removed 50 rows containing non-finite values (`stat_smooth()`). Warning: Removed 9 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpgffsTo/rawDiag-17188c32e8844d.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292349, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:23", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:41:23", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344591, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:24", createdby = "tobiasko", deletable = "true", filechecksum = "4ba9cc6537e5a8c7cbec41afa78fdb27", junk = "false", modified = "2023-08-11 09:41:24", modifiedby = "tobiasko", name = "WU292349-20230811-0941-rawDiag.pdf", relativepath = "container_32266/workunit_292349/WU292349-20230811-0941-rawDiag.pdf", size = "165745", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292349/WU292349-20230811-0941-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292349/WU292349-20230811-0941-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292349))) The current plot is available as workunit 292349 #rows are 216432 output$download 1... #rows are 216432 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c3a930973.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c3a930973.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292350, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:49", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:41:49", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344593, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:41:51", createdby = "tobiasko", deletable = "true", filechecksum = "52aaf38b574a59876eb59e3f6c57f537", junk = "false", modified = "2023-08-11 09:41:51", modifiedby = "tobiasko", name = "WU292350-20230811-0941-rawDiag.pdf", relativepath = "container_32266/workunit_292350/WU292350-20230811-0941-rawDiag.pdf", size = "949354", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292350/WU292350-20230811-0941-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292350/WU292350-20230811-0941-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292350))) The current plot is available as workunit 292350 #rows are 216432 output$download 1... #rows are 216432 output$download 2... #rows are 216432 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c4f9254b0.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c4f9254b0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292352, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:42:14", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:42:14", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344595, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:42:15", createdby = "tobiasko", deletable = "true", filechecksum = "077641d0bef5ef2b5f4df5bca0cdbc68", junk = "false", modified = "2023-08-11 09:42:15", modifiedby = "tobiasko", name = "WU292352-20230811-0942-rawDiag.pdf", relativepath = "container_32266/workunit_292352/WU292352-20230811-0942-rawDiag.pdf", size = "9637", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292352/WU292352-20230811-0942-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292352/WU292352-20230811-0942-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292352))) The current plot is available as workunit 292352 #rows are 216432 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: '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: `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 216432 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c659607f3.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c659607f3.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292353, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:42:31", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230809/20230809_C32266_002_S534380_GFP_wtS_1_control_wt_beads.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` = 2344561), list(`_classname` = "resource", `_id` = 2344560), list(`_classname` = "resource", `_id` = 2344559), list(`_classname` = "resource", `_id` = 2344558), list(`_classname` = "resource", `_id` = 2344557), list(`_classname` = "resource", `_id` = 2344556), list(`_classname` = "resource", `_id` = 2344555), list(`_classname` = "resource", `_id` = 2344554)), modified = "2023-08-11 09:42:31", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344597, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:42:32", createdby = "tobiasko", deletable = "true", filechecksum = "2234f81087790622aef0834766a72826", junk = "false", modified = "2023-08-11 09:42:32", modifiedby = "tobiasko", name = "WU292353-20230811-0942-rawDiag.pdf", relativepath = "container_32266/workunit_292353/WU292353-20230811-0942-rawDiag.pdf", size = "69771", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292353/WU292353-20230811-0942-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292353/WU292353-20230811-0942-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292353))) The current plot is available as workunit 292353 #rows are 216432 output$download 1... Warning: Error in if: argument is of length zero 168: renderPlot [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#841] 166: func 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$xic 1: runApp #rows are 216432 output$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#841] 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//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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 #rows are 695485 output$download 2... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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 output$tic.basepeak <- renderPlot({ #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c3ad2dd93.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c3ad2dd93.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292354, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:46:15", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:46:15", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344603, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:46:16", createdby = "tobiasko", deletable = "true", filechecksum = "4e58cbc7289fcf42959d5d9072e69e47", junk = "false", modified = "2023-08-11 09:46:16", modifiedby = "tobiasko", name = "WU292354-20230811-0946-rawDiag.pdf", relativepath = "container_32266/workunit_292354/WU292354-20230811-0946-rawDiag.pdf", size = "120707", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292354/WU292354-20230811-0946-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292354/WU292354-20230811-0946-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292354))) The current plot is available as workunit 292354 #rows are 695485 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c5c38fdfc.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpgffsTo/rawDiag-17188c5c38fdfc.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292356, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:46:36", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:46:36", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344606, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:46:37", createdby = "tobiasko", deletable = "true", filechecksum = "9cf5f976cfc9fd96b10f266714ccf931", junk = "false", modified = "2023-08-11 09:46:37", modifiedby = "tobiasko", name = "WU292356-20230811-0946-rawDiag.pdf", relativepath = "container_32266/workunit_292356/WU292356-20230811-0946-rawDiag.pdf", size = "211851", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292356/WU292356-20230811-0946-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292356/WU292356-20230811-0946-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292356))) The current plot is available as workunit 292356 #rows are 695485 output$download 1... output$tic.basepeak <- renderPlot({ #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c6e10a75e.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c6e10a75e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292357, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:47:59", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:47:59", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344608, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:48:00", createdby = "tobiasko", deletable = "true", filechecksum = "a26b6e5e5fc473a11b1487da92c439ff", junk = "false", modified = "2023-08-11 09:48:00", modifiedby = "tobiasko", name = "WU292357-20230811-0947-rawDiag.pdf", relativepath = "container_32266/workunit_292357/WU292357-20230811-0947-rawDiag.pdf", size = "120707", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292357/WU292357-20230811-0947-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292357/WU292357-20230811-0947-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292357))) The current plot is available as workunit 292357 #rows are 695485 output$download 1... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c1e26c735.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpgffsTo/rawDiag-17188c1e26c735.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292358, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:48:12", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:48:12", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344610, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:48:13", createdby = "tobiasko", deletable = "true", filechecksum = "7771e8cb89426d15da552cbd49ab1c6b", junk = "false", modified = "2023-08-11 09:48:13", modifiedby = "tobiasko", name = "WU292358-20230811-0948-rawDiag.pdf", relativepath = "container_32266/workunit_292358/WU292358-20230811-0948-rawDiag.pdf", size = "211851", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292358/WU292358-20230811-0948-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292358/WU292358-20230811-0948-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292358))) The current plot is available as workunit 292358 #rows are 695485 output$download 1... Warning: Removed 48 rows containing non-finite values (`stat_smooth()`). Warning: Removed 10 rows containing missing values (`geom_line()`). #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c1fdae237.pdf Warning: Removed 48 rows containing non-finite values (`stat_smooth()`). Warning: Removed 10 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpgffsTo/rawDiag-17188c1fdae237.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292359, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:48:29", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:48:29", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344611, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:48:30", createdby = "tobiasko", deletable = "true", filechecksum = "55aa0f73ed37d3ce896aea84c7f3d7d0", junk = "false", modified = "2023-08-11 09:48:30", modifiedby = "tobiasko", name = "WU292359-20230811-0948-rawDiag.pdf", relativepath = "container_32266/workunit_292359/WU292359-20230811-0948-rawDiag.pdf", size = "67274", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292359/WU292359-20230811-0948-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292359/WU292359-20230811-0948-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292359))) The current plot is available as workunit 292359 #rows are 695485 output$download 1... #rows are 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188cb9b9c57.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188cb9b9c57.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292360, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:49:39", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:49:39", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344613, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:49:40", createdby = "tobiasko", deletable = "true", filechecksum = "e3736fb04ca7f219792c64d539ee9958", junk = "false", modified = "2023-08-11 09:49:40", modifiedby = "tobiasko", name = "WU292360-20230811-0949-rawDiag.pdf", relativepath = "container_32266/workunit_292360/WU292360-20230811-0949-rawDiag.pdf", size = "1216525", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292360/WU292360-20230811-0949-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292360/WU292360-20230811-0949-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292360))) The current plot is available as workunit 292360 #rows are 695485 output$download 1... #rows are 695485 output$download 2... #rows are 695485 output$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: '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 695485 output$download 2... ggsave to file /tmp/RtmpgffsTo/rawDiag-17188c1c1af89f.pdf generated pdf /tmp/RtmpgffsTo/rawDiag-17188c1c1af89f.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 292362, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:50:28", createdby = "tobiasko", deletable = "true", description = "input files:\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_002_S534380_GFP_wtS_1_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_007_S534382_TRIM28_wtS_1_TRIM28_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_008_S534381_GFP_prS_1_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_009_S535137_GFP_wtS_2_control_wt_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_004_S535140_TRIM28_prS_2_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_010_S535138_GFP_prS_2_control_protease_resistant_beads.raw \np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_003_S534383_TRIM28_prS_1_TRIM28_protease_resistant_beads.raw\np32266/Proteomics/EXPLORIS_2/analytic_20230810_dia/20230810_C32266_005_S535139_TRIM28_wtS_2_TRIM28_wt_beads.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` = 2344551), list(`_classname` = "resource", `_id` = 2344550), list(`_classname` = "resource", `_id` = 2344549), list(`_classname` = "resource", `_id` = 2344548), list(`_classname` = "resource", `_id` = 2344547), list(`_classname` = "resource", `_id` = 2344546), list(`_classname` = "resource", `_id` = 2344545), list(`_classname` = "resource", `_id` = 2344544)), modified = "2023-08-11 09:50:28", modifiedby = "tobiasko", name = "XIC plot", status = "AVAILABLE", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2344616, container = list(`_classname` = "order", `_id` = 32266), created = "2023-08-11 09:50:29", createdby = "tobiasko", deletable = "true", filechecksum = "66003927421cb1d79113dfdaf492e391", junk = "false", modified = "2023-08-11 09:50:29", modifiedby = "tobiasko", name = "WU292362-20230811-0950-rawDiag.pdf", relativepath = "container_32266/workunit_292362/WU292362-20230811-0950-rawDiag.pdf", size = "56864", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32266/workunit_292362/WU292362-20230811-0950-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32266/workunit_292362/WU292362-20230811-0950-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 292362))) The current plot is available as workunit 292362 #rows are 695485 output$download 1... #rows are 695485 output$download 2... #rows are 695485 output$download 2... #rows are 695485 output$download 2... Execution halted