Listening on http://127.0.0.1:44247 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' ... Warning: The select input "bfabric8-workunit" contains a large number of options; consider using server-side selectize for massively improved performance. See the Details section of the ?selectizeInput help topic. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.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 missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed AGCPSMode to PrescanMode 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 117545 output$tic.basepeak <- renderPlot({ #rows are 117545 output$download 2... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.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 missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode output$tic.basepeak <- renderPlot({ #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c642d62e0.pdf generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c642d62e0.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296552, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:07:30", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:07:30", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399432, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:07:31", createdby = "tobiasko", filechecksum = "0955cfbfc1507c876af1639b278aedaa", junk = "false", modified = "2023-11-24 10:07:31", modifiedby = "tobiasko", name = "WU296552-20231124-1007-rawDiag.pdf", relativepath = "container_33494/workunit_296552/WU296552-20231124-1007-rawDiag.pdf", size = "182400", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296552/WU296552-20231124-1007-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296552/WU296552-20231124-1007-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296552))) The current plot is available as workunit 296552 #rows are 117545 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c51d36b96.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c51d36b96.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296553, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:07:45", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:07:45", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399433, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:07:46", createdby = "tobiasko", filechecksum = "1bfb428ac92d01306fb2b74d09337838", junk = "false", modified = "2023-11-24 10:07:46", modifiedby = "tobiasko", name = "WU296553-20231124-1007-rawDiag.pdf", relativepath = "container_33494/workunit_296553/WU296553-20231124-1007-rawDiag.pdf", size = "169020", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296553/WU296553-20231124-1007-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296553/WU296553-20231124-1007-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296553))) The current plot is available as workunit 296553 #rows are 117545 output$download 1... `geom_smooth()` using formula = 'y ~ x' #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61cc6e1391.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61cc6e1391.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296554, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:07:59", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:07:59", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399434, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:08:00", createdby = "tobiasko", filechecksum = "95d13bbf74f88e4eb8188ec18905c585", junk = "false", modified = "2023-11-24 10:08:00", modifiedby = "tobiasko", name = "WU296554-20231124-1007-rawDiag.pdf", relativepath = "container_33494/workunit_296554/WU296554-20231124-1007-rawDiag.pdf", size = "168710", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296554/WU296554-20231124-1007-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296554/WU296554-20231124-1007-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296554))) The current plot is available as workunit 296554 #rows are 117545 output$download 1... Warning: Removed 68 rows containing non-finite values (`stat_smooth()`). #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c11b3f9db.pdf Warning: Removed 68 rows containing non-finite values (`stat_smooth()`). generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c11b3f9db.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296555, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:08:36", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:08:36", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399435, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:08:38", createdby = "tobiasko", filechecksum = "a33aa03529bbfaff09da4c1120ace502", junk = "false", modified = "2023-11-24 10:08:38", modifiedby = "tobiasko", name = "WU296555-20231124-1008-rawDiag.pdf", relativepath = "container_33494/workunit_296555/WU296555-20231124-1008-rawDiag.pdf", size = "113555", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296555/WU296555-20231124-1008-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296555/WU296555-20231124-1008-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296555))) The current plot is available as workunit 296555 #rows are 117545 output$download 1... #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c555ed7d6.pdf generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c555ed7d6.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296556, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:09:18", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:09:18", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399436, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:09:19", createdby = "tobiasko", filechecksum = "2bb9716ec4904977cdfa78961460f6c5", junk = "false", modified = "2023-11-24 10:09:19", modifiedby = "tobiasko", name = "WU296556-20231124-1009-rawDiag.pdf", relativepath = "container_33494/workunit_296556/WU296556-20231124-1009-rawDiag.pdf", size = "563242", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296556/WU296556-20231124-1009-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296556/WU296556-20231124-1009-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296556))) The current plot is available as workunit 296556 #rows are 117545 output$download 1... #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c533f1d12.pdf generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c533f1d12.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296557, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:09:30", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:09:30", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399437, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:09:32", createdby = "tobiasko", filechecksum = "df589ac9b1836b2755104151350b1091", junk = "false", modified = "2023-11-24 10:09:32", modifiedby = "tobiasko", name = "WU296557-20231124-1009-rawDiag.pdf", relativepath = "container_33494/workunit_296557/WU296557-20231124-1009-rawDiag.pdf", size = "130675", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296557/WU296557-20231124-1009-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296557/WU296557-20231124-1009-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296557))) The current plot is available as workunit 296557 #rows are 117545 output$download 1... #rows are 117545 output$download 2... ggsave to file /tmp/RtmpFOiCG5/rawDiag-16e61c48b8a20e.pdf generated pdf /tmp/RtmpFOiCG5/rawDiag-16e61c48b8a20e.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296558, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:10:06", createdby = "tobiasko", description = "input files:\np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_004_S598768_ccar1_IP_rep3_FLAG-IP.raw\np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_008_S598770_IgG_IP_rep2_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123_QC_redig/20231123_C33494_003_S598769_IgG_IP_rep1_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_005_S598771_IgG_IP_rep3_Control.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_009_S598767_ccar1_IP_rep2_FLAG-IP.raw \np33494/Proteomics/QEXACTIVE_1/analytic_20231123/20231123_C33494_007_S598766_ccar1_IP_rep1_FLAG-IP.raw \n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.23.\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` = 2398890), list(`_classname` = "resource", `_id` = 2398889), list(`_classname` = "resource", `_id` = 2398888), list(`_classname` = "resource", `_id` = 2398887), list(`_classname` = "resource", `_id` = 2398886), list(`_classname` = "resource", `_id` = 2398885)), modified = "2023-11-24 10:10:06", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2399438, container = list(`_classname` = "order", `_id` = 33494), created = "2023-11-24 10:10:07", createdby = "tobiasko", filechecksum = "a0af2110f370524920b20befa9bcd6f4", junk = "false", modified = "2023-11-24 10:10:07", modifiedby = "tobiasko", name = "WU296558-20231124-1010-rawDiag.pdf", relativepath = "container_33494/workunit_296558/WU296558-20231124-1010-rawDiag.pdf", size = "11975", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33494/workunit_296558/WU296558-20231124-1010-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33494/workunit_296558/WU296558-20231124-1010-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296558))) The current plot is available as workunit 296558 #rows are 117545 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: `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 117545 output$download 2... DEBUG renderPlot plotQCs #rows are 117545 output$download 2... DEBUG renderPlot plotQCs #rows are 117545 output$download 2... DEBUG renderPlot plotQCs #rows are 117545 output$download 2... Execution halted