Listening on http://127.0.0.1:38851 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$employee <- renderUI({ Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$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//p32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw qc ... missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode missing column name(s): MasterScanNumber, LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode MasterScanNumber calculated renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 92737 output$tic.basepeak <- renderPlot({ #rows are 92737 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d4448d5bab.pdf generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d4448d5bab.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290355, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:00", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:19:00", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317951, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:01", createdby = "tobiasko", deletable = "true", filechecksum = "fa159f7c301901945189ffd43c8a9257", junk = "false", modified = "2023-06-22 11:19:01", modifiedby = "tobiasko", name = "WU290355-20230622-1119-rawDiag.pdf", relativepath = "container_32079/workunit_290355/WU290355-20230622-1119-rawDiag.pdf", size = "251492", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290355/WU290355-20230622-1119-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290355/WU290355-20230622-1119-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290355))) The current plot is available as workunit 290355 #rows are 92737 output$download 1... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d46622290a.pdf generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d46622290a.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290356, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:03", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:19:03", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317952, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:05", createdby = "tobiasko", deletable = "true", filechecksum = "2435b4995b2cb285e6c4cf5f121a6e75", junk = "false", modified = "2023-06-22 11:19:05", modifiedby = "tobiasko", name = "WU290356-20230622-1119-rawDiag.pdf", relativepath = "container_32079/workunit_290356/WU290356-20230622-1119-rawDiag.pdf", size = "251492", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290356/WU290356-20230622-1119-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290356/WU290356-20230622-1119-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290356))) The current plot is available as workunit 290356 #rows are 92737 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 92737 output$download 2... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d440f2a577.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d440f2a577.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290357, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:35", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:19:35", modifiedby = "tobiasko", name = "scan frequency plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317953, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:36", createdby = "tobiasko", deletable = "true", filechecksum = "49638fa950fd9631f5fae2c15f010c66", junk = "false", modified = "2023-06-22 11:19:36", modifiedby = "tobiasko", name = "WU290357-20230622-1119-rawDiag.pdf", relativepath = "container_32079/workunit_290357/WU290357-20230622-1119-rawDiag.pdf", size = "134661", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290357/WU290357-20230622-1119-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290357/WU290357-20230622-1119-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290357))) The current plot is available as workunit 290357 #rows are 92737 output$download 1... #rows are 92737 output$download 2... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d4103e06f1.pdf generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d4103e06f1.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290358, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:52", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:19:52", modifiedby = "tobiasko", name = "lock mass correction plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317954, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:19:53", createdby = "tobiasko", deletable = "true", filechecksum = "a268135410d7f38bb344228d0814810b", junk = "false", modified = "2023-06-22 11:19:53", modifiedby = "tobiasko", name = "WU290358-20230622-1119-rawDiag.pdf", relativepath = "container_32079/workunit_290358/WU290358-20230622-1119-rawDiag.pdf", size = "141902", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290358/WU290358-20230622-1119-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290358/WU290358-20230622-1119-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290358))) The current plot is available as workunit 290358 #rows are 92737 output$download 1... #rows are 92737 output$download 2... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d41afba4a8.pdf generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d41afba4a8.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290359, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:20:10", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:20:10", modifiedby = "tobiasko", name = "injection time plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317955, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:20:12", createdby = "tobiasko", deletable = "true", filechecksum = "356c99df67655c755b4b272f39d36d44", junk = "false", modified = "2023-06-22 11:20:12", modifiedby = "tobiasko", name = "WU290359-20230622-1120-rawDiag.pdf", relativepath = "container_32079/workunit_290359/WU290359-20230622-1120-rawDiag.pdf", size = "406760", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290359/WU290359-20230622-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290359/WU290359-20230622-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290359))) The current plot is available as workunit 290359 #rows are 92737 output$download 1... #rows are 92737 output$download 2... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d42c62ca47.pdf generated pdf /tmp/RtmpOxljqu/rawDiag-36b0d42c62ca47.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 290360, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:20:55", createdby = "tobiasko", deletable = "true", description = "input files:\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_008_S525521_TFAMoplexprotein_Group_4.raw\np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_006_S525520_sfGFP-Avi_Group_3.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_004_S525519_onlyDNA_Group_2.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_010_S525522_TFAMoplexDNA_Group_5.raw \np32079/Proteomics/QEXACTIVE_1/analytic_20230621/20230621_C32079_002_S525518_only-protein_Group_1.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` = 2317933), list(`_classname` = "resource", `_id` = 2317932), list(`_classname` = "resource", `_id` = 2317931), list(`_classname` = "resource", `_id` = 2317930), list(`_classname` = "resource", `_id` = 2317929)), modified = "2023-06-22 11:20:55", modifiedby = "tobiasko", name = "charge state plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2317956, container = list(`_classname` = "order", `_id` = 32079), created = "2023-06-22 11:20:56", createdby = "tobiasko", deletable = "true", filechecksum = "70f16660e15aab7d23c97b6642baa989", junk = "false", modified = "2023-06-22 11:20:56", modifiedby = "tobiasko", name = "WU290360-20230622-1120-rawDiag.pdf", relativepath = "container_32079/workunit_290360/WU290360-20230622-1120-rawDiag.pdf", size = "10420", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_32079/workunit_290360/WU290360-20230622-1120-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_32079/workunit_290360/WU290360-20230622-1120-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 290360))) The current plot is available as workunit 290360 #rows are 92737 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: `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 92737 output$download 2... DEBUG renderPlot plotQCs #rows are 92737 output$download 2... ggsave to file /tmp/RtmpOxljqu/rawDiag-36b0d420cab507.pdf Warning: Error in +: non-numeric argument to binary operator 1: runApp #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 Execution halted