Listening on http://127.0.0.1:33065 Loading required package: bfabricShiny Attaching package: 'bfabricShiny' The following object is masked from 'package:base': save Loading required package: protViz Loading required package: rawDiag Loading required package: parallel Loading required package: tidyr Loading required package: rmarkdown Loading required package: base64enc Loading required package: ggplot2 Loading required package: lattice Loading required package: PKI #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw qc ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.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 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber 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 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 missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed AGCPSMode to PrescanMode renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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 #rows are 358982 output$tic.basepeak <- renderPlot({ #rows are 358982 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc22607b344.pdf generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc22607b344.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296644, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:15:15", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:15:15", modifiedby = "tobiasko", name = "TIC and basepeak plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400792, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:15:17", createdby = "tobiasko", filechecksum = "e3395e0a194de758fb45436b937a445d", junk = "false", modified = "2023-11-27 09:15:17", modifiedby = "tobiasko", name = "WU296644-20231127-0915-rawDiag.pdf", relativepath = "container_33324/workunit_296644/WU296644-20231127-0915-rawDiag.pdf", size = "511013", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296644/WU296644-20231127-0915-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296644/WU296644-20231127-0915-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296644))) The current plot is available as workunit 296644 #rows are 358982 output$download 1... saving 'login and webservicepassword' ... output$scan.frequency <- renderPlot Warning: Removed 29 rows containing missing values (`geom_line()`). #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc27d90bf64.pdf Warning: Removed 29 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc27d90bf64.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296645, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:15:53", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:15:53", modifiedby = "tobiasko", name = "scan frequency plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400793, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:15:55", createdby = "tobiasko", filechecksum = "76f4dd75f55f04f623c819aa6a124928", junk = "false", modified = "2023-11-27 09:15:55", modifiedby = "tobiasko", name = "WU296645-20231127-0915-rawDiag.pdf", relativepath = "container_33324/workunit_296645/WU296645-20231127-0915-rawDiag.pdf", size = "408343", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296645/WU296645-20231127-0915-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296645/WU296645-20231127-0915-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296645))) The current plot is available as workunit 296645 #rows are 358982 output$download 1... #rows are 358982 output$download 2... `geom_smooth()` using formula = 'y ~ x' #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc263389b89.pdf `geom_smooth()` using formula = 'y ~ x' generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc263389b89.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296647, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:17:26", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:17:26", modifiedby = "tobiasko", name = "cycle load plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400794, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:17:27", createdby = "tobiasko", filechecksum = "880550ac305153f1f21b3757bc4e8140", junk = "false", modified = "2023-11-27 09:17:27", modifiedby = "tobiasko", name = "WU296647-20231127-0917-rawDiag.pdf", relativepath = "container_33324/workunit_296647/WU296647-20231127-0917-rawDiag.pdf", size = "1534726", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296647/WU296647-20231127-0917-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296647/WU296647-20231127-0917-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296647))) The current plot is available as workunit 296647 #rows are 358982 output$download 1... Warning: Removed 52571 rows containing non-finite values (`stat_smooth()`). Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Removed 7 rows containing missing values (`geom_line()`). #rows are 358982 output$download 2... #rows are 358982 output$download 2... Warning: Removed 52571 rows containing non-finite values (`stat_smooth()`). Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Removed 7 rows containing missing values (`geom_line()`). #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc2d9b10e9.pdf Warning: Removed 52571 rows containing non-finite values (`stat_smooth()`). Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `smooth.construct.cr.smooth.spec()`: ! x has insufficient unique values to support 10 knots: reduce k. Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Computation failed in `stat_smooth()` Caused by error in `gam.reparam()`: ! NA/NaN/Inf in foreign function call (arg 3) Warning: Removed 7 rows containing missing values (`geom_line()`). generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc2d9b10e9.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296648, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:18:28", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:18:28", modifiedby = "tobiasko", name = "lock mass correction plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400798, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:18:29", createdby = "tobiasko", filechecksum = "7512bbb7bb481d6c855dbc84115d16c5", junk = "false", modified = "2023-11-27 09:18:29", modifiedby = "tobiasko", name = "WU296648-20231127-0918-rawDiag.pdf", relativepath = "container_33324/workunit_296648/WU296648-20231127-0918-rawDiag.pdf", size = "26017", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296648/WU296648-20231127-0918-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296648/WU296648-20231127-0918-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296648))) The current plot is available as workunit 296648 #rows are 358982 output$download 1... #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc2508da7b.pdf generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc2508da7b.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296649, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:19:06", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:19:06", modifiedby = "tobiasko", name = "injection time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400799, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:19:07", createdby = "tobiasko", filechecksum = "be2103162c9fac90db23d38f0cdd6e79", junk = "false", modified = "2023-11-27 09:19:07", modifiedby = "tobiasko", name = "WU296649-20231127-0919-rawDiag.pdf", relativepath = "container_33324/workunit_296649/WU296649-20231127-0919-rawDiag.pdf", size = "1471312", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296649/WU296649-20231127-0919-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296649/WU296649-20231127-0919-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296649))) The current plot is available as workunit 296649 #rows are 358982 output$download 1... #rows are 358982 output$download 2... #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc2e5926a7.pdf generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc2e5926a7.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296650, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:20:11", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:20:11", modifiedby = "tobiasko", name = "cycle time plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400800, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:20:12", createdby = "tobiasko", filechecksum = "676742523893aa2353abd9b2b4d07dea", junk = "false", modified = "2023-11-27 09:20:12", modifiedby = "tobiasko", name = "WU296650-20231127-0920-rawDiag.pdf", relativepath = "container_33324/workunit_296650/WU296650-20231127-0920-rawDiag.pdf", size = "339440", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296650/WU296650-20231127-0920-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296650/WU296650-20231127-0920-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296650))) The current plot is available as workunit 296650 #rows are 358982 output$download 1... #rows are 358982 output$download 2... ggsave to file /tmp/RtmpntGRq8/rawDiag-3a3dc2111a07cf.pdf generated pdf /tmp/RtmpntGRq8/rawDiag-3a3dc2111a07cf.pdf bfabricShiny::uploadResource ... list(list(`_classname` = "workunit", `_id` = 296651, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:20:33", createdby = "tobiasko", description = "input files:\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_010_S586606_75-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_007_S586599_68-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_014_S586598_65-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_013_S586608_77-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_005_S586605_74-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_009_S586610_79-KO-DIST_Group_4.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_016_S586604_73-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_008_S586603_72-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_018_S586607_76-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_004_S586597_64-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_003_S586601_70-WT-PROX_Group_1.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_015_S586609_78-KO-PROX_Group_3.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_019_S586602_71-WT-DIST_Group_2.raw\np33324/Proteomics/EXPLORIS_2/analytic_20231124/20231124_C33324_002_S586600_69-KO-DIST_Group_4.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` = 2400373), list(`_classname` = "resource", `_id` = 2400372), list(`_classname` = "resource", `_id` = 2400371), list(`_classname` = "resource", `_id` = 2400368), list(`_classname` = "resource", `_id` = 2400367), list(`_classname` = "resource", `_id` = 2400366), list(`_classname` = "resource", `_id` = 2400365), list(`_classname` = "resource", `_id` = 2400362), list(`_classname` = "resource", `_id` = 2400361), list( `_classname` = "resource", `_id` = 2400360)), modified = "2023-11-27 09:20:33", modifiedby = "tobiasko", name = "charge state plot", status = "AVAILABLE"))list(list(`_classname` = "resource", `_id` = 2400801, container = list(`_classname` = "order", `_id` = 33324), created = "2023-11-27 09:20:34", createdby = "tobiasko", filechecksum = "b2bab3959fa3b387833ccd4bb598ebca", junk = "false", modified = "2023-11-27 09:20:34", modifiedby = "tobiasko", name = "WU296651-20231127-0920-rawDiag.pdf", relativepath = "container_33324/workunit_296651/WU296651-20231127-0920-rawDiag.pdf", size = "13938", status = "available", storage = list(`_classname` = "storage", `_id` = 10), uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_33324/workunit_296651/WU296651-20231127-0920-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_33324/workunit_296651/WU296651-20231127-0920-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 296651))) The current plot is available as workunit 296651 #rows are 358982 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: '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 358982 output$download 2... DEBUG renderPlot plotQCs #rows are 358982 output$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") 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 in mclapply(rf, function(file) { : all scheduled cores encountered errors in user code Warning: Error in : All inputs to rbind.fill must be data.frames 123: stop 122: plyr::rbind.fill 121: [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#424] 105: rawXICAUCData 104: exprFunc [/usr/local/lib/R/site-library/bfabricShiny/shiny/bfabric_rawDiag/server.R#860] 103: widgetFunc 102: :: htmlwidgets shinyRenderWidget 101: func 88: renderFunc 87: renderFunc 83: renderFunc 82: output$tableXICAUC 1: runApp saving 'login and webservicepassword' ... Execution halted