Listening on http://127.0.0.1:33135 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$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 76241 output$tic.basepeak <- renderPlot({ #rows are 76241 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee7a310a55.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee7a310a55.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUEFALSEFALSEFALSEFALSEFALSEFALSE END BEGIN 2305505:2305499c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") The current plot is available as workunit #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p3000/Proteomics/EXPLORIS_1/spfammatter_20211110/20211110_007r_S326787_TMT_sample_o25473_IE70_OE100.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 12226 executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 76241 output$tic.basepeak <- renderPlot({ #rows are 76241 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2eed58069.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2eed58069.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUEFALSEFALSEFALSEFALSEFALSEFALSE 2305505:2305499c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505230550423055032305502230550123055002305499 END BEGIN The current plot is available as workunit #rows are 0 saving 'login and webservicepassword' ... output$employee <- renderUI({ read bfabricposturl https://fgcz-c-072.uzh.ch:5000/. Warning in .read(login = login, webservicepassword = webservicepassword, : query failed. bfabricConnectionWorking FALSE output$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 76241 output$tic.basepeak <- renderPlot({ #rows are 76241 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee12e04695.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee12e04695.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN The current plot is available as workunit ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee24b62f9a.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee24b62f9a.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN The current plot is available as workunit #rows are 0 /scratch/cpanse/ 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$employee <- renderUI({ bfabricConnectionWorking TRUE 'empdegree' found. saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... saving 'login and webservicepassword' ... executing mono /usr/local/lib/R/site-library/rawDiag/exec/fgcz_raw.exe /srv/www/htdocs//p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw qc ... missing column name(s): LMCorrection, ElapsedScanTimesec, transient, AGCMode, PrescanMode NA values replaced in MasterScanNumber renamed LMmZCorrectionppm to LMCorrection renamed AGCPSMode to PrescanMode #rows are 76241 output$tic.basepeak <- renderPlot({ #rows are 76241 output$download 2... saving 'login and webservicepassword' ... ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee52dc1cd5.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee52dc1cd5.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN list(list(errorreport = "Input Resource 2305505 was created with application EXPLORIS_1. This is not an input/preceding application of rawDiag!"))list(list(errorreport = "No value specified for workunitid!")) The current plot is available as workunit ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee3ea455d1.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee3ea455d1.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN list(list(errorreport = "Input Resource 2305505 was created with application EXPLORIS_1. This is not an input/preceding application of rawDiag!"))list(list(errorreport = "No value specified for workunitid!")) The current plot is available as workunit ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee422d1d1a.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee422d1d1a.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN list(list(errorreport = "Input Resource 2305505 was created with application EXPLORIS_1. This is not an input/preceding application of rawDiag!"))list(list(errorreport = "No value specified for workunitid!")) The current plot is available as workunit ggsave to file /tmp/RtmpulBaJ1/rawDiag-21f2ee57ceb4dc.pdf generated pdf /tmp/RtmpulBaJ1/rawDiag-21f2ee57ceb4dc.pdf bfabricShiny::uploadResource ... DEBUG BEGIN TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE 2305505:2305499, c("p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_007_S509067_EPIC-XS-0000405_sample_A5_p2.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_002_S509063_EPIC-XS-0000405_sample_A1_P2_testInjection.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_004_S509065_EPIC-XS-0000405_sample_A3_P3.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_008_S509068_EPIC-XS-0000405_sample_A6_P1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_005_S509066_EPIC-XS-0000405_sample_A4_c1.raw", "p31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_009_S509069_EPIC-XS-0000405_sample_A7_C2.raw") 2305505, 2305504, 2305503, 2305502, 2305501, 2305500, 2305499 END BEGIN list(list(`_classname` = "workunit", `_id` = 289702, application = list(`_classname` = "application", `_id` = 225), container = list(`_classname` = "order", `_id` = 31738), created = "2023-06-05 11:51:10", createdby = "cpanse", deletable = "true", description = "input files:\np31738/Proteomics/EXPLORIS_1/analytic_20230601/20230601_C31738_003_S509064_EPIC-XS-0000405_sample_A2_C3.raw\n\nGenerated by Rpkg https://github.com/fgcz/bfabricShiny/ version 0.12.21.\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` = 2305505)), modified = "2023-06-05 11:51:10", modifiedby = "cpanse", name = "TIC and basepeak plot", status = "PENDING", updatable = "true"))list(list(`_classname` = "resource", `_id` = 2305884, container = list(`_classname` = "order", `_id` = 31738), created = "2023-06-05 11:51:11", createdby = "cpanse", deletable = "true", filechecksum = "a5f6ca0800dc7c626e011a6ddc7463b0", junk = "false", modified = "2023-06-05 11:51:11", modifiedby = "cpanse", name = "WU289702-20230605-1151-rawDiag.pdf", relativepath = "container_31738/workunit_289702/WU289702-20230605-1151-rawDiag.pdf", size = "69114", status = "available", storage = list(`_classname` = "storage", `_id` = 10), updatable = "true", uri = list("https://fgcz-bfabric.uzh.ch/dmexternal/container_31738/workunit_289702/WU289702-20230605-1151-rawDiag.pdf", "scp://localhost/export/bfabric/data/b-fabric-external-repo/container_31738/workunit_289702/WU289702-20230605-1151-rawDiag.pdf"), workunit = list(`_classname` = "workunit", `_id` = 289702))) The current plot is available as workunit 289702 #rows are 76241 output$download 1... saving 'login and webservicepassword' ... Execution halted