su: ignoring --preserve-environment, it's mutually exclusive with --login
Warning in warn_if_app_dir_is_package(appDir) :
  Loading R/ subdirectory for Shiny application, but this directory appears to contain an R package. Sourcing files in R/ may cause unexpected behavior. See `?loadSupport` for more details.
[ImmunoFusion] R package source detected → pkgload::load_all()

[2026-06-26 15:54:13] [INFO] Deploying ImmunoFusion on 0.0.0.0 : 40771

Listening on http://127.0.0.1:40771
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/ImmunoFusion/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/ImmunoFusion/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/ImmunoFusion/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/ImmunoFusion/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/ImmunoFusion/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/ImmunoFusion/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/ImmunoFusion/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/ImmunoFusion/app_cache/sass'. Using temp dir instead.
Warning in dir.create(cache_dir, recursive = TRUE) :
  cannot create dir '/srv/shiny-server/ImmunoFusion/app_cache', reason 'Permission denied'
Warning in value[[3L]](cond) :
  Error using cache directory at '/srv/shiny-server/ImmunoFusion/app_cache/sass'. Using temp dir instead.
Warning in dir.create(d, recursive = TRUE) :
  cannot create dir '/databases/fusiondb_v4/appdata/cache', reason 'Permission denied'
Warning in dir.create(d, recursive = TRUE) :
  cannot create dir '/databases/fusiondb_v4/appdata/cache', reason 'Permission denied'
Warning in gzfile(file, mode) :
  cannot open compressed file '/databases/fusiondb_v4/appdata/cache/cohorts.rds', probable reason 'No such file or directory'
Warning: Error in gzfile: cannot open the connection
  103: h
  102: .handleSimpleError
  101: gzfile
  100: saveRDS
   99: load_cohort_list [/srv/shiny-server/ImmunoFusion/R/data_io.R#34]
   98: load_cohort_metadata [/srv/shiny-server/ImmunoFusion/R/data_io.R#94]
   97: stats::setNames
   96: lapply
   95: listify
   94: choicesWithNames
   93: shinyWidgets::pickerInput
   92: rlang::list2
   91: bslib::card
   90: rlang::list2
   89: separate_arguments
   88: bslib::layout_column_wrap
   87: rlang::list2
   86: bslib::card
   85: rlang::list2
   84: separate_arguments
   83: bslib::layout_column_wrap
   82: dots_list
   81: div
   80: list2
   79: bootstrapPage
   78: shiny::fluidPage
   77: as_page
   76: page_fluid
   75: mod_analysis_surv_ui [/srv/shiny-server/ImmunoFusion/R/mod_analysis_surv.R#9]
   74: dots_list
   73: div
   72: tabPanel_
   71: bslib::nav_panel
   70: list2
   69: structure
   68: navbarMenu_
   67: bslib::nav_menu
   66: list2
   65: dropNulls
   64: buildTabset
   63: navbarPage_
   62: navs_bar_
   61: bslib::page_navbar
   60: ui [/srv/shiny-server/ImmunoFusion/R/ui.R#8]
   59: ..stacktraceon..
   58: force
   57: withRestoreContext
   56: appObj()$httpHandler
   55: handler
   54: handler
   53: handler
   52: handlers$invoke
   51: withCallingHandlers
   50: domain$wrapSync
   49: promises::with_promise_domain
   48: captureStackTraces
   47: withCallingHandlers
   46: withLogErrors
   45: withCallingHandlers
   44: force
   43: withVisible
   42: withCallingHandlers
   41: domain$wrapSync
   40: promises::with_promise_domain
   39: captureStackTraces
   38: doTryCatch
   37: tryCatchOne
   36: tryCatchList
   35: tryCatch
   34: do
   33: hybrid_chain
   32: force
   31: withVisible
   30: withCallingHandlers
   29: domain$wrapSync
   28: promises::with_promise_domain
   27: captureStackTraces
   26: doTryCatch
   25: tryCatchOne
   24: tryCatchList
   23: tryCatch
   22: do
   21: hybrid_chain
   20: handler
   19: func
   18: compute
   17: doTryCatch
   16: tryCatchOne
   15: tryCatchList
   14: tryCatch
   13: rookCall
   12: <Anonymous>
   11: execCallbacks
   10: run_now
    9: service
    8: serviceApp
    7: ..stacktracefloor..
    6: withCallingHandlers
    5: domain$wrapSync
    4: promises::with_promise_domain
    3: captureStackTraces
    2: ..stacktraceoff..
    1: runApp
Downloading google font Inter to local cache (/srv/shiny-server/ImmunoFusion/app_cache/sass)
Downloading google font JetBrains Mono to local cache (/srv/shiny-server/ImmunoFusion/app_cache/sass)
[2026-06-26 16:03:05] [INFO] New user session started
[2026-06-26 16:03:05] [INFO] Module initialized: Home
[2026-06-26 16:03:05] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:03:05] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:03:26] [INFO] New user session started
[2026-06-26 16:03:26] [INFO] Module initialized: Home
[2026-06-26 16:03:26] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:03:26] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:03:45] [INFO] New user session started
[2026-06-26 16:03:45] [INFO] Module initialized: Home
[2026-06-26 16:03:45] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:03:45] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:05:19] [INFO] Navigate to: Data Summary
[2026-06-26 16:05:19] [INFO] Module initialized: Data Summary
[2026-06-26 16:05:23] [INFO] Navigate to: Fusion
[2026-06-26 16:05:23] [INFO] Module initialized: Fusion
[2026-06-26 16:05:25] [INFO] Gene selected: A1BG
[2026-06-26 16:05:28] [INFO] Gene selected: A1CF
[2026-06-26 16:05:31] [INFO] Navigate to: Cohort
[2026-06-26 16:05:31] [INFO] Module initialized: Cohort
[2026-06-26 16:05:32] [INFO] Navigate to: Fusion
[2026-06-26 16:05:43] [INFO] Navigate to: Cohort
[2026-06-26 16:05:45] [INFO] Navigate to: Dist - Distribution
[2026-06-26 16:05:45] [INFO] Module initialized: Distribution
[2026-06-26 16:05:54] [INFO] Navigate to: Cohort
[2026-06-26 16:05:55] [INFO] Navigate to: Fusion
[2026-06-26 16:05:56] [INFO] Navigate to: Data Summary
[2026-06-26 16:05:57] [INFO] Navigate to: Home
[2026-06-26 16:05:58] [INFO] Navigate to: Cohort
[2026-06-26 16:06:00] [INFO] Navigate to: Comp - Comparison
[2026-06-26 16:06:00] [INFO] Module initialized: Comparison
[2026-06-26 16:06:04] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:06:04] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:06:04] [DEBUG] cohorts changed: CPTAC-BRCA, CPTAC-COAD, CPTAC-GBM, CPTAC-HNSC, CPTAC-KIRC, CPTAC-LUAD, CPTAC-LUSC, CPTAC-NORMAL, CPTAC-OV, CPTAC-PAAD, CPTAC-UCEC, EGAD00001003977, EGAD00001004183, EGAD00001006282, EGAD00001006619, EGAD00001007575, EGAD00001008548, EGAD00001008549, HRA000524, PHS000452_CTLA4, PHS000452_PD1, PHS001038, PHS001427, PHS001493, PHS001919, PHS002176, PHS003284, PHS003316, PRJEB23709, PRJEB25780, PRJNA312948, PRJNA356761, PRJNA476140, PRJNA482620, PRJNA498500, PRJNA744780, PRJNA795330, PRJNA923698, PRJNA940989, TARGET-CELL, TARGET-GNB, TARGET-LAML, TARGET-NBL, TARGET-NORMAL, TCGA-ACC, TCGA-BLCA, TCGA-BRCA, TCGA-CESC, TCGA-CHOL, TCGA-COAD, TCGA-DLBC, TCGA-ESCA, TCGA-GBM, TCGA-HNSC, TCGA-KICH, TCGA-KIRC, TCGA-KIRP, TCGA-LAML, TCGA-LGG, TCGA-LIHC, TCGA-LUAD, TCGA-LUSC, TCGA-MESO, TCGA-NORMAL, TCGA-OV, TCGA-PAAD, TCGA-PCPG, TCGA-PRAD, TCGA-READ, TCGA-SARC, TCGA-SKCM, TCGA-STAD, TCGA-TGCT, TCGA-THCA, TCGA-THYM, TCGA-UCEC, TCGA-UCS, TCGA-UVM
[2026-06-26 16:06:04] [DEBUG] cohorts change ignored during cooldown
[2026-06-26 16:06:04] [DEBUG] cohort_groups changed: Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:06:04] [DEBUG] cohort_groups change ignored during cooldown
[2026-06-26 16:06:06] [DEBUG] Apply clicked: cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:06:06] [DEBUG] Apply clicked: cohorts = CPTAC-BRCA, CPTAC-COAD, CPTAC-GBM, CPTAC-HNSC, CPTAC-KIRC, CPTAC-LUAD, CPTAC-LUSC, CPTAC-NORMAL, CPTAC-OV, CPTAC-PAAD, CPTAC-UCEC, EGAD00001003977, EGAD00001004183, EGAD00001006282, EGAD00001006619, EGAD00001007575, EGAD00001008548, EGAD00001008549, HRA000524, PHS000452_CTLA4, PHS000452_PD1, PHS001038, PHS001427, PHS001493, PHS001919, PHS002176, PHS003284, PHS003316, PRJEB23709, PRJEB25780, PRJNA312948, PRJNA356761, PRJNA476140, PRJNA482620, PRJNA498500, PRJNA744780, PRJNA795330, PRJNA923698, PRJNA940989, TARGET-CELL, TARGET-GNB, TARGET-LAML, TARGET-NBL, TARGET-NORMAL, TCGA-ACC, TCGA-BLCA, TCGA-BRCA, TCGA-CESC, TCGA-CHOL, TCGA-COAD, TCGA-DLBC, TCGA-ESCA, TCGA-GBM, TCGA-HNSC, TCGA-KICH, TCGA-KIRC, TCGA-KIRP, TCGA-LAML, TCGA-LGG, TCGA-LIHC, TCGA-LUAD, TCGA-LUSC, TCGA-MESO, TCGA-NORMAL, TCGA-OV, TCGA-PAAD, TCGA-PCPG, TCGA-PRAD, TCGA-READ, TCGA-SARC, TCGA-SKCM, TCGA-STAD, TCGA-TGCT, TCGA-THCA, TCGA-THYM, TCGA-UCEC, TCGA-UCS, TCGA-UVM
[2026-06-26 16:06:07] [INFO] Filters applied: 78 cohorts, genes=[], excl_nonIO=FALSE, excl_nonIO_tx=FALSE, tools=[arriba,starfusion,arriba,starfusion], fusion_types=[CodingFusion,NoHeadGene,SameGene,TruncatedCoding,TruncatedNoncoding]
[2026-06-26 16:13:06] [INFO] Navigate to: Home
[2026-06-26 16:13:14] [INFO] Navigate to: Cohort
[2026-06-26 16:13:17] [INFO] Navigate to: Land - Landscape
[2026-06-26 16:13:17] [INFO] Module initialized: Landscape
[2026-06-26 16:13:23] [INFO] Analysis: Landscape
Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'
  97: h
  96: .handleSimpleError
  95: <Anonymous>
  94: grid.Call
  93: convertUnit
  92: convertWidth
  91: update_anno_extend
  90: ComplexHeatmap::anno_oncoprint_barplot
  89: build_oncoprint [/srv/shiny-server/ImmunoFusion/R/vis.R#2033]
  88: eval [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#236]
  87: eval
  86: withProgress
  85: observe [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#235]
  84: <observer:observeEvent(input$landscape_run)>
  83: ..stacktraceon..
  82: valueFunc
  81: ..stacktraceon..
  80: contextFunc
  79: env$runWith
  78: withCallingHandlers
  77: domain$wrapSync
  76: promises::with_promise_domain
  75: captureStackTraces
  74: force
  73: with_otel_span_context
  72: force
  71: domain$wrapSync
  70: promises::with_promise_domain
  69: withReactiveDomain
  68: domain$wrapSync
  67: promises::with_promise_domain
  66: ctx$run
  65: ..stacktraceoff..
  64: isolate
  63: func
  62: withVisible
  61: f
  60: Reduce
  59: withCallingHandlers
  58: domain$wrapSync
  57: promises::with_promise_domain
  56: captureStackTraces
  55: doTryCatch
  54: tryCatchOne
  53: tryCatchList
  52: tryCatch
  51: do
  50: hybrid_chain
  49: observeEvent(input$landscape_run)
  48: contextFunc
  47: env$runWith
  46: withCallingHandlers
  45: domain$wrapSync
  44: promises::with_promise_domain
  43: captureStackTraces
  42: force
  41: with_otel_span_context
  40: force
  39: domain$wrapSync
  38: promises::with_promise_domain
  37: withReactiveDomain
  36: domain$wrapSync
  35: promises::with_promise_domain
  34: ctx$run
  33: run
  32: withCallingHandlers
  31: domain$wrapSync
  30: promises::with_promise_domain
  29: captureStackTraces
  28: withCallingHandlers
  27: shinyCallingHandlers
  26: force
  25: withVisible
  24: withCallingHandlers
  23: domain$wrapSync
  22: promises::with_promise_domain
  21: captureStackTraces
  20: doTryCatch
  19: tryCatchOne
  18: tryCatchList
  17: tryCatch
  16: do
  15: hybrid_chain
  14: flushCallback
  13: FUN
  12: lapply
  11: ctx$executeFlushCallbacks
  10: .getReactiveEnvironment()$flush
   9: flushReact
   8: serviceApp
   7: ..stacktracefloor..
   6: withCallingHandlers
   5: domain$wrapSync
   4: promises::with_promise_domain
   3: captureStackTraces
   2: ..stacktraceoff..
   1: runApp
[2026-06-26 16:13:25] [INFO] Analysis: Landscape
Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'
  97: h
  96: .handleSimpleError
  95: <Anonymous>
  94: grid.Call
  93: convertUnit
  92: convertWidth
  91: update_anno_extend
  90: ComplexHeatmap::anno_oncoprint_barplot
  89: build_oncoprint [/srv/shiny-server/ImmunoFusion/R/vis.R#2033]
  88: eval [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#236]
  87: eval
  86: withProgress
  85: observe [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#235]
  84: <observer:observeEvent(input$landscape_run)>
  83: ..stacktraceon..
  82: valueFunc
  81: ..stacktraceon..
  80: contextFunc
  79: env$runWith
  78: withCallingHandlers
  77: domain$wrapSync
  76: promises::with_promise_domain
  75: captureStackTraces
  74: force
  73: with_otel_span_context
  72: force
  71: domain$wrapSync
  70: promises::with_promise_domain
  69: withReactiveDomain
  68: domain$wrapSync
  67: promises::with_promise_domain
  66: ctx$run
  65: ..stacktraceoff..
  64: isolate
  63: func
  62: withVisible
  61: f
  60: Reduce
  59: withCallingHandlers
  58: domain$wrapSync
  57: promises::with_promise_domain
  56: captureStackTraces
  55: doTryCatch
  54: tryCatchOne
  53: tryCatchList
  52: tryCatch
  51: do
  50: hybrid_chain
  49: observeEvent(input$landscape_run)
  48: contextFunc
  47: env$runWith
  46: withCallingHandlers
  45: domain$wrapSync
  44: promises::with_promise_domain
  43: captureStackTraces
  42: force
  41: with_otel_span_context
  40: force
  39: domain$wrapSync
  38: promises::with_promise_domain
  37: withReactiveDomain
  36: domain$wrapSync
  35: promises::with_promise_domain
  34: ctx$run
  33: run
  32: withCallingHandlers
  31: domain$wrapSync
  30: promises::with_promise_domain
  29: captureStackTraces
  28: withCallingHandlers
  27: shinyCallingHandlers
  26: force
  25: withVisible
  24: withCallingHandlers
  23: domain$wrapSync
  22: promises::with_promise_domain
  21: captureStackTraces
  20: doTryCatch
  19: tryCatchOne
  18: tryCatchList
  17: tryCatch
  16: do
  15: hybrid_chain
  14: flushCallback
  13: FUN
  12: lapply
  11: ctx$executeFlushCallbacks
  10: .getReactiveEnvironment()$flush
   9: flushReact
   8: serviceApp
   7: ..stacktracefloor..
   6: withCallingHandlers
   5: domain$wrapSync
   4: promises::with_promise_domain
   3: captureStackTraces
   2: ..stacktraceoff..
   1: runApp
[2026-06-26 16:13:51] [INFO] New user session started
[2026-06-26 16:13:51] [INFO] Module initialized: Home
[2026-06-26 16:13:51] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:13:51] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:14:18] [INFO] Navigate to: Cox - Cox Regression
[2026-06-26 16:14:18] [INFO] Module initialized: Cox Regression
[2026-06-26 16:14:32] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=RAB3IP, endpoint=OS
[2026-06-26 16:14:52] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=RAB3IP, endpoint=OS
Warning: Error in invokeRestart: no 'restart' 'muffleWarning' found
  97: h
  96: .handleSimpleError
  95: stop
  94: invokeRestart
  93: value[[3L]] [/srv/shiny-server/ImmunoFusion/R/analysis_core.R#100]
  92: tryCatchOne
  91: tryCatchList
  90: tryCatch
  89: with_run_guard [/srv/shiny-server/ImmunoFusion/R/analysis_core.R#78]
  88: eval [/srv/shiny-server/ImmunoFusion/R/mod_analysis_cox.R#187]
  87: eval
  86: withProgress
  85: observe [/srv/shiny-server/ImmunoFusion/R/mod_analysis_cox.R#186]
  84: <observer:observeEvent(input$cox_run)>
  83: ..stacktraceon..
  82: valueFunc
  81: ..stacktraceon..
  80: contextFunc
  79: env$runWith
  78: withCallingHandlers
  77: domain$wrapSync
  76: promises::with_promise_domain
  75: captureStackTraces
  74: force
  73: with_otel_span_context
  72: force
  71: domain$wrapSync
  70: promises::with_promise_domain
  69: withReactiveDomain
  68: domain$wrapSync
  67: promises::with_promise_domain
  66: ctx$run
  65: ..stacktraceoff..
  64: isolate
  63: func
  62: withVisible
  61: f
  60: Reduce
  59: withCallingHandlers
  58: domain$wrapSync
  57: promises::with_promise_domain
  56: captureStackTraces
  55: doTryCatch
  54: tryCatchOne
  53: tryCatchList
  52: tryCatch
  51: do
  50: hybrid_chain
  49: observeEvent(input$cox_run)
  48: contextFunc
  47: env$runWith
  46: withCallingHandlers
  45: domain$wrapSync
  44: promises::with_promise_domain
  43: captureStackTraces
  42: force
  41: with_otel_span_context
  40: force
  39: domain$wrapSync
  38: promises::with_promise_domain
  37: withReactiveDomain
  36: domain$wrapSync
  35: promises::with_promise_domain
  34: ctx$run
  33: run
  32: withCallingHandlers
  31: domain$wrapSync
  30: promises::with_promise_domain
  29: captureStackTraces
  28: withCallingHandlers
  27: shinyCallingHandlers
  26: force
  25: withVisible
  24: withCallingHandlers
  23: domain$wrapSync
  22: promises::with_promise_domain
  21: captureStackTraces
  20: doTryCatch
  19: tryCatchOne
  18: tryCatchList
  17: tryCatch
  16: do
  15: hybrid_chain
  14: flushCallback
  13: FUN
  12: lapply
  11: ctx$executeFlushCallbacks
  10: .getReactiveEnvironment()$flush
   9: flushReact
   8: serviceApp
   7: ..stacktracefloor..
   6: withCallingHandlers
   5: domain$wrapSync
   4: promises::with_promise_domain
   3: captureStackTraces
   2: ..stacktraceoff..
   1: runApp
[2026-06-26 16:15:02] [INFO] New user session started
[2026-06-26 16:15:02] [INFO] Module initialized: Home
[2026-06-26 16:15:02] [DEBUG] MODAL REOPEN: selected_cohort_groups = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:15:02] [DEBUG] render all_pickers: ct_sel = Hematologic, Bladder, Neuroblastoma, Breast, Brain, Colorectum, Endocrine, Esophageal, Head & Neck, Kidney, Liver, Lung, Ovary, Pancreas, Prostate, Sarcoma, Skin, Stomach, Testicle, Uterine, CellLine, Normal / Control, Others
[2026-06-26 16:15:15] [INFO] Navigate to: Cox - Cox Regression
[2026-06-26 16:15:15] [INFO] Module initialized: Cox Regression
[2026-06-26 16:16:13] [INFO] Navigate to: Land - Landscape
[2026-06-26 16:16:13] [INFO] Module initialized: Landscape
[2026-06-26 16:22:13] [INFO] Navigate to: Home
[2026-06-26 16:22:20] [INFO] Navigate to: Data Summary
[2026-06-26 16:22:20] [INFO] Module initialized: Data Summary
Warning: plotly.js does not (yet) support horizontal legend items 
You can track progress here: 
https://github.com/plotly/plotly.js/issues/53 

[2026-06-26 16:22:27] [INFO] Navigate to: Fusion
[2026-06-26 16:22:27] [INFO] Module initialized: Fusion
[2026-06-26 16:22:27] [INFO] Gene selected: A1BG
[2026-06-26 16:22:28] [INFO] Navigate to: Cohort
[2026-06-26 16:22:28] [INFO] Module initialized: Cohort
[2026-06-26 16:22:29] [INFO] Cohort detail: EGAD00001003977
[2026-06-26 16:33:05] [INFO] Navigate to: Land - Landscape
[2026-06-26 16:33:08] [INFO] Analysis: Landscape
Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'
  97: h
  96: .handleSimpleError
  95: <Anonymous>
  94: grid.Call
  93: convertUnit
  92: convertWidth
  91: update_anno_extend
  90: ComplexHeatmap::anno_oncoprint_barplot
  89: build_oncoprint [/srv/shiny-server/ImmunoFusion/R/vis.R#2033]
  88: eval [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#236]
  87: eval
  86: withProgress
  85: observe [/srv/shiny-server/ImmunoFusion/R/mod_analysis_landscape.R#235]
  84: <observer:observeEvent(input$landscape_run)>
  83: ..stacktraceon..
  82: valueFunc
  81: ..stacktraceon..
  80: contextFunc
  79: env$runWith
  78: withCallingHandlers
  77: domain$wrapSync
  76: promises::with_promise_domain
  75: captureStackTraces
  74: force
  73: with_otel_span_context
  72: force
  71: domain$wrapSync
  70: promises::with_promise_domain
  69: withReactiveDomain
  68: domain$wrapSync
  67: promises::with_promise_domain
  66: ctx$run
  65: ..stacktraceoff..
  64: isolate
  63: func
  62: withVisible
  61: f
  60: Reduce
  59: withCallingHandlers
  58: domain$wrapSync
  57: promises::with_promise_domain
  56: captureStackTraces
  55: doTryCatch
  54: tryCatchOne
  53: tryCatchList
  52: tryCatch
  51: do
  50: hybrid_chain
  49: observeEvent(input$landscape_run)
  48: contextFunc
  47: env$runWith
  46: withCallingHandlers
  45: domain$wrapSync
  44: promises::with_promise_domain
  43: captureStackTraces
  42: force
  41: with_otel_span_context
  40: force
  39: domain$wrapSync
  38: promises::with_promise_domain
  37: withReactiveDomain
  36: domain$wrapSync
  35: promises::with_promise_domain
  34: ctx$run
  33: run
  32: withCallingHandlers
  31: domain$wrapSync
  30: promises::with_promise_domain
  29: captureStackTraces
  28: withCallingHandlers
  27: shinyCallingHandlers
  26: force
  25: withVisible
  24: withCallingHandlers
  23: domain$wrapSync
  22: promises::with_promise_domain
  21: captureStackTraces
  20: doTryCatch
  19: tryCatchOne
  18: tryCatchList
  17: tryCatch
  16: do
  15: hybrid_chain
  14: flushCallback
  13: FUN
  12: lapply
  11: ctx$executeFlushCallbacks
  10: .getReactiveEnvironment()$flush
   9: flushReact
   8: serviceApp
   7: ..stacktracefloor..
   6: withCallingHandlers
   5: domain$wrapSync
   4: promises::with_promise_domain
   3: captureStackTraces
   2: ..stacktraceoff..
   1: runApp


Execution halted