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] Installed package -> library(ImmunoFusion) [2026-08-01 04:10:30] [INFO] Deploying ImmunoFusion on 0.0.0.0 : 37595 Listening on http://127.0.0.1:37595 [2026-08-01 04:10:41] [INFO] New user session started [2026-08-01 04:10:42] [INFO] Module initialized: Home [2026-08-01 04:10:42] [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 Registered S3 method overwritten by 'bit64': method from print.bitstring tools [2026-08-01 04:11:52] [INFO] Navigate to: Land - Landscape [2026-08-01 04:11:52] [INFO] Module initialized: Landscape [2026-08-01 04:11:54] [INFO] Analysis: Landscape [2026-08-01 04:12:02] [INFO] Analysis: Landscape All mutation types: CodingFusion, TruncatedCoding, SameGene, TruncatedNoncoding, NoHeadGene. [2026-08-01 04:12:24] [INFO] New user session started [2026-08-01 04:12:24] [INFO] Module initialized: Home [2026-08-01 04:12:24] [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 [2026-08-01 04:12:27] [INFO] Navigate to: Land - Landscape [2026-08-01 04:12:27] [INFO] Module initialized: Landscape [2026-08-01 04:12:29] [INFO] Analysis: Landscape All mutation types: CodingFusion, TruncatedCoding, SameGene, TruncatedNoncoding, NoHeadGene. [2026-08-01 04:15:18] [INFO] Navigate to: Fusion [2026-08-01 04:15:18] [INFO] Module initialized: Fusion [2026-08-01 04:15:18] [INFO] Gene selected: A1BG [2026-08-01 04:15:21] [INFO] Navigate to: Data Summary [2026-08-01 04:15:21] [INFO] Module initialized: Data Summary [2026-08-01 04:15:21] [INFO] Navigate to: Home [2026-08-01 04:15:30] [INFO] New user session started [2026-08-01 04:15:30] [INFO] Module initialized: Home [2026-08-01 04:15:30] [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 [2026-08-01 04:15:48] [INFO] Navigate to: Fusion [2026-08-01 04:15:48] [INFO] Module initialized: Fusion [2026-08-01 04:15:49] [INFO] Gene selected: A1BG [2026-08-01 04:16:37] [INFO] New user session started [2026-08-01 04:16:37] [INFO] Module initialized: Home [2026-08-01 04:16:37] [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 [2026-08-01 04:25:06] [INFO] New user session started [2026-08-01 04:25:06] [INFO] Module initialized: Home [2026-08-01 04:25:06] [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 [2026-08-01 04:25:22] [INFO] New user session started [2026-08-01 04:25:22] [INFO] Module initialized: Home [2026-08-01 04:25:22] [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 [2026-08-01 04:30:00] [INFO] Navigate to: Home [2026-08-01 04:44:33] [INFO] New user session started [2026-08-01 04:44:33] [INFO] Module initialized: Home [2026-08-01 04:44:34] [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 [2026-08-01 04:46:06] [INFO] New user session started [2026-08-01 04:46:06] [INFO] Module initialized: Home [2026-08-01 04:46:07] [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 [2026-08-01 04:46:12] [INFO] New user session started [2026-08-01 04:46:12] [INFO] Module initialized: Home [2026-08-01 04:46:12] [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 [2026-08-01 05:04:51] [INFO] New user session started [2026-08-01 05:04:51] [INFO] Module initialized: Home [2026-08-01 05:04:51] [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 [2026-08-01 08:14:36] [INFO] New user session started [2026-08-01 08:14:36] [INFO] Module initialized: Home [2026-08-01 08:14:36] [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 [2026-08-01 08:15:06] [INFO] Navigate to: Fusion [2026-08-01 08:15:06] [INFO] Module initialized: Fusion [2026-08-01 08:15:08] [INFO] Gene selected: A1BG [2026-08-01 08:15:22] [INFO] Navigate to: Data Summary [2026-08-01 08:15:22] [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 [2026-08-01 08:15:42] [INFO] Navigate to: Fusion [2026-08-01 08:15:48] [INFO] Navigate to: Cohort [2026-08-01 08:15:48] [INFO] Module initialized: Cohort [2026-08-01 08:15:52] [INFO] Cohort detail: EGAD00001003977 [2026-08-01 08:16:43] [INFO] Navigate to: Dist - Distribution [2026-08-01 08:16:43] [INFO] Module initialized: Distribution [2026-08-01 08:16:48] [INFO] Analysis: Distribution - Frequency Warning in ggplot2::scale_y_continuous(trans = "log10", breaks = c(0, 1, : log-10 transformation introduced infinite values. Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp [2026-08-01 08:18:58] [INFO] New user session started [2026-08-01 08:18:58] [INFO] Module initialized: Home [2026-08-01 08:18:58] [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 [2026-08-01 08:19:07] [INFO] Navigate to: Data Summary [2026-08-01 08:19:07] [INFO] Module initialized: Data Summary [2026-08-01 08:19:15] [INFO] Navigate to: Dist - Distribution [2026-08-01 08:19:15] [INFO] Module initialized: Distribution [2026-08-01 08:19:25] [INFO] Analysis: Distribution - Frequency Warning in ggplot2::scale_y_continuous(trans = "log10", breaks = c(0, 1, : log-10 transformation introduced infinite values. [2026-08-01 08:20:37] [INFO] Navigate to: Cohort [2026-08-01 08:20:37] [INFO] Module initialized: Cohort [2026-08-01 08:20:56] [INFO] Navigate to: Fusion [2026-08-01 08:20:56] [INFO] Module initialized: Fusion [2026-08-01 08:20:57] [INFO] Gene selected: A1BG [2026-08-01 08:21:01] [INFO] Gene selected: A2M [2026-08-01 08:21:05] [INFO] Gene selected: A3GALT2 [2026-08-01 08:21:12] [INFO] Gene selected: SLC66A2 Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp [2026-08-01 08:22:55] [INFO] Analysis: Distribution - Ideogram [2026-08-01 08:31:20] [INFO] Analysis: Distribution - Frequency Warning: Error in dplyr::arrange: ℹ In argument: `..1 = n`. Caused by error: ! object 'n' not found 132: 131: signalCondition 130: signal_abort 129: abort 128: h 127: .handleSimpleError 126: eval 125: mask$eval_all_mutate 124: mutate_col 123: withCallingHandlers 122: mutate_cols 121: mutate.data.frame 120: mutate 119: arrange_rows 118: arrange.data.frame 117: dplyr::arrange 116: :: htmlwidgets shinyRenderWidget 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$dist-freq_table 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 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 [2026-08-01 08:31:38] [INFO] Analysis: Distribution - Frequency Warning: Error in dplyr::arrange: ℹ In argument: `..1 = n`. Caused by error: ! object 'n' not found 132: 131: signalCondition 130: signal_abort 129: abort 128: h 127: .handleSimpleError 126: eval 125: mask$eval_all_mutate 124: mutate_col 123: withCallingHandlers 122: mutate_cols 121: mutate.data.frame 120: mutate 119: arrange_rows 118: arrange.data.frame 117: dplyr::arrange 116: :: htmlwidgets shinyRenderWidget 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$dist-freq_table 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 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 [2026-08-01 08:32:03] [INFO] Analysis: Distribution - Ideogram [2026-08-01 08:33:07] [INFO] Navigate to: Data Summary [2026-08-01 08:33:13] [INFO] Navigate to: Fusion [2026-08-01 08:33:14] [INFO] Gene selected: A3GALT2 [2026-08-01 08:33:19] [INFO] Navigate to: Cohort [2026-08-01 08:33:21] [INFO] Navigate to: Surv - KM Survival [2026-08-01 08:33:21] [INFO] Module initialized: KM Survival [2026-08-01 08:33:24] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS [2026-08-01 08:33:54] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=FGFR3::TACC3, endpoint=OS [2026-08-01 08:34:06] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=DPY19L4::ESRP1, endpoint=OS [2026-08-01 08:34:12] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=AFF1::PTPN13, endpoint=OS [2026-08-01 08:36:14] [INFO] Navigate to: Cohort [2026-08-01 08:36:19] [INFO] Navigate to: Fusion [2026-08-01 08:36:26] [INFO] Gene selected: A1BG [2026-08-01 08:36:31] [INFO] Navigate to: Data Summary [2026-08-01 08:36:40] [INFO] New user session started [2026-08-01 08:36:40] [INFO] Module initialized: Home [2026-08-01 08:36:40] [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 [2026-08-01 08:36:52] [INFO] Navigate to: Fusion [2026-08-01 08:36:52] [INFO] Module initialized: Fusion [2026-08-01 08:36:52] [INFO] Gene selected: A1BG [2026-08-01 08:36:54] [INFO] Navigate to: Cohort [2026-08-01 08:36:54] [INFO] Module initialized: Cohort [2026-08-01 11:16:01] [INFO] New user session started [2026-08-01 11:16:01] [INFO] Module initialized: Home [2026-08-01 11:16:01] [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 [2026-08-01 11:18:17] [INFO] Navigate to: Data Summary [2026-08-01 11:18:17] [INFO] Module initialized: Data Summary [2026-08-01 11:18:22] [INFO] Navigate to: Comp - Comparison [2026-08-01 11:18:22] [INFO] Module initialized: Comparison [2026-08-01 11:18:25] [INFO] Analysis: Comparison - TME - cohort=EGAD00001003977, approach=CIBERSORT, feature=B_cells_memory [2026-08-01 11:18:26] [DEBUG] [run_iobr] cohort=EGAD00001003977 tools= types= filtered=1954 unique_samples=250 mols= [2026-08-01 11:18:38] [INFO] Analysis: Comparison - TME - cohort=EGAD00001003977, approach=TIMER, feature=B_cell [2026-08-01 11:18:39] [DEBUG] [run_iobr] cohort=EGAD00001003977 tools= types= filtered=1954 unique_samples=250 mols= [2026-08-01 11:19:09] [INFO] Analysis: Comparison - Signature - cohort=EGAD00001003977, approach=PCA, feature=APM [2026-08-01 11:19:09] [DEBUG] [run_iobr] cohort=EGAD00001003977 tools= types= filtered=1954 unique_samples=250 mols= [2026-08-01 11:19:17] [INFO] Navigate to: Asso - Association [2026-08-01 11:19:17] [INFO] Module initialized: Association [2026-08-01 11:19:20] [INFO] Analysis: Association - Correlation - type=Signature, approach=PCA, feature=APM, cohorts=EGAD00001003977 Warning in cor.test.default(dt$value, dt$fusion_count, method = corr_method) : cannot compute exact p-value with ties Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp [2026-08-01 11:20:13] [INFO] Analysis: Association - Response - cohorts=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, gene=all, type=Gene [2026-08-01 11:21:51] [INFO] Navigate to: Land - Landscape [2026-08-01 11:21:51] [INFO] Module initialized: Landscape [2026-08-01 11:21:56] [INFO] Analysis: Landscape All mutation types: CodingFusion, TruncatedCoding, SameGene, TruncatedNoncoding, NoHeadGene. [2026-08-01 11:22:05] [INFO] Navigate to: Data Summary [2026-08-01 11:23:45] [INFO] Navigate to: Cohort [2026-08-01 11:23:45] [INFO] Module initialized: Cohort [2026-08-01 11:23:58] [INFO] Navigate to: Home [2026-08-01 11:25:21] [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 [2026-08-01 11:27:13] [INFO] Navigate to: Fusion [2026-08-01 11:27:13] [INFO] Module initialized: Fusion [2026-08-01 11:27:14] [INFO] Gene selected: A1BG [2026-08-01 11:27:20] [INFO] Gene selected: A2ML1 [2026-08-01 11:27:24] [INFO] Gene selected: A2M [2026-08-01 15:08:14] [INFO] New user session started [2026-08-01 15:08:14] [INFO] Module initialized: Home [2026-08-01 15:08:14] [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 [2026-08-01 15:08:19] [INFO] Navigate to: Dist - Distribution [2026-08-01 15:08:19] [INFO] Module initialized: Distribution [2026-08-01 15:08:21] [INFO] Analysis: Distribution - Frequency Warning in ggplot2::scale_y_continuous(trans = "log10", breaks = c(0, 1, : log-10 transformation introduced infinite values. Warning: Error in Cairo: Graphics API version mismatch 96: 95: stop 94: func 93: withVisible 92: f 91: Reduce 90: withCallingHandlers 89: domain$wrapSync 88: promises::with_promise_domain 87: captureStackTraces 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: tryCatch 82: do 81: hybrid_chain 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: domain$wrapSync 75: with_promise_domain 74: contextFunc 73: env$runWith 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: force 67: with_otel_span_context 66: force 65: domain$wrapSync 64: promises::with_promise_domain 63: withReactiveDomain 62: domain$wrapSync 61: promises::with_promise_domain 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 58: force 57: domain$wrapSync 56: promises::with_promise_domain 55: withReactiveDomain 54: handler 53: handler 52: handlers$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$wrapSync 28: promises::with_promise_domain 27: captureStackTraces 26: doTryCatch 25: tryCatchOne 24: tryCatchList 23: tryCatch 22: do 21: hybrid_chain 20: handler 19: func 18: compute 17: doTryCatch 16: tryCatchOne 15: tryCatchList 14: tryCatch 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Session terminated, killing shell... ...killed.