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 03:40:10] [INFO] Deploying ImmunoFusion on 0.0.0.0 : 32771

Listening on http://127.0.0.1:32771
[2026-08-01 03:40:17] [INFO] New user session started
Registered S3 method overwritten by 'bit64':
  method          from 
  print.bitstring tools
[2026-08-01 03:40:19] [INFO] Module initialized: Home
[2026-08-01 03:40:19] [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 03:40:20] [INFO] No filter config found — auto-building from Arrow (one-time).
[2026-08-01 03:40:20] [INFO] Building filter configuration from database...
[2026-08-01 03:40:25] [INFO] Filter config cached to /databases/fusiondb_v4/appdata/cache/filter_config.yml (78 cohorts, 3 sample types, 5 fusion types, 3 tools)
[2026-08-01 03:40:42] [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
[2026-08-01 03:40:47] [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
[2026-08-01 03:40:47] [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
[2026-08-01 03:40:47] [INFO] Filters applied: 78 cohorts, genes=[], excl_nonIO=FALSE, excl_nonIO_tx=FALSE, tools=[arriba,arriba,starfusion,starfusion], fusion_types=[CodingFusion,NoHeadGene,SameGene,TruncatedCoding,TruncatedNoncoding]
[2026-08-01 03:40:48] [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
[2026-08-01 03:40:48] [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
[2026-08-01 03:40:48] [INFO] Filters applied: 78 cohorts, genes=[], excl_nonIO=FALSE, excl_nonIO_tx=FALSE, tools=[arriba,arriba,starfusion,starfusion], fusion_types=[CodingFusion,NoHeadGene,SameGene,TruncatedCoding,TruncatedNoncoding]
[2026-08-01 03:40:52] [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
[2026-08-01 03:40:52] [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
[2026-08-01 03:40:52] [INFO] Filters applied: 78 cohorts, genes=[], excl_nonIO=FALSE, excl_nonIO_tx=FALSE, tools=[arriba,arriba,starfusion,starfusion], fusion_types=[CodingFusion,NoHeadGene,SameGene,TruncatedCoding,TruncatedNoncoding]
[2026-08-01 03:40:59] [INFO] Navigate to: Surv - KM Survival
[2026-08-01 03:40:59] [INFO] Module initialized: KM Survival
[2026-08-01 03:41:02] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS
[2026-08-01 03:41:04] [ERROR] Analysis ERROR [KM Survival]: Can't add `p$table` to a <ggplot> object.
[2026-08-01 03:41:09] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS
[2026-08-01 03:41:09] [ERROR] Analysis ERROR [KM Survival]: Can't add `p$table` to a <ggplot> object.
[2026-08-01 03:41:21] [INFO] Navigate to: Cox - Cox Regression
[2026-08-01 03:41:21] [INFO] Module initialized: Cox Regression
[2026-08-01 03:41:26] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=RAB3IP, endpoint=OS

Session terminated, killing shell... ...killed.