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 03:50:34] [INFO] Deploying ImmunoFusion on 0.0.0.0 : 40115

Listening on http://127.0.0.1:40115
[2026-08-01 03:55:19] [INFO] New user session started
[2026-08-01 03:55:19] [INFO] Module initialized: Home
[2026-08-01 03:55:19] [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
Registered S3 method overwritten by 'bit64':
  method          from 
  print.bitstring tools
[2026-08-01 03:55:30] [INFO] Navigate to: Data Summary
[2026-08-01 03:55:30] [INFO] Module initialized: Data Summary
[2026-08-01 03:55:36] [INFO] Navigate to: Fusion
[2026-08-01 03:55:36] [INFO] Module initialized: Fusion
[2026-08-01 03:55:37] [INFO] Gene selected: A1BG
[2026-08-01 03:55:52] [INFO] Navigate to: Cohort
[2026-08-01 03:55:52] [INFO] Module initialized: Cohort
[2026-08-01 03:55:54] [INFO] Cohort detail: PRJNA498500
Warning in as.data.table.list(jval, .named = NULL) :
  Item 1 has 187 rows but longest item has 196; recycled with remainder.
Warning in as.data.table.list(jval, .named = NULL) :
  Item 3 has 187 rows but longest item has 196; recycled with remainder.
Warning in as.data.table.list(jval, .named = NULL) :
  Item 4 has 187 rows but longest item has 196; recycled with remainder.
Warning in as.data.table.list(jval, .named = NULL) :
  Item 5 has 187 rows but longest item has 196; recycled with remainder.
[2026-08-01 03:56:13] [INFO] Navigate to: Dist - Distribution
[2026-08-01 03:56:13] [INFO] Module initialized: Distribution
[2026-08-01 03:56:15] [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 03:56:22] [INFO] Analysis: Distribution - Ideogram

[2026-08-01 03:56:45] [INFO] Analysis: Distribution - Lollipop
[2026-08-01 03:56:48] [INFO] Analysis: Distribution - Lollipop
[2026-08-01 03:57:08] [INFO] Analysis: Distribution - Composition
[2026-08-01 03:57:11] [INFO] Analysis: Distribution - Composition
[2026-08-01 03:57:20] [INFO] Navigate to: Comp - Comparison
[2026-08-01 03:57:20] [INFO] Module initialized: Comparison
[2026-08-01 03:57:22] [INFO] Analysis: Comparison - TME - cohort=EGAD00001003977, approach=CIBERSORT, feature=B_cells_memory
[2026-08-01 03:57:23] [DEBUG] [run_iobr] cohort=EGAD00001003977 tools= types= filtered=1954 unique_samples=250 mols=
[2026-08-01 03:57:28] [INFO] Analysis: Comparison - Signature - cohort=EGAD00001003977, approach=PCA, feature=APM
[2026-08-01 03:57:28] [DEBUG] [run_iobr] cohort=EGAD00001003977 tools= types= filtered=1954 unique_samples=250 mols=
[2026-08-01 03:57:34] [INFO] Navigate to: Asso - Association
[2026-08-01 03:57:34] [INFO] Module initialized: Association
[2026-08-01 03:57:35] [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
[2026-08-01 03:57:42] [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 03:57:59] [INFO] Analysis: Association - Interaction - genes=VPS13B,PPARG,EIF4A2,MYO1D,PLEKHA7, type=Gene
[2026-08-01 03:58:10] [INFO] Navigate to: Surv - KM Survival
[2026-08-01 03:58:10] [INFO] Module initialized: KM Survival
[2026-08-01 03:58:12] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS
[2026-08-01 03:58:18] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=FRS2, endpoint=OS
[2026-08-01 03:58:26] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS
[2026-08-01 03:58:51] [INFO] Analysis: KM Survival - cohort=EGAD00001003977, gene=RAB3IP, endpoint=OS
[2026-08-01 03:59:04] [INFO] Navigate to: Cox - Cox Regression
[2026-08-01 03:59:04] [INFO] Module initialized: Cox Regression
[2026-08-01 03:59:09] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=FGFR3, endpoint=OS
[2026-08-01 03:59:18] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=FGFR3, endpoint=OS
[2026-08-01 03:59:20] [INFO] Analysis: Cox Regression - cohort=EGAD00001003977, genes=FGFR3, endpoint=OS
exponentiate estimates of model(s) constructed from coxph method at default
[2026-08-01 03:59:36] [INFO] Navigate to: Land - Landscape
[2026-08-01 03:59:36] [INFO] Module initialized: Landscape
[2026-08-01 03:59:40] [INFO] Analysis: Landscape
[2026-08-01 03:59:40] [WARN] OncoPrint build error: cannot open file 'Rplots.pdf'
[2026-08-01 03:59:49] [INFO] Analysis: Landscape
[2026-08-01 03:59:49] [WARN] OncoPrint build error: cannot open file 'Rplots.pdf'
[2026-08-01 03:59:55] [INFO] Analysis: Landscape
[2026-08-01 03:59:55] [WARN] OncoPrint build error: cannot open file 'Rplots.pdf'
[2026-08-01 04:00:03] [INFO] Analysis: Landscape
[2026-08-01 04:00:03] [WARN] OncoPrint build error: cannot open file 'Rplots.pdf'

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