su: ignoring --preserve-environment, it's mutually exclusive with --login Attaching package: ‘DT’ The following objects are masked from ‘package:shiny’: dataTableOutput, renderDataTable Attaching package: ‘bs4Dash’ The following objects are masked from ‘package:shiny’: actionButton, column, insertTab, navbarMenu, tabsetPanel The following object is masked from ‘package:graphics’: box Attaching package: ‘shinyWidgets’ The following object is masked from ‘package:bs4Dash’: progressBar Attaching package: ‘zip’ The following objects are masked from ‘package:utils’: unzip, zip Loading required package: DBI Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Attaching package: ‘dbplyr’ The following objects are masked from ‘package:dplyr’: ident, sql ========================================================================== IOBR v2.2.3.9000 Immuno-Oncology Biological Research For Documentation: https://iobr.github.io/IOBR/ For Tutorial: https://iobr.github.io/book/ For Help: https://github.com/IOBR/IOBR/issues If you use IOBR in published research, please cite: DQ Zeng, YR Fang, ..., GC Yu*, WJ Liao*, Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0. Cell Rep Methods 4, 100910 (2024). & YR Fang, ..., WJ Liao*, DQ Zeng*, Systematic Investigation of Tumor Microenvironment and Antitumor Immunity With IOBR, Med Research (2025). https://onlinelibrary.wiley.com/doi/epdf/10.1002/mdr2.70001 ========================================================================== IOBRportal database mode: enabled. Listening on http://127.0.0.1:39403 ℹ Best number of TME clusters: 2 ℹ Cluster distribution: ℹ Creating heatmap with 1 features tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling tidyHeatmap says: If you use tidyHeatmap for scientific research, please cite: Mangiola, S. and Papenfuss, A.T., 2020. 'tidyHeatmap: an R package for modular heatmap production based on tidy principles.' Journal of Open Source Software. doi:10.21105/joss.02472. This message is displayed once per session. Warning: `when()` was deprecated in purrr 1.0.0. ℹ Please use `if` instead. ℹ The deprecated feature was likely used in the tidyHeatmap package. Please report the issue at . ℹ Creating heatmap with 1 features ℹ Best number of TME clusters: 3 ℹ Cluster distribution: ℹ Creating heatmap with 25 features ℹ Creating heatmap with 25 features ℹ Groups: "Female" and "Male" ℹ Features: 24 ✔ Wilcoxon test complete ℹ Survival follow-up time range: 0.03 to 132.3 months ℹ Best cutoff for "T_cells_CD8_CIBERSORT": 0.01 ✔ Best cutoff for "T_cells_CD8_CIBERSORT": 0.01 ℹ High T_cells_CD8_CIBERSORT: 586 ℹ Low T_cells_CD8_CIBERSORT: 143 ℹ Maximum follow-up time is 132.3 months; divided into 6 sections Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the ggpubr package. Please report the issue at . Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" ℹ Computing spearman correlation for 1 feature Warning in cor.test.default(data[[feat]], data[[target]], method = method, : Cannot compute exact p-value with ties ✔ Correlation analysis complete ℹ Best number of TME clusters: 2 ℹ Cluster distribution: Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Ran out of iterations and did not converge ℹ Input data preview: ℹ Random palettes: 1 (palette1), 2 (palette2), 3 (palette3), 4 (palette4) Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls < cases Setting levels: control = 0, case = 1 Setting direction: controls > cases Setting levels: control = 0, case = 1 Setting direction: controls < cases ℹ Follow-up time ranges from 0.03 to 211.35 months TME1 TME2 38 8 ℹ Maximum follow-up time is 211.3 months; divided into 6 sections ℹ Reference group not defined, using alphabetical order Ignoring unknown labels: • colour : "Strata" ℹ Survival follow-up time range: 0.03 to 211.35 months ℹ Best cutoff for "T_cells_CD8_CIBERSORT": 0.19 ✔ Best cutoff for "T_cells_CD8_CIBERSORT": 0.187 Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. ℹ High T_cells_CD8_CIBERSORT: 8 ℹ Low T_cells_CD8_CIBERSORT: 38 Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Loglik converged before variable 1 ; coefficient may be infinite. ℹ Maximum follow-up time is 211.3 months; divided into 6 sections Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" Ignoring unknown labels: • colour : "Strata" User session ended. Running garbage collection... User session ended. Running garbage collection... Closed TCGA pool. Closed OtherCohort pool. Closed Immunotherapy pool. Closed CancerCohort pool. Execution halted