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://127.0.0.1:42763 User session ended. Running garbage collection... User session ended. Running garbage collection... ℹ Best number of TME clusters: 3 ℹ Cluster distribution: ℹ Creating heatmap with 258 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 . User session ended. Running garbage collection... ℹ Best number of TME clusters: 3 ℹ Cluster distribution: ℹ Creating heatmap with 258 features # A tibble: 5 × 5 # Groups: KRAS_mutation [3] KRAS_mutation EGFR_mutation Freq Prop count 1 Mutant Mutant 1 0.04 28 2 Mutant WT 27 0.96 28 3 WT Mutant 21 0.45 47 4 WT WT 26 0.55 47 5 103 1 103 ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2 '#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF' ℹ Groups: "WT" and "Mutant" ℹ Features: 182 ✔ Wilcoxon test complete ℹ Groups: 2 ("WT" and "Mutant") ℹ Features: 182 ✔ Kruskal-Wallis test complete ℹ Creating heatmap with 20 features User session ended. Running garbage collection... User session ended. Running garbage collection... User session ended. Running garbage collection... User session ended. Running garbage collection... User session ended. Running garbage collection... User session ended. Running garbage collection... 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