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 v2.2.0.9000 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://127.0.0.1:35687 ℹ Best number of TME clusters: 3 ℹ Cluster distribution: ℹ Creating heatmap with 4 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 . # A tibble: 5 × 5 # Groups: Gender [2] Gender M_Stage Freq Prop count 1 Female M0 38 0.79 48 2 Female M1 10 0.21 48 3 Male M0 24 0.77 31 4 Male M1 5 0.16 31 5 Male 2 0.06 31 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' # A tibble: 5 × 5 # Groups: Gender [2] Gender M_Stage Freq Prop count 1 Female M0 38 0.79 48 2 Female M1 10 0.21 48 3 Male M0 24 0.77 31 4 Male M1 5 0.16 31 5 Male 2 0.06 31 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' # A tibble: 5 × 5 # Groups: Gender [2] Gender M_Stage Freq Prop count 1 Female M0 38 0.79 48 2 Female M1 10 0.21 48 3 Male M0 24 0.77 31 4 Male M1 5 0.16 31 5 Male 2 0.06 31 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' Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. ℹ The deprecated feature was likely used in the IOBR package. Please report the issue at . Warning: Error in ggsave: could not find function "ggsave" 96: 95: stop 94: func 92: f 91: Reduce 82: do 81: hybrid_chain 74: contextFunc 73: env$runWith 60: Context$new(getDefaultReactiveDomain(), "[download]")$run 59: shinysession$handleRequest 54: handler 53: handler 52: handlers$invoke 20: handler 19: func 18: compute 13: rookCall 12: 11: execCallbacks 10: run_now 9: service 8: serviceApp 1: runApp Closed TCGA pool. Closed OtherCohort pool. Closed Immunotherapy pool. Closed CancerCohort pool. Execution halted