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://127.0.0.1:35931
ℹ Best number of TME clusters: 3
ℹ Cluster distribution:
ℹ Creating heatmap with 185 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
  <https://github.com/stemangiola/tidyHeatmap/issues>.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'TGFβ_myCAF' in 'mbcsToSbcs': for β (U+03B2)
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'IFNγ_iCAF' in 'mbcsToSbcs': for γ (U+03B3)
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 <https://github.com/IOBR/IOBR/issues>.
Warning: Error in ggsave: could not find function "ggsave"
  96: <Anonymous>
  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$invoke
  20: handler
  19: func
  18: compute
  13: rookCall
  12: <Anonymous>
  11: execCallbacks
  10: run_now
   9: service
   8: serviceApp
   1: runApp
# A tibble: 11 × 5
# Groups:   T_Stage [5]
   T_Stage Cluster  Freq  Prop count
   <chr>   <chr>   <dbl> <dbl> <dbl>
 1 T1      TME1        5  0.56     9
 2 T1      TME2        2  0.22     9
 3 T1      TME3        2  0.22     9
 4 T2      TME1       34  0.81    42
 5 T2      TME2        8  0.19    42
 6 T3      TME1        7  0.88     8
 7 T3      TME3        1  0.12     8
 8 T4      TME1       14  0.78    18
 9 T4      TME2        2  0.11    18
10 T4      TME3        2  0.11    18
11 <NA>    TME1        2  1        2
ℹ Available categories: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap
ℹ Box palettes: nrc, jama, aaas, jco, paired1, paired2, paired3, paired4, accent, set2
'#374E55FF', '#DF8F44FF', '#00A1D5FF', '#B24745FF', '#79AF97FF', '#6A6599FF', '#80796BFF'
ℹ Groups: 4 ("Stage III", "Stage II", "Stage IV", and "Stage I")
ℹ Features: 183
✔ Kruskal-Wallis test complete
ℹ Creating heatmap with 20 features
ℹ Showing top 10 signatures
`height` was translated to `width`.
Warning: Error in ggsave: could not find function "ggsave"
  96: <Anonymous>
  95: stop
  94: func
  92: f
  91: Reduce
  82: do
  81: hybrid_chain
  74: contextFunc
  73: env$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: <Anonymous>
  11: execCallbacks
  10: run_now
   9: service
   8: serviceApp
   1: runApp
ℹ Survival follow-up time range: 4.11 to 153.72 months
ℹ Best cutoff for "EMT3": 0.1
✔ Best cutoff for "EMT3": 0.104
ℹ High EMT3: 38
ℹ Low EMT3: 41
ℹ Maximum follow-up time is 153.7 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 <https://github.com/kassambara/ggpubr/issues>.
ℹ Follow-up time ranges from 4.11 to 153.72 months
Female   Male 
    48     31 
ℹ Maximum follow-up time is 153.7 months; divided into 6 sections
ℹ Reference group not defined, using alphabetical order
ℹ Time range: 4.11 to 153.72
Warning: Error in ggsave: could not find function "ggsave"
  96: <Anonymous>
  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: <Anonymous>
  11: execCallbacks
  10: run_now
   9: service
   8: serviceApp
   1: runApp
ℹ Input data preview:
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 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
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
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
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
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
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
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
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
Setting levels: control = 0, case = 1
Setting direction: controls < cases
ℹ Input data preview:
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 Input data preview:
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 Input data preview:
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 Computing spearman correlation for 184 features
Warning in cor.test.default(data[[feat]], data[[target]], method = method,  :
  Cannot compute exact p-value with ties
Warning in cor.test.default(data[[feat]], data[[target]], method = method,  :
  Cannot compute exact p-value with ties
Warning in cor.test.default(data[[feat]], data[[target]], method = method,  :
  Cannot compute exact p-value with ties
✔ Correlation analysis complete
ℹ Calculating spearman correlation (n = 79)
ℹ Exact p-value: 2.1e-04
ℹ Groups: "TME1", "TME2", and "TME3"
ℹ Calculating pearson correlation: 5 x 5
Warning: Error in ggsave: could not find function "ggsave"
  96: <Anonymous>
  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: <Anonymous>
  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