Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.

[teng-gao]

Hi, I now receive this warning while plotting phylogenies using ggtree:

#> Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if
#> `.name_repair` is omitted as of tibble 2.0.0.
#> ℹ Using compatibility `.name_repair`.
#> ℹ The deprecated feature was likely used in the treeio package.
#>   Please report the issue at <https://github.com/YuLab-SMU/treeio/issues>.

Sessioninfo:

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] numbat_1.1.0      pagoda2_1.0.9     igraph_1.3.4      data.table_1.14.2
[5] glue_1.6.2        ggplot2_3.3.6     stringr_1.4.1     dplyr_1.0.9      
[9] Matrix_1.4-0     

loaded via a namespace (and not attached):
  [1] uuid_0.1-4             N2R_0.1.1              parallelDist_0.2.6    
  [4] fastmatch_1.1-3        plyr_1.8.7             repr_1.1.3            
  [7] lazyeval_0.2.2         splines_4.1.2          listenv_0.8.0         
 [10] scattermore_0.7        urltools_1.7.3         digest_0.6.29         
 [13] yulab.utils_0.0.5      htmltools_0.5.2        viridis_0.6.2         
 [16] fansi_1.0.3            magrittr_2.0.3         RMTstat_0.3           
 [19] tensor_1.5             cluster_2.1.2          ROCR_1.0-11           
 [22] globals_0.14.0         graphlayouts_0.8.1     RcppParallel_5.1.5    
 [25] matrixStats_0.61.0     R.utils_2.11.0         spatstat.sparse_2.0-0 
 [28] sccore_0.1.3           colorspace_2.0-3       ggrepel_0.9.1         
 [31] crayon_1.5.1           jsonlite_1.8.0         spatstat.data_2.1-0   
 [34] brew_1.0-6             survival_3.2-13        zoo_1.8-10            
 [37] phangorn_2.9.0         ape_5.6-2              polyclip_1.10-0       
 [40] gtable_0.3.0           leiden_0.3.9           Rook_1.1-1            
 [43] future.apply_1.8.1     abind_1.4-5            scales_1.2.1          
 [46] DBI_1.1.1              miniUI_0.1.1.1         Rcpp_1.0.9            
 [49] viridisLite_0.4.1      xtable_1.8-4           spatstat.core_2.3-0   
 [52] gridGraphics_0.5-1     tidytree_0.4.0         reticulate_1.20       
 [55] bit_4.0.4              htmlwidgets_1.5.3      httr_1.4.2            
 [58] RColorBrewer_1.1-3     ellipsis_0.3.2         Seurat_4.0.4          
 [61] ica_1.0-2              pkgconfig_2.0.3        R.methodsS3_1.8.1     
 [64] farver_2.1.1           uwot_0.1.10            deldir_0.2-10         
 [67] utf8_1.2.2             reshape2_1.4.4         ggplotify_0.1.0       
 [70] tidyselect_1.1.2       labeling_0.4.2         rlang_1.0.6           
 [73] later_1.3.0            munsell_0.5.0          tools_4.1.2           
 [76] cli_3.4.1              generics_0.1.3         ggridges_0.5.3        
 [79] evaluate_0.14          fastmap_1.1.0          goftest_1.2-2         
 [82] ggtree_3.0.4           bit64_4.0.5            RhpcBLASctl_0.21-247.1
 [85] fitdistrplus_1.1-5     tidygraph_1.2.2        purrr_0.3.4           
 [88] RANN_2.6.1             ggraph_2.0.6           pbapply_1.4-3         
 [91] future_1.21.0          nlme_3.1-152           mime_0.12             
 [94] R.oo_1.24.0            aplot_0.1.6            hdf5r_1.3.5           
 [97] compiler_4.1.2         plotly_4.9.4           png_0.1-7             
[100] spatstat.utils_2.2-0   treeio_1.16.2          tibble_3.1.8          
[103] tweenr_2.0.1           stringi_1.7.8          drat_0.2.0            
[106] logger_0.2.2           lattice_0.20-45        IRdisplay_1.0         
[109] vctrs_0.5.1            pillar_1.8.1           lifecycle_1.0.3       
[112] spatstat.geom_2.2-2    triebeard_0.3.0        lmtest_0.9-38         
[115] RcppAnnoy_0.0.18       cowplot_1.1.1          irlba_2.3.3           
[118] httpuv_1.6.2           patchwork_1.1.2        R6_2.5.1              
[121] scistreer_1.0.1        promises_1.2.0.1       KernSmooth_2.23-20    
[124] gridExtra_2.3          parallelly_1.25.0      codetools_0.2-18      
[127] MASS_7.3-54            assertthat_0.2.1       rjson_0.2.21          
[130] withr_2.5.0            SeuratObject_4.0.2     sctransform_0.3.2     
[133] mgcv_1.8-38            parallel_4.1.2         rpart_4.1-15          
[136] quadprog_1.5-8         grid_4.1.2             ggfun_0.0.6           
[139] IRkernel_1.1.1         tidyr_1.2.0            dendsort_0.3.4        
[142] Cairo_1.5-12.2         Rtsne_0.15             pbdZMQ_0.3-5          
[145] ggforce_0.3.4.9000     shiny_1.6.0            base64enc_0.1-3      

[teng-gao]

To reproduce:

install.packages('numbat')

p = plot_phylo_heatmap(
    gtree = phylogeny_example,
    joint_post = joint_post_example,
    segs_consensus = segs_example)

[xiangpin]

This warning does not cause any problem for the following codes, but it will be fixed in the next version.