Error - 'X' is not a dendrogram when running Numbat example dataset

[sunjh22]

Hi Gao,

When running the run_numbat using example data, an error throws out:

Running under parameters:
t = 0.001
alpha = 1e-04
gamma = 20
min_cells = 20
init_k = 3
sample_size = 1e+05
max_cost = 51.9
max_iter = 2
min_depth = 0
use_loh = auto
multi_allelic = TRUE
min_LLR = 50
max_entropy = 0.6
skip_nj = FALSE
exclude_normal = FALSE
diploid_chroms =
ncores = 20
common_diploid = TRUE
Input metrics:
173 cells
Approximating initial clusters using smoothed expression ..
number of genes left: 10242
Error in dendrapply(dend, get_attr_from_leaf) : 'X' is not a dendrogram
In addition: Warning message:
In dendextend::get_leaves_attr(den, attribute = "label") :
'dend' should be a dendrogram.

Do you have any comments about this error?

Ryan Sun

[teng-gao]

Hi Ryan,

Thanks for reporting this. Could you give us more information on your R version and package versions?

> library(numbat)
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /home/tenggao/R-4.1.0/lib/libRblas.so
LAPACK: /home/tenggao/R-4.1.0/lib/libRlapack.so

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_0.1.0

loaded via a namespace (and not attached):
 [1] treeio_1.16.2      tidyselect_1.1.1   purrr_0.3.4        graphlayouts_0.8.0
 [5] lattice_0.20-44    ggfun_0.0.5        colorspace_2.0-2   vctrs_0.3.8       
 [9] generics_0.1.2     viridisLite_0.4.0  utf8_1.2.2         gridGraphics_0.5-1
[13] rlang_1.0.1        pillar_1.7.0       glue_1.6.1         tweenr_1.0.2      
[17] lifecycle_1.0.1    stringr_1.4.0      munsell_0.5.0      gtable_0.3.0      
[21] parallel_4.1.0     fansi_1.0.2        tidygraph_1.2.0    Rcpp_1.0.8        
[25] scales_1.1.1       jsonlite_1.7.3     farver_2.1.0       gridExtra_2.3     
[29] ggforce_0.3.3      ggplot2_3.3.5      digest_0.6.29      aplot_0.1.2       
[33] stringi_1.7.6      dplyr_1.0.8        ggrepel_0.9.1      polyclip_1.10-0   
[37] grid_4.1.0         ggtree_3.0.4       cli_3.1.1          tools_4.1.0       
[41] yulab.utils_0.0.4  logger_0.2.2       magrittr_2.0.2     lazyeval_0.2.2    
[45] patchwork_1.1.1    tibble_3.1.6       ggraph_2.0.5       crayon_1.4.2      
[49] ape_5.6-1          tidyr_1.2.0        pkgconfig_2.0.3    MASS_7.3-54       
[53] ellipsis_0.3.2     tidytree_0.3.7     data.table_1.14.2  ggplotify_0.1.0   
[57] extraDistr_1.9.1   viridis_0.6.2      R6_2.5.1           igraph_1.2.11     
[61] nlme_3.1-152       compiler_4.1.0    

[sunjh22]

Hi Teng,

Thanks for your response, following is my R session information, so is it a must to run numbat under R4.0?

> library(numbat)
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so_

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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_0.1.0

loaded via a namespace (and not attached):
 [1] ggrepel_0.8.1       Rcpp_1.0.4.6        ape_5.3             lattice_0.20-41     tidyr_1.1.2         gtools_3.8.1        digest_0.6.27      
 [8] ggforce_0.3.3       R6_2.4.0            plyr_1.8.4          evaluate_0.14       ggplot2_3.3.2       pillar_1.4.6        gplots_3.0.1.1     
[15] rlang_0.4.11        lazyeval_0.2.2      rstudioapi_0.13     data.table_1.14.0   gdata_2.18.0        Matrix_1.2-18       rmarkdown_1.14     
[22] stringr_1.4.0       igraph_1.2.11       polyclip_1.10-0     munsell_0.5.0       compiler_3.6.0      xfun_0.20           pkgconfig_2.0.3    
[29] htmltools_0.5.1.1   tidyselect_1.1.0    tibble_3.0.4        gridExtra_2.3       graphlayouts_0.7.1  viridisLite_0.3.0   crayon_1.3.4       
[36] dplyr_1.0.2         MASS_7.3-51.6       bitops_1.0-6        grid_3.6.0          nlme_3.1-147        jsonlite_1.7.1      gtable_0.3.0       
[43] lifecycle_1.0.0     magrittr_1.5        scales_1.0.0        KernSmooth_2.23-17  tidytree_0.3.3      stringi_1.4.3       farver_2.0.1       
[50] viridis_0.5.1       ggtree_1.16.6       logger_0.2.2        ellipsis_0.3.1      rvcheck_0.1.8       generics_0.1.0      vctrs_0.3.4        
[57] RColorBrewer_1.1-2  tools_3.6.0         treeio_1.10.0       glue_1.4.0          tweenr_1.0.2        purrr_0.3.4         ggraph_2.0.5       
[64] parallel_3.6.0      yaml_2.2.0          colorspace_1.4-1    extraDistr_1.9.1    BiocManager_1.30.10 caTools_1.17.1.2    tidygraph_1.2.0    
[71] knitr_1.23          patchwork_1.0.0    

[teng-gao]

Thanks - I will try to reproduce this issue using your R version. Meanwhile could you try with R4 and see if the problem persists? If so please also provide your code for running the example.

[sunjh22]

Hi Teng,

I have tried it with R4.1 and it worked well! Thanks!

Ryan

[evanbiederstedt]

Thanks @sunjh22

If we could track down precisely why R-3.6 isn't working, we could revise the DESCRIPTION file. It's a bit confusing at the moment.

It's true that 3.6 is already 3 years old; I'm guessing there's a dependency issue somewhere....we really should track this down.

Thanks for the issue!

[teng-gao]

Thanks @sunjh22

If we could track down precisely why R-3.6 isn't working, we could revise the DESCRIPTION file. It's a bit confusing at the moment.

It's true that 3.6 is already 3 years old; I'm guessing there's a dependency issue somewhere....we really should track this down.

Thanks for the issue!

I changed the R version requirement to 4 for now

[mmfalco]

I had the same problem with R version 4.0. Rather than R version I think the problem was dendextend or stats package version. For those with the same problem try first to update the package to the latest version of both packages:

install.packages(c("dendextend","stats"))