`ggtree::read.tree` crashes RStudio

[bschilder]

Hello,

ggtree::read.tree aborts RStudio, both on my Desktop Rstudio and within a Bioconductor Docker container.

Reprex

tree_path <- tempfile()
download.file("http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/",
              tree_path)
tr <- ggtree::read.tree(file = tree_path) 

Sounds a bit similar to #428

Session info

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] phytools_1.0-1  maps_3.4.0      caper_1.0.1     mvtnorm_1.1-3   MASS_7.3-55    
 [6] ape_5.6-1       rotl_3.0.12     orthogene_1.1.2 dplyr_1.0.8     ggplot2_3.3.5  
[11] ggtree_3.2.1   

loaded via a namespace (and not attached):
 [1] nlme_3.1-155              progress_1.2.2            httr_1.4.2               
 [4] numDeriv_2016.8-1.1       tools_4.1.0               backports_1.4.1          
 [7] utf8_1.2.2                R6_2.5.1                  DBI_1.1.2                
[10] lazyeval_0.2.2            colorspace_2.0-2          withr_2.4.3              
[13] prettyunits_1.1.1         tidyselect_1.1.1          mnormt_2.0.2             
[16] phangorn_2.8.1            compiler_4.1.0            cli_3.2.0                
[19] expm_0.999-6              plotly_4.10.0             scales_1.1.1             
[22] quadprog_1.5-8            digest_0.6.29             yulab.utils_0.0.4        
[25] rmarkdown_2.11            rentrez_1.2.3             pkgconfig_2.0.3          
[28] htmltools_0.5.2           plotrix_3.8-2             fastmap_1.1.0            
[31] htmlwidgets_1.5.4         rlang_1.0.1               gridGraphics_0.5-1       
[34] generics_0.1.2            combinat_0.0-8            jsonlite_1.7.3           
[37] car_3.0-12                homologene_1.4.68.19.3.27 magrittr_2.0.2           
[40] ggplotify_0.1.0           GenomeInfoDbData_1.2.7    patchwork_1.1.1          
[43] Matrix_1.4-0              Rcpp_1.0.8                munsell_0.5.0            
[46] fansi_1.0.2               abind_1.4-5               babelgene_21.4           
[49] lifecycle_1.0.1           scatterplot3d_0.3-41      yaml_2.2.2               
[52] carData_3.0-5             clusterGeneration_1.3.7   brio_1.1.3               
[55] grid_4.1.0                parallel_4.1.0            crayon_1.5.0             
[58] rncl_0.8.4                lattice_0.20-45           hms_1.1.1                
[61] magick_2.7.3              tmvnsim_1.0-2             knitr_1.37               
[64] pillar_1.7.0              igraph_1.2.11             ggpubr_0.4.0             
[67] ggsignif_0.6.3            codetools_0.2-18          fastmatch_1.1-3          
[70] XML_3.99-0.8              glue_1.6.1                gprofiler2_0.2.1         
[73] evaluate_0.14             ggimage_0.3.0             ggfun_0.0.5              
[76] data.table_1.14.2         BiocManager_1.30.16       vctrs_0.3.8              
[79] treeio_1.18.1             testthat_3.1.2            gtable_0.3.0             
[82] purrr_0.3.4               tidyr_1.2.0               assertthat_0.2.1         
[85] xfun_0.29                 broom_0.7.12              tidytree_0.3.7           
[88] coda_0.19-4               rstatix_0.7.0             viridisLite_0.4.0        
[91] tibble_3.1.6              aplot_0.1.2               ellipsis_0.3.2  

Many thanks in advance, Brian

[bschilder]

Realizing this was a silly mistake on my part. I was trying to import the link to the README rather than the file itself. Still, unsure why that would cause RStudio to crash.

URL <- "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.commonNames.nh"
tree_path <- file.path("~/Desktop",basename(URL))
download.file(URL,
              destfile = tree_path,
              method = "wget")
tr <- ggtree::read.tree(tree_path)

Though I am getting an error now:

Error in FUN(X[[i]], ...) : 
  numbers of left and right parentheses in Newick string not equal

[bschilder]

Seems there some issues with reading in tree files with ";".

However, after removing this, read.tree just returns NULL without any messages.

URL <- "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.commonNames.nh"
tree_path <- file.path("~/Desktop",basename(URL))
download.file(URL,
              destfile = tree_path,
              method = "wget")
#### Remove ";" at the end, which causes errors ####
l <- readLines(tree_path)
l2 <- gsub(";","",l)
writeLines(l2,tree_path)

## Both of these return NULL
tr <- ape::read.tree(file = tree_path)
tr <- ape::read.tree(text = l2)

The only thing that worked for me was using the package aphylo (after removing ";"):

if(!require("aphylo")) remotes::install_github("USCbiostats/aphylo")
tr <- aphylo::read_nhx(tree_path)

[bschilder]

There may actually be an underlying issue with the CommonNames newick itself, because the other two versions that use other taxonomic naming schemes seem to work fine:

hg38.100way.scientificNames.nh hg38.100way.nh

URL <- "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.scientificNames.nh"
tree_path <- file.path("~/Desktop",basename(URL))
download.file(URL,
              destfile = tree_path,
              method = "wget")
tr <- ape::read.tree(file = tree_path) 

[GuangchuangYu]

[bschilder]

Hm, this is odd, running the same code doesn't seem to produce the same result for me (unless I'm missing something). Same result with both read.newick and read.nhx

Which version of treeio are you using?

thanks, Brian

[GuangchuangYu]

v1.18.1 as displayed in the screenshot.

[bschilder]

sorry, missed that

weird, that's the same version I'm using. Not sure why we're getting totally different results. Only other thing I can think of is the OS: I'm on macOS Big Sur 11.4