multiple ggtree functions error with "could not find function "offspring.tbl_tree_item""

[nelsonruth11]

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The functions I'm attempting to use are get_taxa_name and collapse. get_taxa_name works when I don't specify a node, but breaks when I do specify a node. Collapse breaks every time.

hc_tree<-structure(list(edge = structure(c(11L, 11L, 12L, 13L, 14L, 15L, 
15L, 14L, 13L, 16L, 17L, 18L, 19L, 19L, 18L, 17L, 16L, 12L, 1L, 
12L, 13L, 14L, 15L, 2L, 3L, 4L, 16L, 17L, 18L, 19L, 5L, 6L, 7L, 
8L, 9L, 10L), .Dim = c(18L, 2L)), Nnode = 9L, tip.label = c("XPA.85.007", 
"XPA.85.002", "XPA.85.001", "XPA.85.009", "XPA.85.013", "XPA.85.012", 
"XPA.85.011", "XPA.85.010", "XPA.85.014", "XPA.85.003"), edge.length = c(0.0218860096110355, 
0.0218860096110355, 0.0157703305873459, 0.0253235785955029, 0.0304972457273817, 
0.0480189746562429, 0.0500981691928612, 0.135321566311564, 0.0432215089373018, 
0.112235851237383, 0.243285688496605, 0.0742303504425568, 0.0271071192052938, 
0.0260784098242765, 0.134848138865602, 0.374765735649553, 0.159653881377338, 
0.093950590734575), node.label = c("", "", "58", "66", "92", 
"88", "99", "100", "100"), root.edge = 0), .Names = c("edge", 
"Nnode", "tip.label", "edge.length", "node.label", "root.edge"
), class = "phylo", order = "cladewise")

hc_annot_clean <- structure(list(XPA = c("XPA.85.001", "XPA.85.002", "XPA.85.003", 
"XPA.85.007", "XPA.85.009", "XPA.85.010", "XPA.85.011", "XPA.85.012", 
"XPA.85.013", "XPA.85.014"), HCfam = c("H03", "H03", "H03", "H03", 
"H03", "H04", "H01", "H01", "H01", "H03")), class = c("tbl_df", 
"tbl", "data.frame"), row.names = c(NA, -10L), .Names = c("XPA", 
"HCfam"))

#creating and annotating tree works
p <- ggtree(hc_tree, linetype="solid", layout="circular") %>% collapse(node=17)
p <- p %<+% hc_annot_clean

#highlighting node works
p + geom_nodelab(aes(label=node)) 
  geom_hilight(node=17)

#can print every taxa name
get_taxa_name(p)

#breaks when I specify which node to print taxa from
get_taxa_name(p, node=17)

#collapse also breaks when I specify a node
p <- ggtree(hc_tree, linetype="solid", layout="circular")
p <- collapse(p, node=17)

Both provide the same error message:

Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly,  : 
  could not find function "offspring.tbl_tree_item

I have seen this issue: YuLab-SMU/tidytree#42 and done the troubleshooting methods there, but nothing worked.

The solutions proposed here did not work either: https://support.bioconductor.org/p/9153297/#9153353

Thanks,

-Nelson

[xiangpin]

Did you try re-install ggtree using BiocManager::install("ggtree", force=T, type = 'source') ?

[nelsonruth11]

I have, but that also errored:

> BiocManager::install("ggtree", force=T, type = 'source')
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.22), R 4.2.1 (2022-06-23)
Installing package(s) 'ggtree'
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/ggtree_3.4.4.tar.gz'
Content type 'application/gzip' length 356386 bytes (348 KB)
==================================================
downloaded 348 KB

* installing *source* package ‘ggtree’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warning_wrap' not found
Error: unable to load R code in package ‘ggtree’
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/Users/nruth/Library/R/x86_64/4.2/library/ggtree’
* restoring previous ‘/Users/nruth/Library/R/x86_64/4.2/library/ggtree’

The downloaded source packages are in
	‘/private/var/folders/30/w80ljzj12zxdg2rn5tqr9th40015b6/T/RtmpEoEOmK/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.2/Resources/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'classInt', 'flextable', 'Matrix', 'MatrixModels', 'mvtnorm', 'RcppArmadillo', 'terra', 'tidytree'

Rolling back tidytree to 0.4.2 didn't work either

[xiangpin]

This is because you use Bioconductor version 3.15, an old version. Now the released version of Bioconductor is 3.17. You should update Bioconductor first, Or you can try re-install ggtree using remotes::install_github('YuLab-SMU/ggtree').

[nelsonruth11]

I stepped away for a few days and now things work. Still on the same BiocManager, ggtree 3.4.4, ggtreeExtra 1.6.1. Thanks for your help and a great package, closing.

[alephreish]

I'm not sure it belongs here, but I want to mention the following experience:

I stumbled upon this (getting could not find function "offspring.tbl_tree_item with geom_cladelab) today when creating a conda environment with the latest version of bioconda/bioconductor-ggtree which is 3.8.0, under Linux. Updating to 3.8.2 manually is highly undesirable under this scenario.

[ewallace]

Noting that I ran into the same bug, (getting could not find function "offspring.tbl_tree_item with geom_cladelab) today.

I fixed it by reinstalling packages as described:

devtools::install_version("tidytree", version = "0.4.2")
BiocManager::install("ggtree", force=T, type = 'source')

It would still be great to fix the most recent package versions to remove the bug.