search

YuLab-SMU / treeio

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
https://yulab-smu.top/treedata-book/
94 stars 24 forks source link

S3 overwrite warning in R version 4.3.1 (2023-06-16) with treeio 1.24.3 #109

Open ckeeling opened 1 year ago

ckeeling commented 1 year ago

I get a warning every time I start RStudio before any code has been executed:

Registered S3 methods overwritten by 'treeio':
  method              from    
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
  Ntip.treedata       tidytree
  ancestor.phylo      tidytree
  ancestor.treedata   tidytree
  child.phylo         tidytree
  child.treedata      tidytree
  full_join.phylo     tidytree
  full_join.treedata  tidytree
  groupClade.phylo    tidytree
  groupClade.treedata tidytree
  groupOTU.phylo      tidytree
  groupOTU.treedata   tidytree
  inner_join.phylo    tidytree
  inner_join.treedata tidytree
  is.rooted.treedata  tidytree
  nodeid.phylo        tidytree
  nodeid.treedata     tidytree
  nodelab.phylo       tidytree
  nodelab.treedata    tidytree
  offspring.phylo     tidytree
  offspring.treedata  tidytree
  parent.phylo        tidytree
  parent.treedata     tidytree
  root.treedata       tidytree
  rootnode.phylo      tidytree
  sibling.phylo       tidytree

Any suggestions how I can fix this, or is this something for you @GuangchuangYu ? treeio is a dependency for clusterProfiler that I am using.

Thanks, Chris

dansmith01 commented 11 months ago

It's not just RStudio. Even in the RGui app that ships with R, that message pops up. I'm a package developer and since my package suggests ggtree (which depends on treeio), anyone who loads my package also sees that ugly message. Would really appreciate a fix.

> library(treeio)
Registered S3 methods overwritten by 'treeio':
  method              from    
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
  Ntip.treedata       tidytree
  ancestor.phylo      tidytree
  ancestor.treedata   tidytree
  child.phylo         tidytree
  child.treedata      tidytree
  full_join.phylo     tidytree
  full_join.treedata  tidytree
  groupClade.phylo    tidytree
  groupClade.treedata tidytree
  groupOTU.phylo      tidytree
  groupOTU.treedata   tidytree
  inner_join.phylo    tidytree
  inner_join.treedata tidytree
  is.rooted.treedata  tidytree
  nodeid.phylo        tidytree
  nodeid.treedata     tidytree
  nodelab.phylo       tidytree
  nodelab.treedata    tidytree
  offspring.phylo     tidytree
  offspring.treedata  tidytree
  parent.phylo        tidytree
  parent.treedata     tidytree
  root.treedata       tidytree
  rootnode.phylo      tidytree
  sibling.phylo       tidytree

R 4.3.1; windows 10; all packages up to date from CRAN/Bioconductor as of today.

dansmith01 commented 11 months ago

@ckeeling, @joshua-theisen I was able to solve this by updating the development version of treeio on github.

remotes::install_github('YuLab-SMU/treeio')

Hopefully the fix will get pushed to Bioconductor soon!