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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treeio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treeio_1.35.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/treeio.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-10 00:28:30 UTC
* using option ‘--no-vignettes’
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.35.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘treeio’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
  ‘[tidytree:drop.tip-methods]{drop.tip}’
  ‘[tidytree:get.data-methods]{get.data}’
  ‘[tidytree:get.fields-methods]{get.fields}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘treeio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find.hclust
> ### Title: find the hierarchical cluster analysis among the nodes of graph
> ###   based on the length of all the shortest paths in the graph.
> ### Aliases: find.hclust
> 
> ### ** Examples
> 
> library(igraph)
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-spt.R:5:5'): spt for igraph ────────────────────────────────────
  Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
    dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
    Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
    Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-spt.R:5:5
   2.   └─base::library.dynam(lib, package, package.lib)
   3.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 124 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/treeio.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL treeio
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘treeio’ ...
** this is package ‘treeio’ version ‘1.35.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (treeio)

R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(treeio)
treeio v1.35.0 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR
Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package
for phylogenetic tree input and output with richly annotated and
associated data. Molecular Biology and Evolution. 2020, 37(2):599-603.
doi: 10.1093/molbev/msz240
> 
> test_check("treeio")
Saving _problems/test-as-phylo-17.R
Saving _problems/test-as-phylo-28.R
Saving _problems/test-spt-5.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 124 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-as-phylo.R:17:3'): as.phylo for tree igraph ────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Backtrace:
    ▆
 1. ├─ape::as.igraph.phylo(tr) at test-as-phylo.R:17:3
 2. └─base::loadNamespace(x)
 3.   └─base::library.dynam(lib, package, package.lib)
 4.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-as-phylo.R:26:3'): as.phylo for tree igraph with weights ───────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Backtrace:
    ▆
 1. ├─igraph::sample_gnp(18, 0.3) %>% igraph::mst() %>% ... at test-as-phylo.R:26:3
 2. └─base::loadNamespace(x)
 3.   └─base::library.dynam(lib, package, package.lib)
 4.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-spt.R:5:5'): spt for igraph ────────────────────────────────────
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Backtrace:
    ▆
 1. └─base::loadNamespace(x) at test-spt.R:5:5
 2.   └─base::library.dynam(lib, package, package.lib)
 3.     └─base::dyn.load(file, DLLpath = DLLpath, ...)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 124 ]
Error:
! Test failures.
Execution halted