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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ggtreeSpace.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ggtreeSpace_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ggtreeSpace.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtreeSpace/DESCRIPTION’ ... OK
* this is package ‘ggtreeSpace’ version ‘1.5.0’
* 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 ‘ggtreeSpace’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ggplot_add:
  function(object, plot, ...)
ggplot_add.tsheatmap:
  function(object, plot, object_name)

ggplot_add:
  function(object, plot, ...)
ggplot_add.treespace:
  function(object, plot, object_name)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
intern_call: no visible binding for global variable ‘dat’
Undefined global functions or variables:
  dat
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'geom_treespace.Rd':
geom_treespace
  Code: function(tr, trait, mapping = NULL, ...)
  Docs: function(tr, data, mapping = NULL, ...)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

Codoc mismatches from Rd file 'ggtreespace.Rd':
ggtreespace
  Code: function(tr, trait, mapping = NULL, ...)
  Docs: function(tr, data, mapping = NULL, ...)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

Codoc mismatches from Rd file 'make_ts_data.Rd':
make_ts_data
  Code: function(tr, trait)
  Docs: function(tr, data)
  Argument names in code not in docs:
    trait
  Argument names in docs not in code:
    data
  Mismatches in argument names:
    Position: 2 Code: trait Docs: data

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
phylospm 13.269  0.131  13.443
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ggtreeSpace.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ggtreeSpace
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘ggtreeSpace’ ...
** this is package ‘ggtreeSpace’ version ‘1.5.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (ggtreeSpace)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(ggtreeSpace)
> 
> test_check("ggtreeSpace")
ggtree v3.99.1 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
object for visualization of a phylogenetic tree and annotation data.
iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate

Loading required package: maps

Attaching package: 'dplyr'

The following object is masked from 'package:ape':

    where

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining with `by = join_by(node)`
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  5.752   0.283   6.035