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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2136/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeio 1.24.3  (landing page)
Guangchuang Yu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/treeio
git_branch: RELEASE_3_17
git_last_commit: 132fb4d
git_last_commit_date: 2023-07-24 00:02:52 -0400 (Mon, 24 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for treeio on kjohnson2


To the developers/maintainers of the treeio package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: treeio
Version: 1.24.3
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_1.24.3.tar.gz
StartedAt: 2023-10-19 08:09:58 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 08:12:10 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 132.9 seconds
RetCode: 0
Status:   OK  
CheckDir: treeio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.24.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/treeio.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.24.3’
* 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 R 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 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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

treeio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL treeio
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘treeio’ ...
** 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)

Tests output

treeio.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 v1.24.3 For help: https://yulab-smu.top/treedata-book/

If you use the ggtree package suite in published research, please cite
the appropriate paper(s):

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

Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods
for mapping and visualizing associated data on phylogeny using ggtree.
Molecular Biology and Evolution. 2018, 35(12):3041-3043.
doi:10.1093/molbev/msy194

Guangchuang Yu.  Data Integration, Manipulation and Visualization of
Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
doi:10.1201/9781003279242
> 
> test_check("treeio")
{
	"tree": "(K:0.081785{11},N:0.062341{14},(D:0.082021{4},(L:0.005508{12},(J:0.013996{10},(G:0.045746{7},((C:0.02773{3},(E:0.031104{5},O:0.048389{15})23:0.008328{23})22:0.015959{22},(H:0.021007{8},(I:0.014739{9},(B:0.031643{2},(A:0.01034{1},(F:0.006649{6},M:0.009195{13})28:0.028303{28})27:0.008072{27})26:0.0035{26})25:0.020359{25})24:0.000555{24})21:0.023675{21})20:0.045745{20})19:0.014684{19})18:0.059308{18})17:0.231628{17})16{16};",
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    "AA_subs": "",
    "t": 0.001,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0006,
    "N_x_dN": 0,
    "S_x_dS": 0.4
  },
  {
    "edge_num": 25,
    "subs": "G96A / T162C / T214C / G303A / T318C / A366G / C390T / G498A / A1146G / G1425A / C1461T / G1677A / A1902G / A1959G",
    "AA_subs": "",
    "t": 0.02,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.023,
    "N_x_dN": 0,
    "S_x_dS": 14.6
  },
  {
    "edge_num": 26,
    "subs": "G785A / A1067G / C1548T",
    "AA_subs": "R262K / K356R",
    "t": 0.003,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 1.5591,
    "dN": 0.0013,
    "dS": 0.0008,
    "N_x_dN": 2,
    "S_x_dS": 0.5
  },
  {
    "edge_num": 27,
    "subs": "C1168T / G1180A / A1242G / T1249C / T1257C",
    "AA_subs": "D394N",
    "t": 0.008,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0863,
    "dN": 0.0007,
    "dS": 0.0076,
    "N_x_dN": 1,
    "S_x_dS": 4.8
  },
  {
    "edge_num": 28,
    "subs": "A21G / T186A / T211C / G294A / T299C / A348T / C438T / C444T / C582T / A744G / C771T / A785G / G786A / C1374T / C1467T / A1500G / A1869G / G1878A / C2043T",
    "AA_subs": "V100A / K262R",
    "t": 0.028,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0453,
    "dN": 0.0013,
    "dS": 0.0289,
    "N_x_dN": 2,
    "S_x_dS": 18.3
  }
],
	"metadata": {"info": "R-package treeio", "data": "Thu Oct 19 08:11:40 2023"}
}
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 142 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 142 ]
> 
> proc.time()
   user  system elapsed 
  9.126   0.390  17.184

Example timings

treeio.Rcheck/treeio-Ex.timings

nameusersystemelapsed
Nnode.treedata0.0010.0010.002
beast-parser0.2470.0090.455
drop.tip-methods0.1220.0030.220
getNodeNum0.0010.0000.004
read.astral0.0520.0000.094
read.codeml0.3800.0150.722
read.codeml_mlc0.0900.0030.162
read.hyphy0.0490.0030.087
read.hyphy.seq0.0180.0010.041
read.jplace0.0640.0020.112
read.mcmctree0.0790.0020.143
read.nextstrain.json0.9560.0221.756
read.nhx0.0530.0020.102
read.paml_rst0.2520.0070.462
read.phylip0.0380.0020.076
read.phyloxml0.5630.0141.038
read.r8s0.0180.0010.033
read.raxml0.0370.0010.057
read.treeqza0.0530.0510.198
rename_taxa0.0010.0000.002
tree_subset0.0000.0010.000
write.beast0.0140.0020.024
write.beast.newick0.0110.0010.021