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CHECK report for treeio on malbec2

This page was generated on 2020-10-17 11:55:57 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE treeio PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1829/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeio 1.12.0
Guangchuang Yu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/treeio
Branch: RELEASE_3_11
Last Commit: dbe4429
Last Changed Date: 2020-04-27 15:04:25 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: treeio
Version: 1.12.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings treeio_1.12.0.tar.gz
StartedAt: 2020-10-17 06:11:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:12:31 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 64.2 seconds
RetCode: 0
Status:  OK 
CheckDir: treeio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:treeio.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings treeio_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/treeio.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.12.0’
* 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 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 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:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL treeio
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘treeio’ ...
** using staged installation
** R
** inst
** 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 (treeio)

Tests output

treeio.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
treeio v1.12.0  For help: https://yulab-smu.github.io/treedata-book/

If you use treeio in published research, 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")
{
	"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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    "dN_vs_dS": 0.0646,
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    "N_x_dN": 1,
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    "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": "Sat Oct 17 06:12:19 2020"}
}
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 132 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.351   0.129  12.019

Example timings

treeio.Rcheck/treeio-Ex.timings

nameusersystemelapsed
Nnode.treedata0.0010.0000.001
beast-parser0.1040.0120.131
drop.tip-methods0.0220.0040.084
getNodeNum0.0020.0000.002
read.astral0.0020.0030.006
read.codeml0.4670.0200.563
read.codeml_mlc0.0450.0010.045
read.hyphy0.0300.0000.038
read.hyphy.seq0.0290.0000.028
read.jplace0.0690.0000.069
read.nhx0.0120.0000.012
read.paml_rst0.3750.0000.381
read.phylip0.0310.0000.032
read.phyloxml0.9310.0070.950
read.r8s0.0090.0000.009
read.raxml0.0060.0000.007
rename_taxa0.0030.0000.002
tree_subset000
write.beast0.0310.0040.042